Pegasoferae?: Difference between revisions

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Nishihari et al located 4 retroposon insertion events that support Pegasoferae. In the ensuing 2-3 years, it has become possible to reinvestigate these events with additional species utilizing bioinformatic methods on the 10 available Laurasiathere genomes (not all of which will completely cover a given event).
Nishihari et al located 4 retroposon insertion events that support Pegasoferae. In the ensuing 2-3 years, it has become possible to reinvestigate these events with additional species utilizing bioinformatic methods on the 10 available Laurasiathere genomes (not all of which will completely cover a given event).


This can be done fairly rapidly (though only a subset of the putatively informative L1MA9 insertions are analyzed here). First, the primers used by the Okada group are [http://genome.cse.ucsc.edu/cgi-bin/hgBlat?db=hg8 blatted] into the UCSC genome browser of an appropriate species (dog). The reverse strand primer must be first reverse-complemented with the UCSC [http://www.soe.ucsc.edu/~kent/dnaDust/dnadust.html utilities tool] for a single line of Blat output to span the region of interest.
This can be done fairly rapidly (though only a subset of the putatively informative L1MA9 insertions are analyzed here). First, the primers used by the Okada group are [http://genome.soe.ucsc.edu/cgi-bin/hgBlat?db=hg8 blatted] into the UCSC genome browser of an appropriate species (dog). The reverse strand primer must be first reverse-complemented with the UCSC [http://www.soe.ucsc.edu/~kent/dnaDust/dnadust.html utilities tool] for a single line of Blat output to span the region of interest.


In every case studied here, the L1MA9 elements lie within small introns of coding genes. That means typically 30-40 amino acids from each flanking exon are available to create reliable anchors for future blast searches at NCBI. Without these anchors, L1MA9 elements do not necessarily retrieve orthologous elements in other species via blast, for the reason that the active L1MA9 parent element may have spun off subsequent fragments that are closer in sequence.
In every case studied here, the L1MA9 elements lie within small introns of coding genes. That means typically 30-40 amino acids from each flanking exon are available to create reliable anchors for future blast searches at NCBI. Without these anchors, L1MA9 elements do not necessarily retrieve orthologous elements in other species via blast, for the reason that the active L1MA9 parent element may have spun off subsequent fragments that are closer in sequence.


Next, dna spanning the exons and their internal intron are collected from Laurasiatheres with UCSC genome browsers, [http://genome.cse.ucsc.edu/cgi-bin/hgGateway?hgsid=106984621&clade=vertebrate&org=Dog&db=0 notably dog], cat, horse and cow. This dna is then marked up for all retroposons using the RepeatMasker track. Here it is important to track orientation of the repeat element (letting the reading frame of the exons define the positive strand convention), the fragment coordinates relative to an idealized repeat of the given class in the underlying RepeatMasker library, and the percent identity to this element.  
Next, dna spanning the exons and their internal intron are collected from Laurasiatheres with UCSC genome browsers, [http://genome.soe.ucsc.edu/cgi-bin/hgGateway?hgsid=106984621&clade=vertebrate&org=Dog&db=0 notably dog], cat, horse and cow. This dna is then marked up for all retroposons using the RepeatMasker track. Here it is important to track orientation of the repeat element (letting the reading frame of the exons define the positive strand convention), the fragment coordinates relative to an idealized repeat of the given class in the underlying RepeatMasker library, and the percent identity to this element.  


These three steps allow in-depth comparison of putatively orthologous retroposons, noting however in the case of L1MA9 elements that fragment coordinates are very similar in many thousands of these insertions due to the replication mechanism favoring distal fragments of similar lengths. Thus homoplasic events cannot truly be ruled out even upon this closer examination.
These three steps allow in-depth comparison of putatively orthologous retroposons, noting however in the case of L1MA9 elements that fragment coordinates are very similar in many thousands of these insertions due to the replication mechanism favoring distal fragments of similar lengths. Thus homoplasic events cannot truly be ruled out even upon this closer examination.
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The comparative genomics is extended now to additional species using [http://www.ncbi.nlm.nih.gov/blast/Blast.cgi tblastn of the WGS contig division] of GenBank. This target database stores 2x assemblies of species such as microbat, hedgehog, and shrew. The spanning contig GenBank entries are then [http://www.proweb.org/proweb/Tools/WU-blast.html uBlasted] against the growing database of fiducial sequences to locate the exons and intervening sequence. The latter is most conveniently retrieved by screen-scraping of [http://www.expasy.ch/tools/dna.html 6-frame translation], dropping out the alternate lines containing the amino acids.
The comparative genomics is extended now to additional species using [http://www.ncbi.nlm.nih.gov/blast/Blast.cgi tblastn of the WGS contig division] of GenBank. This target database stores 2x assemblies of species such as microbat, hedgehog, and shrew. The spanning contig GenBank entries are then [http://www.proweb.org/proweb/Tools/WU-blast.html uBlasted] against the growing database of fiducial sequences to locate the exons and intervening sequence. The latter is most conveniently retrieved by screen-scraping of [http://www.expasy.ch/tools/dna.html 6-frame translation], dropping out the alternate lines containing the amino acids.


The latter two species exons can sometimes be retrieved faster from the 28-species alignment track at UCSC -- genomic alignment provides more reliable orthologs -- some lineages could have idiosyncratic segmental duplications that could cause cross-matching. If the coding regions are evolving too fast, the whole enterprise becomes questionable. Another pitfall is paralogs. Here [http://genome.cse.ucsc.edu/cgi-bin/hgNear?org=Human&db=hg18&hgsid=106984621 GeneSorter] at the UCSC site can be consulted, at least for human, to rapidly examine the situation.  
The latter two species exons can sometimes be retrieved faster from the 28-species alignment track at UCSC -- genomic alignment provides more reliable orthologs -- some lineages could have idiosyncratic segmental duplications that could cause cross-matching. If the coding regions are evolving too fast, the whole enterprise becomes questionable. Another pitfall is paralogs. Here [http://genome.soe.ucsc.edu/cgi-bin/hgNear?org=Human&db=hg18&hgsid=106984621 GeneSorter] at the UCSC site can be consulted, at least for human, to rapidly examine the situation.  


Next, the est_other and nr divisions of GenBank are probed to retrieve any data that might be available from non-genomic projects. Transcripts per se don't seem useful here (lack the intron of interest) yet they provide precise probes later of the trace archives for the given species.
Next, the est_other and nr divisions of GenBank are probed to retrieve any data that might be available from non-genomic projects. Transcripts per se don't seem useful here (lack the intron of interest) yet they provide precise probes later of the trace archives for the given species.
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The one-residue indel appears cleanly restricted to Pegasoferae. There are 5 Laurasiatheres with it and 5 without it, which needs further buttressing by PCR (adding more basal species has the effect of localizing the event farther back on the stem). The parental gene did not develop the indel in any bioinformatically accessible species.
The one-residue indel appears cleanly restricted to Pegasoferae. There are 5 Laurasiatheres with it and 5 without it, which needs further buttressing by PCR (adding more basal species has the effect of localizing the event farther back on the stem). The parental gene did not develop the indel in any bioinformatically accessible species.


Interestingly, the retrogene CHML landed within intron 1 of encephalopsin OPN3 with the same direction of transcription. This raises some questions about how CHML is translated (as it would apparently be spliced out). Encephalopsin has an [http://genomewiki.ucsc.edu/index.php/Opsin_evolution:_Encephalopsin_gene_loss interesting history in mammals] involving multiple independent losses.
Interestingly, the retrogene CHML landed within intron 1 of encephalopsin OPN3 with the same direction of transcription. This raises some questions about how CHML is translated (as it would apparently be spliced out). Encephalopsin has an [[Opsin_evolution:_Encephalopsin_gene_loss| interesting history in mammals]] involving multiple independent losses.


The region annotated below corresponds to a known domain called GDI (for GDP dissociation inhibitor: pfam00996). The 3D structure of this region is available in the parent gene in rat, PDB 1LTX so the structural location of the indel could be determined. Very likely it lies within a loop and has minimal functional impact.
The region annotated below corresponds to a known domain called GDI (for GDP dissociation inhibitor: pfam00996). The 3D structure of this region is available in the parent gene in rat, PDB 1LTX so the structural location of the indel could be determined. Very likely it lies within a loop and has minimal functional impact.
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=== Analysis of a five residue deletion in DIO1 ===
=== Analysis of a five residue deletion in DIO1 ===


The  five amino acid deletion here occurs in first exon of iodothyronine deiodinase, a [http://genomewiki.ucsc.edu/index.php/Selenoprotein_evolution:_introduction#DIO1.2C_DIO2.2C_and_DIO3:_a_curious_history much-studied gene.]  A consistent picture is seen in dog, bears, cat, horse, macrobat, and microbat with artiodactyls (cow, dolphin, pig, vicuna) and eulipotyphlya (hedgehog and shrew) lacking the deletion, which is evidently the ancestral condition judging by marsupials, more basal Atlantogenata, and Euarchontoglires.  
The  five amino acid deletion here occurs in first exon of iodothyronine deiodinase, a [[Selenoprotein_evolution:_introduction#DIO1.2C_DIO2.2C_and_DIO3:_a_curious_history| much-studied gene.]]  A consistent picture is seen in dog, bears, cat, horse, macrobat, and microbat with artiodactyls (cow, dolphin, pig, vicuna) and eulipotyphlya (hedgehog and shrew) lacking the deletion, which is evidently the ancestral condition judging by marsupials, more basal Atlantogenata, and Euarchontoglires.  


[[Image:Pegasoferae.png|left|]]
[[Image:Pegasoferae.png|left|]]
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=== Possibly informative whole gene duplication in bat opsin ===
=== Possibly informative whole gene duplication in bat opsin ===


An apparental functional duplication of a visual opsin gene has been [http://mbe.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=14660703 reported previously] in the megabat Haplonycteris fischeri that is missing in Pteropus and Myotis. This is another form of rare genomic event, a large insertion indel since most mammals have but [http://genomewiki.ucsc.edu/index.php/Opsin_evolution:_update_blog two imaging opsins].
An apparental functional duplication of a visual opsin gene has been [http://mbe.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=14660703 reported previously] in the megabat Haplonycteris fischeri that is missing in Pteropus and Myotis. This is another form of rare genomic event, a large insertion indel since most mammals have but [[Opsin_evolution:_update_blog| two imaging opsins.]]


This gene duplication might simply be restricted to this one genus (or even this one species). Alternatively it might have greater phylogenetic depth and be somewhat informative in resolving intra-bat taxonomy. This would require PCR of many additional bat species since no further genomic work is anticipated any time soon. It is not relevent to Pegasoferae per se since bats are clearly monophyletic overall, even as the macro/micro distinction remains equivocal as a taxonomic character.  
This gene duplication might simply be restricted to this one genus (or even this one species). Alternatively it might have greater phylogenetic depth and be somewhat informative in resolving intra-bat taxonomy. This would require PCR of many additional bat species since no further genomic work is anticipated any time soon. It is not relevent to Pegasoferae per se since bats are clearly monophyletic overall, even as the macro/micro distinction remains equivocal as a taxonomic character.  
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  mibat GACAAGCATGTCAGGACCTAGTCGGTTCC---CTGTTAGCTCGTCCAGCACTGTCCATCCTAGT
  mibat GACAAGCATGTCAGGACCTAGTCGGTTCC---CTGTTAGCTCGTCCAGCACTGTCCATCCTAGT


=== Insertion in NEK11 in bat, cow, and sheep not shared by pig or dolphin ===


<pre>
EIPEDPLVAEEYYADAFDSYCEESDEEEEE-IALERPEKEIRNEGSQPAYRTNQQ  NEK11_homSap Homo sapiens (human)
EIPEDPLVAEEYYADAFDSYCEESDEEEEE-IALERPEKEIRNEGSQPAYRTNQQ  NEK11_panTro Pan troglodytes (chimp)
EIPEDPLVAEEYYADAFDSYCEESDEEEEE-IVLAGPEKEIKNEGSQPTYRTNQQ  NEK11_ponPyg Pongo pygmaeus (orang_sumatran)
EIPEDPLVAEEYYADAFDSYCEESDEEEEE-IVLAGPEKEIKNEGSQPTYRTNQQ  NEK11_macMul Macaca mulatta (rhesus)
EIPEDPLVAEEYYADTFDSYCEESDEEEEG-TVLSGPEKEIKKES-QPAYRTNQQ  NEK11_calJac Callithrix jacchus (marmoset)
EIPEDPLVAEEYYADVFDS-CSE-EEEEEE-IVFSASEGEVKDEGPQPPYRTHQQ  NEK11_otoGar Otolemur garnettii (bushbaby)
EIPEDPLVAEQYYSDVFDSCSEDSEEQEEE-MIFSEAGGDTKEEESPSVYRTNQQ  NEK11_musMus Mus musculus (mouse)
EIPEDPLVAEQYYADVFDSCSEDSGEQEEE-MAFSEAGGDMREEGSPPTYRTNQQ  NEK11_ratNor Rattus norvegicus (rat)
EIPEDPLVAEVYYADAFDSCSEDSEEQEGE-TGSLGPEVEAQDEGSQPTSRTNHQ  NEK11_cavPor Cavia porcellus (guinea_pig)
.IPEDPFVAEEYYADVFDSCSEESEEQEEE-ILFSGPEREVKD------YRTNQQ  NEK11_oryCun Oryctolagus cuniculus (rabbit)
EIPEDPLVAEEYYTDVFDSCSEESEEQEED-TLFSGPDRETKD-----GNRINQQ  NEK11_ochPri Ochotona princeps (pika)
EIPEDPLVAEEYYADAFDSCSEESEEEEEE-IMFSAPEEEVKDEGPRPAHRIFQQ  NEK11_canFam Canis familiaris (dog)
DIPEDPIVAEEYYADAFDSCSEESEEEEEE-IVFSGPEEEVKDEGPQPAYRTIQQ  NEK11_felCat Felis catus (cat)
EIPEDPLVAEEYYADAFDSCSEESEDEEEE-IVFSGPEEEVKDEVQQPAYRTNQQ  NEK11_equCab Equus caballus (horse)
.IPEDPRVAEEYYADTFDSCSEESEEEEEEEMVLAGLEAEVRDKGPQPDCRANQQ  NEK11_myoLuc Myotis lucifugus (microbat)
EIPEDPLVAEEYYADVFDSCSEESEESEEGKTVFSVKDEEVEDEGPQPVYRTNQQ  NEK11_bosTau Bos taurus (cow)
EIPADPLVAEEYYADVFDSCSEESEESEEEKTVFSVKDEEVEDEGPQPVYRTNQQ  NEK11_oviAri Ovis aries (sheep)
EIPEDPLVAEEYYTDAFDSCSEESEEEEEN-MVFSAGEEEVQDEGSQPAYRTNQQ  NEK11_susScr Sus scrofa (pig)
EIPEDPLVAEEYYADAFDSCSEESEEEEEN-TVFSAGEEEVKDEEPQPAYRTNQQ  NEK11_vicVic Vicugna vicugna (vicugna)
EIPEDPLKAEEYYADVFDSCSEESEEEGEE-TVFSGSE-EVSDDGLQPAHRTNQQ  NEK11_eriEur Erinaceus europaeus (hedgehog)
EIPEDPLVAEEYYADAFDSCSEESEDRGEE-ALFSGSGEDCEEEEPQLSYRTNQQ  NEK11_sorAra Sorex araneus (shrew)
EIPEDPLVAEEYYADVFDSCSEESEEEEEE-TVFSGPEEKAKDEGPQPVYRTNQQ  NEK11_choHof Choloepus hoffmanni (sloth)
EIPEDPLVAEEYYADTFDSCSEESEEEEEE-IVFSGPEEEVKDKEPQPAYRTNQ.  NEK11_loxAfr Loxodonta africana (elephant)
EIPEDPLVAEEYYADTFDSCSEESEEEEDE-TVFSGPGEEVKDEESQPASRTDQQ  NEK11_echTel Echinops telfairi (tenrec)
EIPEDPLVAEEYYDDVFDSCSEESEEEAEE-----KSEEMVEYETSQTVVKTNQQ  NEK11_ornAna Ornithorhynchus anatinus (platypus)
.IPEDPLIAEEYYNDVFDSCSETSEDQEEE-VVEADEVKEDEEEDTLFTYTTNQQ  NEK11_anoCar Anolis carolinensis (lizard)
not available NEK11_micMur Microcebus murinus (mouse_lemur)
not available NEK11_tupBel Tupaia belangeri (tree_shrew)
not available NEK11_speTri Spermophilus tridecemlineatus (squirrel)
not available NEK11_pteVam Pteropus vampyrus (macrobat)
not available NEK11_turTru Tursiops truncatus (dolphin)
not available NEK11_dasNov Dasypus novemcinctus (armadillo)
not available NEK11_monDom Monodelphis domestica (opossum)
not sought    NEK11_tarSyr Tarsius syrichta (tarsier)
not sought    NEK11_proCap Procavia capensis (hyrax)
not sought    NEK11_macEug Macropus eugenii (wallaby)
not sought    NEK11_galGal Gallus gallus (chicken)
not sought    NEK11_taeGut Taeniopygia guttata (finch)
</pre>
Query:    13 EIPEDPLVAEEYYADAFDSYCEESDEEEEEIALERPEKEIRNEGSQPAYRTNQQ genome
            EIPEDPLVAEEYYADAFDSYC ESDEEEEEIALERPEKEIRNEGSQPAYRTNQQ
Sbjct:  467 EIPEDPLVAEEYYADAFDSYCVESDEEEEEIALERPEKEIRNEGSQPAYRTNQQ webb
chr3 132430108 132430168 3
human TTTGATTCCTATTGTGAAGAGAGTGATGAG---GAGGAAGAAGAAATAGCGTTAGAAAGACCA
  cow TTTGATTCCTGTTCTGAAGAAAGTGAGGAGAGTGAGGAAGGAAAAACAGTATTCTCAGTCAAG
 
human TTTGATTCCTATTGTGAAGAGAGT---GATGAGGAGGAAGAAGAAATAGCGTTAGAAAGACCAG
mibat TTTGACTCCTGTTCTGAAGAGAGTGAGGAGGAGGAGGAGGAAGAAATGGTGTTGGCAGGACTGG
=== Deletion in ENAM in microbat and horse not shared by macrobat ===
This one-residue deletion in horse and microbat lies in a very important gene for dentition, enamalin. This particular region of the protein is quite prone to indels with at least 6 other events (at other sites) in 32 other placental mammals. It is not taxonomically informative because macrobat lacks the indel.
PNIRNFPSGRQWYFTGTVMGHRQNRPFY RNQQVQRGPRWN FFAWERKQVAR PGNPVYH  ENAM_homSap Homo sapiens (human)
PNVRNFPSGRQWYFTGTVMGHRQNRPFY RNQQVQRGPRWN SFAWEGKQVAR PGNPVYH  ENAM_panTro Pan troglodytes (chimp)
PNIRNFPSGTQWYFTGTVMGHRQNRPFY RNQQVQRGPRWN SFAWERKQVAR PGNPVYH  ENAM_gorGor Gorilla gorilla (gorilla)
PNIRKFPSGRQWYLTGTVTGHRRNGPFY RNQQVQRGPRWN FFAWEGKQVAR PGNPVYH  ENAM_ponPyg Pongo pygmaeus (orang_sumatran)
PNIRNFPSGRRWYPTGTAMGHRQNGPFY RNRQVQRGPQWN SFAWEGKQVVR PGNPVYH  ENAM_macMul Macaca mulatta (rhesus)
PNIRNFPSGRRWYPTGTAMGHRQNGPFY RNRQVQRGPQWN SFAWEGKQVVR PGNPVYH  ENAM_papAnu Papio anubis (baboon)
PNIRNFPSGRQWYFTGTVMGHRQNRPFY RNQQVPRGPRWN SFAWEGKQVAR PGNPVYH  ENAM_nasLar Nasalis larvatus (proboscis monkey)
PNIRSFPSGRQWYP<span style="color: #6699FF;">T--T</span>MGHRQNGPFY RNRQVQRGLRWN SFPWEGKQVAR PRNPVYH  ENAM_calJac Callithrix jacchus (marmoset)
PNVRRFPSGRQWYPTGTAMGHRQTGPFY RNQQFQRGPRWN SF<span style="color: #6699FF;">V----Q</span>VAR AGNPTYH  ENAM_otoGar Otolemur garnettii (bushbaby)
PNARNVPWVRQWYPAGTAVGRRQNGPLY RSQQFQRVPRWH SFALESKQVAR PVNPPYR  ENAM_micMur Microcebus murinus (mouse_lemur)
PNIRNFPSGRQWHSTGTAMGNRQTRPFY RNQQVQRGPSWN SFALESKQAAH PRTPTYR  ENAM_tupBel Tupaia belangeri (tree_shrew)
YPYPNYPSERQWQTTG<span style="color: #6699FF;">T-Q</span>GPRQNGPGY RNPQVERGPQWN SFAWEGKQATR PGNPTYG  ENAM_musMus Mus musculus (mouse)
YPYPNYPSERQWQTTD<span style="color: #6699FF;">T-Q</span>GPKQNGPGY QNPQIQRGPQWN SFAWEGKQATT<span style="color: #FF0000;">H</span>PGNPTYH  ENAM_ratNor Rattus norvegicus (rat)
PNIRNSPSGRQSNPTHTATGQRPPGPSY RNQPGQWDAQGN SFAWEGKQAAG PKNPTYH  ENAM_cavPor Cavia porcellus (guinea_pig)
PNIRNPPTGRQWHPTGTAMGHRQYGPLY RNQQVQRGPRWN SLAWEGKQATR PGNPTYR  ENAM_speTri Spermophilus tridecemlineatus (squirrel)
.NTRNFPSERQWHHTGTAVGHRPNGPFY RNQQVQRGTQWN SFAWESKQATR PENPTYR  ENAM_oryCun Oryctolagus cuniculus (rabbit)
.NTRNFPSGRQWHQTGTAVGQRPNGPFY RNQQVQKNSQWN SFAWENKQATN PGNPASH  ENAM_ochPri Ochotona princeps (pika)
PNIRNFPAGRQWRPTGTFMGHRQNGPFY RNQQVQRGPRWN SFALERKQAMR PGNPIYR  ENAM_canFam Canis familiaris (dog)
PNIRNFPAGRQWRPTGTIMGRRQNGPFY RNQQVQRGPRWN SFALEGKQAFR SGNPIYR  ENAM_felCat Felis catus (cat)
<span style="color: #990099;">PNIRNFPARRQWRPTGTATGNRQNGPFY RNQ-VQRDPQWN SFAWEGKRTVH PGNPIYR  ENAM_equCab Equus caballus (horse)
.NFPSFPVGRQWRPTGTTVGHRQNGPFY RNP-VQRGPRWN SYAWEGKQAVR PGNPIYH  ENAM_myoLuc Myotis lucifugus (microbat)</span>
PNLQSFPVGRQWRPTGTAMGHGQNGPFY RNQQVQRGPRWN SFALEDRQTVR PGNPIYR  ENAM_pteVam Pteropus vampyrus (macrobat)
PNIRNFPAGRQWHPTGTSMGNRRNGPFY RNQQIQRAPRWN SFVLEGKQAIRLGYPIYRR  ENAM_bosTau Bos taurus (cow)
PNIRNFPAGRQ<span style="color: #FF0000;">WHPT</span>GTFMGHRRNGPFY RNQQIQRGPRWN SFVLEGKQVIRPGYPIYRR  ENAM_oviAri Ovis aries (sheep) whRQWHpt insert
PNIRGFPARRQWRPPGPAMGHRRNGPFY RNQQIQRGPRWN SFTLEGKQAVRPGYPTYRR  ENAM_susScr Sus scrofa (pig)
PNIRSFPAGRQWRPTGTATGHKRNGPFY RNQQIQRGPRWN SFVLEGKQAVRPGYPIYRR  ENAM_turTru Tursiops truncatus (dolphin)
PNIRSFPARRQWRPTGTAMGHRQNGPFY RNQQIQRG.... ...................  ENAM_vicVic Vicugna vicugna (vicugna)
PNIRNYPAGRQWRPTGTILGHRQNWPFY RTQQVQGSPRWH SFALENKQALRPGTPFYRK  ENAM_eriEur Erinaceus europaeus (hedgehog)
PNVRNVPAGRQWRPTGTDTWQRQNVPFY RNQLYQRGPRWN SFTLENKQAIRPGIPFYSK  ENAM_sorAra Sorex araneus (shrew)
PNIRDFPARRPWHPSGNVMGHRENGPFY RN-QVQRGPRWN SFALESKKAVLLGNPAYHK  ENAM_dasNov Dasypus novemcinctus (armadillo)
PSVRGFPTGRQWRPTGTAMGHRQNGPFY RNQQVQRGARWN SFTLEGKQAARPGNPAYRK  ENAM_loxAfr Loxodonta africana (elephant)
PGAQGSPIARQWRPIGTAMGHRQNGPLY RNQQVQRGPRWN SFTLEGKPAARPGNPAYQK  ENAM_proCap Procavia capensis (hyrax)
PNIRGFPARRQWCPTGTTMGHRQNGPY<span style="color: #6699FF;">Y -Q</span>NQVQRGPWWK SFAL...............  ENAM_choHof Choloepus hoffmanni (sloth)
too diverged                                                    ENAM_monDom Monodelphis domestica (opossum)
too diverged                                                    ENAM_macEug Macropus eugenii (wallaby)
too diverged                                                    ENAM_ornAna Ornithorhynchus anatinus (platypus)
not available                                                  ENAM_echTel Echinops telfairi (tenrec)
chr4 71727036 71727099 -3
human AGACAGAATAGGCCTTTTTACAGAAATCAACAAGTTCAAAGGGGTCCTCGGTGGAACTTCTTT
horse AGACAGAATGGGCCTTTCTACCGAAATCAA---GTTCAAAGGGATCCTCAGTGGAACTCCTTT
human AGACAGAATAGGCCTTTTTACAGAAATCAACAAGTTCAAAGGGGTCCTCGGTGGAACTTCTTTG
mibat AGACAGAATGGGCCTTTTTACCGAAATCCA---GTCCAAAGGGGTCCTCGGTGGAACTCCTATG
=== Deletion in CDCP1 in microbat and horse shared by macrobat but homoplasic in rabbit ===
This one-residue deletion in exon 7 of CDCP1 occurs in horse and microbat and also macrobat but also at the same spot in rabbit but not pika. The deletion does not occur in cat, dog, or the 5 artiodactyls. Precise location of the indel is problematic because it occurs in a short EEE repeat (variations have D). Recall glu and asp have but two codons each. Otherwise this is a very well conserved region of the protein. This indel by itself is neither a throwaway nor a showstopper. It would benefit from PCR of additional perissodactyls (rhino etc) to isolate horse or push the event further up the stem.
<span style="color: #0066CC;">ERSGVVCQTGRAFMIIQEQRTRAEEIFSLDEDVLPKPSFHHHSFWVNISNCSPTSGKQLD CDCP1_homSap Homo sapiens (human)
ERSGVVCQTGRAFMIIQEQRTRAEEIFSLDEDVLPKPSFHHHSFWVNISNCSPTSGKQLD CDCP1_panTro Pan troglodytes (chimp)
ERTSVVCQTGRAFMIIQEQRTRAEEIFSLDEDVLPKPSFHHHSFWVNISNCSPASGKQLD CDCP1_ponPyg Pongo pygmaeus (orang_sumatran)
ERTGVVCQTGRAFMIIQEQRTRAEEIFSLDEDALPKPRFHHHSFWVNISNCSPASGKQLD CDCP1_macMul Macaca mulatta (rhesus)
ERTGVVCQTGRAFMIIQEQRTRAEEIFSLDEDVLPKPSFHHHSFWVNISNCSPASGKQLD CDCP1_calJac Callithrix jacchus (marmoset)
ERTGVVCQTGRAFMIIQEQHTRAEEIFSLEEEVLPKPSFHHHSFWVNISNCSPASGKQLD CDCP1_otoGar Otolemur garnettii (bushbaby)
ERTGVVCQTGRAFMVLQEQRTRVEEIFSLEEEALPQAKLHHHSFWVNISNCSPASGKQLD CDCP1_tarSyr Tarsius syrichta (tarsier) bad trace
ERTGVVCQTGRAFMVLQEQRTRVEEIFSLEEEALPQAKLLHHSFWVNISNCSPASGKQLD CDCP1_micMur Microcebus murinus (mouse_lemur) bad trace
...GVVCQTGRAFLIIKEQRTRAEEIFSLEEEALPKPSFRHHSFWLNISNCSPASGKQLD CDCP1_tupBel Tupaia belangeri (tree_shrew)
ERSGLACQSGRAFMIIQEQQSRAEEIFSLEEEVLPKPSFHHHSFWVNISNCSPMNGKQLD CDCP1_musMus Mus musculus (mouse)
ERSGLACQSGRAFMIIQEQQTRAEEIFSLEEEVLPKPSFHHHSFWVNISNCSPMNGKQLD CDCP1_ratNor Rattus norvegicus (rat)
ERSGVVCQSGRAYMIIQEQQSQAEEIFSLEDDILPKPRCYHHSFWVNISNCSPASSKQ.. CDCP1_dipOrd Dipodomys ordii (kangaroo_rat)
ERTGVVCQSERAFMIIQEQRTRAEEIFSLEDDRLPKPSFHRHSFWVNISNCSPASGKQLD CDCP1_cavPor Cavia porcellus (guinea_pig)
ERIGVACQTGWALMIIQEQRSQPEEIFNLEEVMLPKPSFHYHNFWVNISNCSPVSGKQLD CDCP1_speTri Spermophilus tridecemlineatus (squirrel)
ERMGVVCQTGRAFMIIQEQQTRAKEIFSLE</span><span style="color: #FF0000;">E-V</span><span style="color: #0066CC;">LPEPRVRRRSFWVNVSNCSPASGKQLD CDCP1_oryCun Oryctolagus cuniculus (rabbit)
ERTGVVCQTGRAFMIIQEQRSRVEEIFSLEEEVLPKPRVHRHSFWVNVSNCSPASGKQLD CDCP1_ochPri Ochotona princeps (pika)
ERTGVVCQTGRAFMIIQEQRSKAEEIFSLEDEVLPKPSFHHHSFWVNISNCSPVSGKQLD CDCP1_canFam Canis familiaris (dog)
ERTGVVCQTGRAFMIIQEQRTKAEEIFSLEDEVLPKPSFHHHSFWVNISNCSPVSGKQLD CDCP1_felCat Felis catus (cat)
ERTGLVCQTGRAFMIIQEQRMRAEEIFSLE</span><span style="color: #FF0000;">E-V</span><span style="color: #0066CC;">LPKPRFHHHSFWVNISNCSPVSGKQLD CDCP1_equCab Equus caballus (horse)
ERTGLVCQTGRAFMIIQEQLTKAEQIFSLE</span><span style="color: #FF0000;">E-V</span><span style="color: #0066CC;">LPKSSSHHHNFWVNISNCSPVRGKQLD CDCP1_myoLuc Myotis lucifugus (microbat)
EQTGLVCQTGRAFMIVQEQRTRAEEIFSLE</span><span style="color: #FF0000;">E-V</span><span style="color: #0066CC;">LPKPGFRHHSFWVNISNCSPLSGKQLD CDCP1_pteVam Pteropus vampyrus (macrobat)
ERTGVVCQTGRAFMIIQEQRAHAEEIFSLEEEVLPKPSFRYHSFWVNISNCSPMSGKQLD CDCP1_bosTau Bos taurus (cow)
ERTGVVCQTGRAFMIIQEQRARAEEIFSLEEEVLPKPSFHHHSFWVNISNCSPASGKQLD CDCP1_susScr Sus scrofa (pig)
ERTGVVCQTGRAFMIIQEQRAHTEEIFSLEEEVLPKPSFRYHSFWVNISNCSPMSKKQLD CDCP1_turTru Tursiops truncatus (dolphin)
ERTGVVCQTGRAFMIIQEQRSHAEEIFSLEEEVLPKPSFRHHSFWVNISNCSPVSGKQL. CDCP1_vicVic Vicugna vicugna (vicugna)
EKSGVVCQTGRAFMILQDQQHHSEEIFSLEDEVLPKPRFHRHSFWVNISNCSPASGKQLD CDCP1_eriEur Erinaceus europaeus (hedgehog)
ERTGVVCHTGRAFMIIQEQQTHVEEIFSLEEDVLPKPSFYHHSFWVNISNCSPVSGKQLD CDCP1_sorAra Sorex araneus (shrew)
EQTGVVCQTGRAFMIIQEQRTRAEEIFSLEEEVLPKPSFRRHSFWVNISNCSPVSGKQLD CDCP1_dasNov Dasypus novemcinctus (armadillo)
ERTSLVCQTGRAFMIIQEQQTNAEEIFSLEEDMLPKPSFRHHSFWVNISNCSPMSGKQLD CDCP1_choHof Choloepus hoffmanni (sloth)
ERTGVVCQTGRAFMIIQEQQSNAEEIFNLEDQVLPKPRFHHHSFWVNISNCSPMSGKQLD CDCP1_loxAfr Loxodonta africana (elephant)
ERTGVVCQTGRAFMIIQEQQSHAEEIFNLEDQVLPKPRFHHHSFWVNISNCSPMSGKQLD CDCP1_proCap Procavia capensis (hyrax)
ERTGVVCQTGRAFMIIQEQRAHAEEIFNLEDEVLPKPSFRHHSFWVNISNCSPVSGKQFE CDCP1_echTel Echinops telfairi (tenrec)
DRMGVSCETGRAFMIIQEQKAKAEEIVSRDDEPLPKPKDLHHNFWVNISNCSPMNGKQLD CDCP1_monDom Monodelphis domestica (opossum)
ERMGVACETGRAYMIIREQIPKAEEMVTREDELLPKPQVLHHSFWVNVSNCSPMKGKQLD CDCP1_ornAna Ornithorhynchus anatinus (platypus)
DRMGITCETGRAYVNIKEQMPGAEETVRREDELLPQPRNMHYNFWVNISNCKPVDPMQLS CDCP1_galGal Gallus gallus (chicken)
EWMGVTCEENRAHIYIREHNPGAKEMVCRDDEKLPRTLEMHDHFWVNITNCKPAAGKLLS CDCP1_anoCar Anolis carolinensis (lizard)
DRMDIMCETGRAFINIKEQKSWADIVL</span><span style="color: #FF0000;">K-D</span><span style="color: #0066CC;">YDTFPSSINLFYPFWFNITNCKPKSRQKLQ CDCP1_xenTro Xenopus tropicalis (frog)</span>
not available CDCP1_oviAri Ovis aries (sheep)
not sought CDCP1_macEug Macropus eugenii (wallaby)
not sought CDCP1_taeGut Taeniopygia guttata (finch)
=== Insertion in IRS1 in microbat and horse shared by macrobat but quasi-homoplasic in lemur ===
A one-residue insertion occurs in IRS1 in horse, microbat, and macrobat relative to other placentals but also is found at a similar site in lemur but not bushbaby. Close examination of lemur suggests its insertion comes at a slightly further downstream, ie AHHHQ  vs AHHQ in bushbaby. That insertion is supported by 3 traces that
agree on the location of the insertion: ti|1550444960, 1559993096, and 1569281779. Three traces also support no comparable insertion in bushbaby.
For unknown reasons, this region is poorly represented in trace archives, being missing in 8 genome project mammals including several with very high coverage. The insertion is located near a somewhat repetitive area of histidines and glutamines (which have two codons each and differ only in third codon position). Armadillo has a separate 4 amino acid deletion upsteam. Opossum is already rather diverged and chicken/lizard proteins are irrelevent.
Overall, while homoplasy in lemur can be argued away, the region is somewhat prone to indels. Additional species from PCR within Laurasiatheres could strengthen this candidate considerably.
ADDSSSSTSSDSLGGGYCGARLEPSLPH-PHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_homSap Homo sapiens (human)
ADDSSSSTSSDSLGGGYCGARLEPSLPH-PHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_panTro Pan troglodytes (chimp)
ADDSSSSTSSDSLGGGYCGARLEPSLPH-PHHQVLQPHLPRKVDTAAQTNSRLARPTLL IRS1_ponPyg Pongo pygmaeus (orang_sumatran)
VDDSSSSTSSDSLGGGYCGARLEPSLPH-PHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_macMul Macaca mulatta (rhesus)
ADDSSSSTSSDSLGGGYCGARLEPSLPH-PHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_papAnu Papio anubis (baboon)
ADDSSSSTSSDSLGGGYCGARLEPSLPH-PHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_cerAet Cercopithecus aethiops
VEDSSSSTSSDSLGGGYCGARMEPSLSH-SHHQVLQLHLPRKVDSAAQTNSRLARPTRL IRS1_calJac Callithrix jacchus (marmoset)
AEDSSSSTSSDSLGGGYCGARPEPGLPH-PHHQILQSHLPRKVDTAAQTNSRLVRPTRL IRS1_tarSyr Tarsius syrichta (tarsier) bad trace
<span style="color: #0066CC;">AEDSSSSTSSDSLGGGYCGARQEPGLPH</span><span style="color: #FF0000;">-AHH</span><span style="color: #0066CC;">QVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_otoGar Otolemur garnettii (bushbaby)
AEDSSSSTSSDSLGGGYCGARLEPGLPH</span><span style="color: #FF0000;">AHHH</span><span style="color: #0066CC;">QVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_micMur Microcebus murinus (mouse_lemur)</span> <span style="color: #990099;">bad trace</span>
AEDSSSSTSSDSLGGGYCGARPESGLPH-LHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_tupBel Tupaia belangeri (tree_shrew)
AEDSSSSTSSDSLGGGYCGARPESSLTH-PHHHVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_musMus Mus musculus (mouse)
AEDSSSSTSSDSLGGGYCGARPESSVTH-PHHHALQPHLPRKVDTAAQTNSRLARPTRL IRS1_ratNor Rattus norvegicus (rat)
AEDSSSSTSSDSLGGGYCGARPEPGLPH-PHHHILQPRLPRKVDTAAQTNSRLARPTRL IRS1_cavPor Cavia porcellus (guinea_pig)
AEDSSSSTSSDSLGGGYCGARPEPGLPH-PHHHVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_oryCun Oryctolagus cuniculus (rabbit)
AEDSSSSTSSDSLGGGYCGVRPDPGLPH-IHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_canFam Canis familiaris (dog)
AEDSSSSTSSDSLGGGYCGVRPDSGLPH-IHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_felCat Felis catus (cat)
<span style="color: #00CC99;">AEDSSSSTSSDSLGGGYCGARSEPGLPH</span><span style="color: #FF0000;">H</span><span style="color: #00CC99;">LHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_equCab Equus caballus (horse)
AEDSSSSTSNDSLGGGYCGVRPEPSLPQ</span><span style="color: #FF0000;">H</span><span style="color: #00CC99;">LHHQVLQSHLPRKVDSAAQTNSRLARPTRL IRS1_myoLuc Myotis lucifugus (microbat)
AEDSSSSTSSDSLGGGHCGARPEPGLPH</span><span style="color: #FF0000;">H</span><span style="color: #00CC99;">LHHQVLQSHLPRKVDTAAQTNSRLARPTRL IRS1_pteVam Pteropus vampyrus (macrobat)</span>
AEDSSSSTSSDSLGGGYCGARPEPGLPH-LHHQVLQAHLPRKVDTAAQTNNRLARPTRL IRS1_bosTau Bos taurus (cow)
.....SSTSSDSLGGGYCGARPEPGLPH-LHHQVLQPHLPRKVDTAAQTNNRLARPTRL IRS1_susScr Sus scrofa (pig)
ADDSSSSTSSDSLGGGYCGGRPEPGLPH-LHHQVLQPHLPRKVDTAAQTNRRLTRPTKL IRS1_eriEur Erinaceus europaeus (hedgehog)
AEDSSSSTSSDSLGGGYCAARPEPGLPP-LHHQVLQPHLPRKVDTAAQTHSRLTRPTRL IRS1_sorAra Sorex araneus (shrew)
AEDSSSSTSSDSLGGGYCGVRP<span style="color: #FF0000;">E----H</span>-LHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_dasNov Dasypus novemcinctus (armadillo)
AEDSSSSTSSDSLGGGYCGPRPEPGHPH-LHHQVLQPHLPRKVDTAAQTNSRLTRPTRL IRS1_proCap Procavia capensis (hyrax)
AEDSSSSTSSDSLGGGYCGPRPEPGHPP-LHHQVLQPHLPRKVDMAAQTNSRLARPTRL IRS1_echTel Echinops telfairi (tenrec)
AEDSSSSASSDSLGG<span style="color: #FF0000;">G--GGQ-E</span>GVHGH-LHHQALHQHLPRKMDLVAQTKSRLTRPTRL IRS1_monDom Monodelphis domestica (opossum)
not available  IRS1_speTri Spermophilus tridecemlineatus (squirrel)
not available  IRS1_dipOrd Dipodomys ordii (kangaroo_rat)
not available  IRS1_ochPri Ochotona princeps (pika)
not available  IRS1_oviAri Ovis aries (sheep)
not available  IRS1_turTru Tursiops truncatus (dolphin)
not available  IRS1_vicVic Vicugna vicugna (vicugna)
not available  IRS1_choHof Choloepus hoffmanni (sloth)
not available  IRS1_loxAfr Loxodonta africana (elephant)
not available  IRS1_ornAna Ornithorhynchus anatinus (platypus)
not available  IRS1_xenTro Xenopus tropicalis (frog)
not sought    IRS1_macEug Macropus eugenii (wallaby)
not sought    IRS1_taeGut Taeniopygia guttata (finch)
too diverged  IRS1_galGal Gallus gallus (chicken)
too diverged  IRS1_anoCar Anolis carolinensis (lizard)
=== Deletion in KIAA1009 of microbat and horse not shared by macrobat; rabbit indel not shared by pika ===
The one-residue deletion found in horse and microbat is not found in macrobat and so is not informative. They do not appear to be located quite orthologously. A five-residue deletion in rabbit is not supported in pika. This illustrates not that terminal leaf indels are common but rather they do exist and the selection algorithm can find them.
DDIKEAHQITVRNLEAEIDVLKHQNAELDVKKNDKDDEDFQSIEFQVEQAHAKAKLVRLN KIAA1009_homSap Homo sapiens (human)
DDIKEAHQITVRNLEAEIDVLKHQNAELDVKKNDKDDKDFQSIEFQVEQAHAKAKLVRLN KIAA1009_panTro Pan troglodytes (chimp)
DDIKEAHQITVRKLEAEIDVLKHQNAELDVKKNDKDDKDFQSIEFQVEQAHAKAKLVRLN KIAA1009_ponPyg Pongo pygmaeus (orang_sumatran)
DDIKEAHQITVRNLEAEIDILKHQNAELDVKKNDKDDKDFQSIEFQVEQAHAKAKLVRLN KIAA1009_macMul Macaca mulatta (rhesus)
DDTKEAHQITVRKLEAEIDVLKHQNAELDVKKSGKVDKDFQSIEFQVEQAHAKAKLVRLN KIAA1009_calJac Callithrix jacchus (marmoset)
GDIKEAHQITVRKLEAEIDVLKHQNADLEHKKNDKGDQGLQSIEFQVEQAQARAKLARLN KIAA1009_musMus Mus musculus (mouse)
GGIKEAHQITVRKLEAEIDVLKHQNAHLEHKKNDKEDQDLQSIEFQVEQAQARAKLARLN KIAA1009_ratNor Rattus norvegicus (rat)
.DIKETHQTIVRDLEAEIDVLKRQNAELELKKNGTDDKDFQSIELQVEQAHAKAKLVRLN KIAA1009_cavPor Cavia porcellus (guinea_pig)
xxx KIAA1009_speTri Spermophilus tridecemlineatus (squirrel)
.DIKEAHLTTVRNLETEIDLLKHRNTELKHKKNDRDGKDLQSIELQVEQAHAKAKLVRL. KIAA1009_dipOrd Dipodomys ordii (kangaroo_rat)
DDIKEAHQITVRNLEAEIVVLKQRSAELELKKNGKDD-----IEFQVEQAHAKAKLVRLN KIAA1009_oryCun Oryctolagus cuniculus (rabbit)
..IKETHEIAVRNLEAEIDGLKQRNAELELKKNDKDGKDFQSIEFQVEQAHAKAKLVRL. KIAA1009_ochPri Ochotona princeps (pika)
SDIKEAHQITVRNLEAEINILKHQNAELECKKNDKDDKDFQSIEFQVEQAHAKAKLVRLN KIAA1009_canFam Canis familiaris (dog)
SDLKEAHQLTVRNLEAEIDVLKHRNAELELK-NDKDDQDFQSLEFQVEQAHAKAKLVRLN KIAA1009_equCab Equus caballus (horse)
.DIKEAHEITVRNLEAEIDTFKQQNAELELKKN-RDDKDFQSIEFQVEQAHAKAKLARLN KIAA1009_myoLuc Myotis lucifugus (microbat)
DDIKEAHQITVRNLEAEIDTLKHQNAELELKKDDKDDKDFQSIEFQVEQAHAKAKLVRLN KIAA1009_pteVam Pteropus vampyrus (macrobat)
DDVKEAHQITIRNLEAEIDVLKHQNAELELRKTEKDDKDFQSIEFQVEQAHSKAKLVRLN KIAA1009_bosTau Bos taurus (cow)
...KESHQSTVRNLEAEIDVLKHQNAELELKKNDKDDKDFQSIEFQVeQAHSKAKLVRLN KIAA1009_susScr Sus scrofa (pig)
DDVKEAHQITVGNLEAEIDVLKHQNAEWELKKDDKDDQDFQSIEFQVEQAHSKAKLVRL. KIAA1009_turTru Tursiops truncatus (dolphin)
NDLKEAHQITIRNLEAEIDILKNQNADLEHKKNDKDDKDFQSIEFQVEQAHAKAKLVRLN KIAA1009_eriEur Erinaceus europaeus (hedgehog)
.EIKEAHQITVKNLEAEIDVLKHQNAKLELKKNSKDNKDFQSIEFRVEQAHAKAKLVRLN KIAA1009_sorAra Sorex araneus (shrew)
.DLTGAHQITVRNLEAEIDVLKHQNAELELKKNDKHDKDFHSIEFQVEQAHAKAKLVRLN KIAA1009_choHof Choloepus hoffmanni (sloth)
.DIKEAHQITVRNLEAEIDMLKHQNAELELKKNDKDDKDFQSLEFQVEQAHAKAKLVRLN KIAA1009_loxAfr Loxodonta africana (elephant)
.DMKDVHLATVKTLEAEIESLKSQNAQLELKKNEKDDNDFQSLEFQVEQAHTKARLVRLN KIAA1009_monDom Monodelphis domestica (opossum)
.DVKEAHQVTVRNLEAEIEALKKQNAQLELQKSERGDQDFQAIEFQVEQAHTKARLARLN KIAA1009_ornAna Ornithorhynchus anatinus (platypus)
.NLKTTHQITVENLKTEIENLKSQNSQLKLRSK-KDNKDLQSTDWQMKQGKTKEKLLKLN KIAA1009_galGal Gallus gallus (chicken)
.NVNEAHQMTVNNLQAEIDSLRSQIGELERQKNATDNAELQSLEHQVEQAHAKAKMVRLN KIAA1009_anoCar Anolis carolinensis (lizard)
not available KIAA1009_felCat Felis catus (cat)
not available KIAA1009_oviAri Ovis aries (sheep)
not available KIAA1009_vicVic Vicugna vicugna (vicugna)
not sought    KIAA1009_otoGar Otolemur garnettii (bushbaby)
not sought    KIAA1009_micMur Microcebus murinus (mouse_lemur)
not sought    KIAA1009_tupBel Tupaia belangeri (tree_shrew)
not sought    KIAA1009_tarSyr Tarsius syrichta (tarsier)
not sought    KIAA1009_dipOrd Dipodomys ordii (kangaroo_rat)
not sought    KIAA1009_dasNov Dasypus novemcinctus (armadillo)
not sought    KIAA1009_proCap Procavia capensis (hyrax)
not sought    KIAA1009_echTel Echinops telfairi (tenrec)
not sought    KIAA1009_macEug Macropus eugenii (wallaby)
not sought    KIAA1009_taeGut Taeniopygia guttata (finch)
chr6 84919393 84919456 -3
human GACTGAAAATCTTCATCATCTTTATCATTTTTCTTGACGTCTAATTCAGCATTCTGATGTTTA
horse GACTGGAAATCTTGATCATCTTTGTCATTT---TTGAGTTCTAACTCAGCATTCCGATGTTTG


human GACTGAAAATCTTCATCATCTTTATCATTTTTCTTGACGTCTAATTCAGCATTCTGATGTTTAA
mibat GACTGGAAATCTTTATCATCTCT---ATTTTTCTTGAGTTCTAACTCAGCATTCTGTTGTTTAA
=== Insertion in GATA6 in horse and bats not shared by other Laurasiatheres ===
This is an apparently informative one-residue insertion in the well-conserved terminal exon of GATA6 for horse, microbat, and macrobat but no others. Note though that dog but not cat has an upstream insertion of 3 glycines and vicugna has a serine inserted seemingly at this same upstream site. The horse/bat insertion can be located with confidence given the overall conservation even though it was offset slightly in the original nucleotide alignment. There is no observable polymorphism or ambiguity in the relevent traces for horse or bats.
<span style="color: #990099;">TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRPDSWC GATA6_homSap Homo sapiens (human)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_panTro Pan troglodytes (chimp)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_ponPyg Pongo pygmaeus (orang_sumatran)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_macMul Macaca mulatta (rhesus)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_calJac Callithrix jacchus (marmoset)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_tarSyr Tarsius syrichta (tarsier)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_otoGar Otolemur garnettii (bushbaby)
ANPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_micMur Microcebus murinus (mouse_lemur)
TNPENSELKYSGQDGLYIGVSLASPSEVTSS-VRQDSWC GATA6_tupBel Tupaia belangeri (tree_shrew)
.NPENSDLKYSGQDGLYIGVSLSSPAEVTSS-VRQDSWC GATA6_musMus Mus musculus (mouse)
ANPENSDLKYSGQDGLYIGVSLSSPAEVTSS-VRQDSWC GATA6_ratNor Rattus norvegicus (rat)
TNPEGSELKYSGQDGLYIGVSMASPAEVTSS-VRQDSWC GATA6_cavPor Cavia porcellus (guinea_pig)
TNPEYSKLHYSGQNGLHIGFSLALPAEVTSS-VGQDSYC GATA6_speTri Spermophilus tridecemlineatus (squirrel)
PTPENSELKYSVQDGLYIGVSLSSPAEVTSS-VRQDSWC GATA6_dipOrd Dipodomys ordii (kangaroo_rat)
SNPENSELKYSGQDGLYMGVNLASSAEVTSS-VRQDSWC GATA6_oryCun Oryctolagus cuniculus (rabbit)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_ochPri Ochotona princeps (pika)</span>
TNPE<span style="color: #0066CC;">NG</span><span style="color: #6699FF;">EL</span>KYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_canFam Canis familiaris (dog)<span style="color: #0066CC;"> NG</span><span style="color: #FF0000;">GGG</span><span style="color: #6699FF;">EL insert</span>
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_felCat Felis catus (cat)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS<span style="color: #FF0000;">S</span>VRQDSWC GATA6_equCab Equus caballus (horse)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS<span style="color: #FF0000;">S</span>VRQDSWC GATA6_myoLuc Myotis lucifugus (microbat)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS<span style="color: #FF0000;">S</span>VRQDSWC GATA6_pteVam Pteropus vampyrus (macrobat)
ANPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_bosTau Bos taurus (cow)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_oviAri Ovis aries (sheep)
ANPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_susScr Sus scrofa (pig)
ANPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_turTru Tursiops truncatus (dolphin)
ANPE<span style="color: #0066CC;">NS</span><span style="color: #6699FF;">EL</span>KYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_vicVic Vicugna vicugna (vicugna) <span style="color: #0066CC;">NS</span><span style="color: #FF0000;">S</span><span style="color: #6699FF;">EL insert</span>
SNLENSELKYSGQDGLFIGVSLASPAEVTSS-VRQDSWC GATA6_eriEur Erinaceus europaeus (hedgehog)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_sorAra Sorex araneus (shrew)
<span style="color: #990099;">TNPDNSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_dasNov Dasypus novemcinctus (armadillo)
TNPENSELKYSAQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_loxAfr Loxodonta africana (elephant)
TNPENSELKYSAQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_proCap Procavia capensis (hyrax)
.NPETSELKYSAPDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_echTel Echinops telfairi (tenrec)
TSPESTALKYSGQDGLYSGVSLTSTAEVTAS-VRQDSWC GATA6_monDom Monodelphis domestica (opossum)
TSPESTALKYSGQDGLYSGVSLTSTAEVTAS-VRQDSWC GATA6_triVul Trichosurus vulpecula (possum)
RSPESSALKYSGQQGLFPGVSLTSTAEVTAS-VRQESWC GATA6_ornAna Ornithorhynchus anatinus (platypus)</span>
not available GATA6_oviAri Ovis aries (sheep)
not available GATA6_choHof Choloepus hoffmanni (sloth)
not sought    GATA6_macEug Macropus eugenii (wallaby)
not sought    GATA6_taeGut Taeniopygia guttata (finch)
not sought    GATA6_galGal Gallus gallus (chicken)
not sought    GATA6_taeGut Taeniopygia guttata (finch)
not sought    GATA6_anoCar Anolis carolinensis (lizard)
chr18 18034707 18034767 3
human GCGTCAGTCTCGCCTCGCCGGCCGAAGTCA---CGTCCTCCGTGCGACCGGATTCCTGGTGCG
horse GCGTCAGCCTGGCCTCGCCGGCTGAAGTCACATCGTCTTCGGTGAGACAGGATTCCTGGTGCG
human GCGTCAGTCTCGCCTCGCCGGCCGAAGTCACGTCCTCC---GTGCGACCGGATTCCTGGTGCGC
mibat GCGTCAGCCTGGCCTCACCGGCCGAAGTCACGTCCTCCTCGGTGAGACAGGATTCGTGGTGTGC
=== Terminal frameshift in RBP3 (IRBP) ===
The last exon of RBP3, like in many proteins, does not appear to be under a great deal of selective pressure. This surfaces in a certain amount of observed 'terminal wander' as various mutations allow readthru of the original stop codon to the next one that occurs by chance downstream. Here pegasoferae, relative to artiodactyls, all share a one bp indel within coding that causes an altogether novel amino acid sequence to terminate the protein.
The history here is quite complex when tetrapods outside Laurasiatheres are included. Ancestrally, the exon was clearly much shorter, terminating at consistent length just after module M4 ended in the RPB3 internal repeat structure from frog to marsupial divergence. In afrotheres, either the stop codon mutated or a frameshift occured, causing the protein to become longer. The new stop codon in hyrax represents the ancestral placental position. Elephants retain a cryptic stop codon here but evolved an earlier one that is used today. This stop codon and some aspects of sequence was conserved in pegasoferae but not artiodactyls (though by reinstituting the original trinucleotide ggg and former reading frame, residual ancestral sequence as well as the original distal stop codon can still be seen. Shrew and hedgehog diverged by a different scheme and are unhelpful.
In euarchontoglires, the placental stop codon persists only in treeshrew and lemurs. Later diverging primates evolved an earlier stop codon a few residues past the ancestral one; rodents are also short but variable. Despite its complexity, this region of the gene is a strong rare genomic event unlikely to recur. Unfortunately, it is quite clear from outgroup species such as treeshrew and hyrax that the frameshift event took place in stem artiodactyls whose monophylogeny is not in doubt) rather than in stem (bat + horse + carnivores). Note early artiodactyls pig and lama both fixed the frameshift so no phylogenetic resolution is provided within artiodactyls either.
The last exon begins as GERYGSKKSMVILTSSVTAGTAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDTNLYLTIPTARSVGASDGSSWEGVGVTPHVVVPAEEALARAKEM and is followed by the terminal reqions shown below (which are anchored to the QH feature which is reliably locatable in all species:
QHNQLRVKRSPGLQDHL*                                            human
QHNQLRVKRSPGLQDHL*                                            chimp
QHNQLRVKRSPGLQDHL*                                            gorilla
QHNQLRVKRSPGLQDHP*                                            orang
QHNQLRVKRSPGLQDHP*                                            macaque
QQNQLRVKRSPGLQSHL*                                            marmoset
QYNLPRVRRSPGLQ                                                tarsier
QHTLLRSRRSASLQGHQ                                              lemur
QHKLLRLRRSTGLQGHSEGGPHGQSPGAGRTSGPSTTSVS----AHGPA*GSWGQRGACQAL mouse_lemur
QHTLRRARRSPGWQSPGLRGLLGGVRGPSPRLSRTSGPQAKGAPARGPA*DPQGQHRGLLSS treeshrew
QHTLLRARRSL----RGQRLRRQRQGRAGPLGHIQRTLGHEVLTEAP KGWKRGLLHSSWA* pig contig
QHTLLRVRRSAGLRGRHKGLLGQHPGRAGPLGHFQGAPRHEVLTEVP KGRKRGVM...    lama
QHTPLRARRSPRLHGRRKGHHRQSQGRAGSLGRNQGVgRPEVLTEAP SGQKRGLLQCG*  cow
QHTLLRARRSPRLQGRRKGHRSQSQKRPGPPGHVQGAPRHEVLTEAP KGQQRGLLPSG*  dolphin
QHTLLRARRSPGLQGCRDDLFQQSPGVGGTSGHTPRAFQHVVLPEAP EGQQRALLSSD*  horse corrected to artiodactyl
QHTLLRARRSP              RMGGTSRPHTKALRHVVLPEAS GFRKGTC*AP    cat corrected to artiodactyl
QHPARRARRSP-------------RAPGTSRRHTRGWRPWPGLPPEA RGSSGACWAP    dog corrected to artiodactyl
QHTLMRVRRSPGQQGPQEGLRGQSPRVSGISGPHIMNAKAPQARGPA*KGQKRALLSSG*  macrobat
QHTLLRARRSPGLQGCRDDLFQQSPGVGGTSGPYPKGI---PACGPA*EGQQRALLSSD*  horse 
QHTLLRARRSP--------------RMGGTSRPHTKGT---PARGPA*              cat
QHPARRARRSP--------------RAPGTSRRHTRRV-AALARAPA*GQGQLRGLLGST  dog
QPTVLRAKRSPSL* 0                                              shrew
QNVQLRVKRNLA-QQGHWESIQGHSSGVGGVTELNIKGA*                      hedgehog
HHSLQMV*RLNAGLQGHRRGLGG*WIEPRAGGASGPRTEGTRARGPA*RSGGQQRGLLSP  elephant
QDSLKAVKLSAGLQGLRAGFGVQSSWVGGTSGPH---TESTSEHGPA*VCWEQEKGMLRS*  hyrax
NHHLQRAK*                                                      opossum
IHHLQRAD*                                                      wallaby
RAHLEHRD*                                                      platypus
NAHLHSSR*                                                      finch
SAHLHSSR*                                                      chicken
KAHLH---*                                                      lizard
ESQLEGRR*                                                      frog
cow terminus before and after frameshift:
 
cagcacactccgctaagggcgaggcgcagcccacgcctgcatggccgccgcaagggccaccacaggcagagccagggaagggcgggatctctgggccgcaaccaaggggtgggcaggcctgaggtcctgactgaggcccccagtgggcagaaaaggggcctgctgcagtgtggt
  Q  H  T  P  L  R  A  R  R  S  P  R  L  H  G  R  R  K  G  H  H  R  Q  S  Q  G  R  A  G  S  L  G  R  N  Q  G  V  G  R  P  E  V  L  T  E  A  P  S  G  Q  K  R  G  L  L  Q  C  G 


cagcacactccgctaagggcgaggcgcagcccacgcctgcatggccgccgcaagggccaccacaggcagagccagggaagggcggatctctgggccgcaaccaaggggtgggcaggcctgaggtcctgactgaggcccccagtgggcagaaaaggggcctgctgcagtgtggt
  Q  H  T  P  L  R  A  R  R  S  P  R  L  H  G  R  R  K  G  H  H  R  Q  S  Q  G  R  A  D  L  W  A  A  T  K  G  W  A  G  L  R  S  -  L  R  P  P  V  G  R  K  G  A  C  C  S  V 


=== SWS1 deletion restricted to Caniformia ===


This is a one-residue deletion in the second transmembrane helix of this shortwave imaging opsin considered under informative opsin indels. This is too phylogenetically narrow to illuminate Pegasoferae.


SWS1_homSap  LNAMVLVATLRYKKLRQPLNYILVNVSFG G FLLCIFSV F PVFVASCNGYFVFGRHVC human
SWS1_tarSyr  LNAMVLVATLHYRKLRQPLNYILVNVSLG G FLLCIFSV L PVFIASCRGYFVFGRHVC tarsier
SWS1_oryCun  LNAMVLVATLRYKKLRQPLNYILVNISLA G FLACIFSV F NVFVASCYGYFVFGRFVC rabbit
SWS1_ratNor  LNATVLVATLHYKKLRQPLNYILVNVSLG G FLFCIFSV F TVFIASCHGYFLFGRHVC rat
<font color ="blue">SWS1_ailMel  LNATVLVATLRYRKLRQPLNYILVNVSLA G FVYCI<font color ="red">-</font>SV S TVFIASCHGYFIFGRHVC panda
SWS1_canFam  LNGTVLVATLRYKKLRQPLNYILVNVSLG G FLYCI<font color ="red">-</font>SV S TVFIASCQGYFVFGRHVC dog
SWS1_enhLut  LNATVLVATLRYKKLRQPLNYILVNVSLG G FIYCI<font color ="red">-</font>SV S SVFIASCHGYFIFGHHIC otter
SWS1_phoVit  LNASVLVATLRYKKLRQPLNYILVNVSLG G FLYCI<font color ="red">-</font>SV S SVFIASCQGYFIFGRHVC seal
SWS1_ursMar  LNATVLVATLRYRKLRQPLNYILVNVSLA G FVYCI<font color ="red">-</font>SV S TVFIASCHGYFIFGRHVC bear</font>
<font color ="green">SWS1_felCat  LNATVLVATLRYRKLRQPLNYILVNVSLG G FLYCVSSV S IVFITSCHAYFIFGRHVC cat</font>
<font color ="brown">SWS1_hipAmp  LNATVLVATLRYRKLRQPLNYILVNVSLG G FIYCIFSV F VVFITSCHGYFVFGRHVC hippo
SWS1_ptePum  LNATVLVATLRYRKLRQPLNYILVNVSLG G FLFCIFSV F TVFIASCQGYFVFGRHVC bat
SWS1_talEur  LNATVLVATLRYRKLRQPLNYILVNVSLG G FLFCIFSV L TVFIASCKGYFIFGRHVC mole
SWS1_sorAra  LNATVLVPTLRYRKLRQPLNYILVNVSLG G FLFCIFSV F TVIIASCKGYFVIGRHVC shrew
SWS1_susScr  LNATVLVATLRYRKLRQPLNYILVNVSLG G FIYCIFSV F SVFIASCHGYFVFGRRVC pig
SWS1_bosTau  LNATVLVATLRYRKLRQPLNYILVNVSLG G FIYCIFSV F IVFITSCYGYFVFGRHVC cow
SWS1_lamPac  LNATVLIATLRYRKLRQPLNYILVNVSLG G FIYCMFSV F CVFVASCYGYFVFGRRVC lama
SWS1_turTru  LDATVLVATLRYRKLRQPLNYILVNVSLG G FIYCIFSV F VVFITSCHGYFVFGRHVC dolphin</font>
SWS1_echTel  LNAVVLVATLRYRKLRQPLNYILVNVSLA S VLFCVISV F TVFVASCHGYFIFGRHVC hyrax
SWS1_monDom  LNAVVLVATLRYKKLRQPLNYILVNVSLC G FIFCIFAV F TVFISSSQGYFIFGRHVC
SWS1_smiCri  LNGVVLIATLRYKKLRQPLNYILVNISLA G FIFCVFSV F TVFVSSSQGYFVFGRHVC
SWS1_tarRom  LNAVVLIATLRYKKLRQPLNYILVNISLA G FIFCVISV F TVFISSSQGYFIFGRHVC
SWS1_galGal  LNAVVLWVTVRYKRLRQPLNYILVNISAS G FVSCVLSV F VVFVASARGYFVFGKRVC
[[Category:Comparative Genomics]]
[[Category:Comparative Genomics]]

Latest revision as of 08:07, 1 September 2018

Can rare genomic events establish Pegasoferae?

Pegasoferae is a novel proposal using rare genomic events involving retroposon insertions to establish the phylogenetic ordering within Laurasiatheres, grouping bats, perissodactyls and carnivores to the exclusion of the other hoofed mammalian group, artiodactyls. Bats have been placed in many previous locations, notably in the Euarchonta wing (outgroup to primates). While that particular idea is clearly refuted by many lines of evidence, the proper placement of bats remains under discussion.

Pegasoferae.png

Rare genomic events may be more useful for this than maximal likelihood because the orders of Laurasiatheres may have diverged relatively rapidly. Retroposon events are so numerous per million years however that they may be able to resolve branching at these tight nodes. However they suffer from homoplasy in that separate insertion events from a given parental element can look very similar and because deletions over time (no selection for their retention) can cause their disappearance and so confusion with lineages that never had the insertion.

Qualifying retroposons need to be situated between two well-conserved flanking markers because orthology is otherwise difficult to decisively establish in intergenic regions. These markers ideally are no more than 1500bp apart to allow tiling of traces for species without assemblies (eg vicugna, pig, dolphin, macrobat in Laurasiatheres) and spanning PCR runs. Higher sampling density greatly enhances the ability to correctly infer the sequence of events.

Short coding indels in coding exons can also be phylogenetically informative. Here if the exon is otherwise quite conserved, the risk of homoplasy (recurrent events at the same or indistinguishably similar position) is fairly low. These events are inherantly rare first because conserved regions of a protein may not admit indels structurally (ie are inactivated) and second because the window of relevancy for a given tree topology issue may only be a small fraction of elapsed evolutionary time (eg 1 million year stem on a 85 myr branch).

Coding indels can exhibit the usual problems of lineage-sorting: two co-existing alleles at the time of speciation that resolve differently in descendent lineages. Insertions, while a third as common as deletions and so less likely to have arise multiple times, are more subject to subsequent confusing reversion; deletions are less likely to revert to ancestral length for lack of genetic mechanism. It goes without saying that indels from repetitive regions or in dna of anomalous composition are wholly unsuitable for taxonomic purposes.

Methods for re-analysis and supplementation of L1MA9 data

Nishihari et al located 4 retroposon insertion events that support Pegasoferae. In the ensuing 2-3 years, it has become possible to reinvestigate these events with additional species utilizing bioinformatic methods on the 10 available Laurasiathere genomes (not all of which will completely cover a given event).

This can be done fairly rapidly (though only a subset of the putatively informative L1MA9 insertions are analyzed here). First, the primers used by the Okada group are blatted into the UCSC genome browser of an appropriate species (dog). The reverse strand primer must be first reverse-complemented with the UCSC utilities tool for a single line of Blat output to span the region of interest.

In every case studied here, the L1MA9 elements lie within small introns of coding genes. That means typically 30-40 amino acids from each flanking exon are available to create reliable anchors for future blast searches at NCBI. Without these anchors, L1MA9 elements do not necessarily retrieve orthologous elements in other species via blast, for the reason that the active L1MA9 parent element may have spun off subsequent fragments that are closer in sequence.

Next, dna spanning the exons and their internal intron are collected from Laurasiatheres with UCSC genome browsers, notably dog, cat, horse and cow. This dna is then marked up for all retroposons using the RepeatMasker track. Here it is important to track orientation of the repeat element (letting the reading frame of the exons define the positive strand convention), the fragment coordinates relative to an idealized repeat of the given class in the underlying RepeatMasker library, and the percent identity to this element.

These three steps allow in-depth comparison of putatively orthologous retroposons, noting however in the case of L1MA9 elements that fragment coordinates are very similar in many thousands of these insertions due to the replication mechanism favoring distal fragments of similar lengths. Thus homoplasic events cannot truly be ruled out even upon this closer examination.

The comparative genomics is extended now to additional species using tblastn of the WGS contig division of GenBank. This target database stores 2x assemblies of species such as microbat, hedgehog, and shrew. The spanning contig GenBank entries are then uBlasted against the growing database of fiducial sequences to locate the exons and intervening sequence. The latter is most conveniently retrieved by screen-scraping of 6-frame translation, dropping out the alternate lines containing the amino acids.

The latter two species exons can sometimes be retrieved faster from the 28-species alignment track at UCSC -- genomic alignment provides more reliable orthologs -- some lineages could have idiosyncratic segmental duplications that could cause cross-matching. If the coding regions are evolving too fast, the whole enterprise becomes questionable. Another pitfall is paralogs. Here GeneSorter at the UCSC site can be consulted, at least for human, to rapidly examine the situation.

Next, the est_other and nr divisions of GenBank are probed to retrieve any data that might be available from non-genomic projects. Transcripts per se don't seem useful here (lack the intron of interest) yet they provide precise probes later of the trace archives for the given species.

Finally, the trace achives are consulted for residual species such as macrobat, vicugna, sheep, pig, and dolphin. Note too that contigs and genomes often leave out singleton traces so these species can be completed here as necessary. The approach here is to tile in from both directions extending the reliable exon matches (if any). Since the L1MA9 elements needed to occur in small introns given the Nishihari et al discovery approach, usually 3 traces suffice to tile the intron successfully.

Trace reads are inherently error-prone (hence the need for 6x coverage to obtain a reliable genomic assembly). However here it is unlikely that a whole L1MA9 element would be missing unless the species in question had two distinct alleles. In evaluating rare genomic events, it is important to check all high-quality covering traces to rule out such polymorphisms because these would seriously undercut the whole exercise.

After obtaining data from all available Laurasiatheres, the sequences are marked up with different colors for their various constituent elements as illustrated below. Note the fasta header can carry the exonic sequence as well as quantitative information about the repeat elements. By extracting header lines only, a simple flatfile database emerges suitable for making simple summary comparative diagrams/

Analysis of L1MA9 retroposon INT189

The phlogenetic distribution of the L1MA9 retroposon INT189 has been taken as evidence for bats being the immediate outgroup of horse + dog. That interpretation can be revisited using newly available genomes. Yet only two sequences representing perissodactyl and carnivore are at GenBank as cat assembly has a gap in the critical region. But other new data in 3 bats and 4 cetartiodactyls and 2 shrew/hedgehog confirm the lack of L1MA9 near the distal exon.

The trouble is a second L1MA9 element lies upstream of the MER58A middle marker. This is lacking in both carnivores. Evidently it was deleted in stem carnivore -- otherwise it would be providing evidence for carnivores being outgroup to cows + bats + horse. In short this single intron is providing 'support' for two contradictory topologies.

The sizes of many bat genomes have been experimentally determined: the 30-genus average of 2.6 gbp is about 500,000,000 bp less than human. Since bats in essence have the same 20,000 coding genes as other mammals, that discrepancy has to arise from less intronic and intergenic dna. Possibly bats had fewer active retroposing elements. Far more likely, bats they have an average number and the discrepancy arises from a faster rate of deletions than insertions.

Thus for taxonomically informative (ancestral laurasiathere) retroposons, many millions of deletion events have occured. Since the L1MA9 elements here are only 100bp or so, it would come as no surprise if a high percentage of the older relevent ones have experienced partial (or full) deletions making them unrecognizable with RepeatMasker.

Thus presence of a retroposon in a given orthologous position bat can be informative but absence is not so informative. INT189 is an absence. That one event isn't insufficient anyway to establish branching order. So bat/horse/carnivore tree topology remains unresolved. If horse is the outgroup to carnivore + bat -- and cow outgroup to all of these -- then hoofed animals are parsimoniously ancestral (rather than arising twice by convergent evolution) and bat and carnivore lost hooves (a bit unreasonable as dog and bats retain the ancestral 5 digits). 

Summary of the phylogenetic distribution of the L1MA9 retroposon INT189:

>PGM2_canFam Canis familiaris (dog)           abseny               -MER58 182-265 23% -L1MA9 6069-6302 27%
>PGM2_felCat Felis catus (cat)   genomic del  absent               -MER58              no data
>PGM2_equCab Equus caballus (horse)          -L1MA9 6172-6264 26%  -MER58A  1-145 23% -L1MA9 6050-6302 23%
>PGM2_myoLuc Myotis lucifugus (microbat)     -L1MA9 6174-6264 20%  -MER58A 38-157 26%
>PGM2_pteVam Pteropus vampyrus (macrobat)    -L1MA9 6161-6291 25%  -MER58A 35-145 29%
>PGM2_pipAbr Pipistrellus abramus (microbat) -L1MA9 6180-6301 252% -MER58A 38-157 24%
>PGM2_bosTau Bos taurus (cow)                -L1MA9 6155-6263 28%  -MER58A  7-157 21%
>PGM2_turTru Tursiops truncatus (dolphin)    -L1MA9 6155-6265 29%  -MER58A 37-148 21%
>PGM2_susScr Sus scrofa (pig) cdna + tiled   -L1MA9 6159-6264 27%  -MER58 212-271 28%
>PGM2_vicVic Vicugna vicugna (vicugna) tiled -L1MA9 6162-6310 24%  -MER58A 35-157 20%
>PGM2_ateAlb Atelerix albiventris (hedgehog) ...                   ...
>PGM2_sorAra Sorex araneus (shrew)           ...                   ...

>PGM2_canFam Canis familiaris (dog) -MER58 182-265 23% -L1MA9 6069-6302 27% VISAELASFLATKNLSLSQQLKAIYVE YGYHITKASYFICHDQGTIKKLFENLRNY 
GTCATCAGCGCCGAGTTGGCTAGCTTTCTAGCAACCAAGAATTTGTCTTTGTCTCAGCAGCTAAAGGCCATTTATGTTGAGTACGTTTCTATTAACTCTG 
TTTAATTGAAATAATACTTTTTAAAAGTTTTATTATGTTTTTATGTGTGACACTAATATTCTAACCCTCTTACTTTGGGTGAGGGTTCTTCTGAAAACTA 
AAGGATCACTTTTTCTTTTAATGCTTAACTATTCAATACTAATTATCACTTATGACTGTGTTAATCCTTAACAAATGAGAACATCAGTTGCAGAAATAGC 
TAATTGAGGAGGGTGATTCCCTGATGTCAGAAAGGACAAAGGTTTTCGTGAAACATCTATTACGTGTTTAGAgccactagtcaagtctgcctttgtagtg 
caaaagcagctgatggcaagacgtacaggaatgggtgtggtgtggctgcaatgaaaTGAAACTTTCACCTCCCAAGATAGGCCGAAGGCCAGGCAGCAGT 
TTGGCAATACCTGGGGTCAATAGTTATACCTCTTTTTTATGCTAAATTATTCCTTTGAAGCTAGTCATTGTTATCGTTTCATTTAGCTTAAAATATACTG 
ATTGCTACATGTTCTGTATACACCACGTGAGATTATTTGTTCCTCATTTTGCATATTTGTACTTTTtttattgagatgtaattgacattaatgtcaggta 
taataacataatgattcgatatttatatattattacaaagtgatcaccatagtaagtcgagttaacatccacaccacatataatcacaaatattcattct 
tgtgatgatagcttttatgatctgtggtcttagcaactttcaaatatacagtacaatactagtagatacagtcaccaagttatatatATATAATTTTATT 
TCTTTTGATAGATATGGCTACCATATTACCAAAGCTTCCTATTTTATCTGCCATGATCAAGGCACCATTAAAAAATTGTTTGAAAACCTTAGAAACTAC 

>PGM2_felCat Felis catus (cat) genomic del incomplete coverage -MER58 ASFLATKNLsLSQQLKAIYGE YGYRITKASYFICHDQGTIKQLFENLRNY 
GCTAGCTTTCTAGCAACCAAGAATTTGTTTGTCTCAGCAGCTAAAGGCCATCTACGGCGAGTAAGTGTCTTCTAACCTGGTAAAGAAGTAATAG 
TGTTAAATATTTTCTTATGGTTCTACGTGTGAGATATTAATATTCTTTCTAATGCTCTTTGGTTGTGAATTCTATTTCTTTTTCTTTTTTTAATGTTTAT 
TTATTTTTGAGAGAGAGAGAGAGAGAGATGGAGTATGAGCAGGGGAGGGGCAGAGAGAGAGGGAGATACAGAATCCAAAGCAGGCTCCAGGCTCTGAGCT 
GTCAGCACAGAGCTCCACACGGGGCTTAAACTCACAAACCATGAGATCATGACCTGAGCTGAAGTCAGACACTCAACCGTTTGAGCCACCCACGTGCCCC 
ATGAATTCTATTTCTTATGAAACTAAATAATCATCTTTTCTTTTGATACTTAACCATGTAATGGTAATTATCATTCACGATTGCACGAATCCTTAACAAA 
TGAGGGCATCAGTTGCAGAAATAGCTAATTGAAGAATGTGATTTTAAGTGTGTGATGTCAAAAAAGATTAAAGGTGTTCATGAAATCTCTATTAAGTTTT 
TAGAGCAATGACCCAGGTCTGCCTTTATAAAGTGCAAAAGCAGCCCGTGGCAACACGTTGCAGTAAGACTCTTACTTACAAATACAGGCTAAAGGCCAGG 
CAGCAGTTTGGCAATCCCCAGGGTTAATTGTTGTACCTCTTTTTTATGCTAAATTATTCCTTTGAAGGTACTCATGGCTATTTGTTTCATTTGGTTTAAA 
ATATACTGGTTGACAAATGTACACTGTGTGGAATTATGTGTTCCTCATTTTGCATATTTGTATTTCCTTAACTGAGATATAACTGACATTAGTTTCAGGT 
ATGCGATACAGTGTTTCAATATCTGTATATATTACAAAATGATCATCACAGTACATCTAGTAACAGTCGCACCACACTTAATACAAAAGT  
TCCaTATGGCTACCGTATTACCAAAGCTTCATATTTTATTTGCCATGATCAAGGCACCATTAAACAATTATTTGAAAACCTTAGAAACTAT 

>PGM2_equCab Equus caballus (horse) -L1MA9 6172-6264 24% -MER58A 1-145 23% -L1MA9 6172-6264 26%-L1MA9 6050-6302 23% VISAELASFLATKNLSLSQQLKAIYVE YGYHITKASYFICYDQDTIKKLFENLRNY 
GTCATAAGCGCAGAGTTGGCTAGCTTTCTAGCAACCAAGAATTTGTCTTTGTCTCAGCAGCTAAAGGCCATCTATGTTGAGTAAGTTTCTATTAACTCTC 
TTTAACTGAGGTAATTTTTTTTATTAGtttcaaatgtacaacataatgattcaatgtatgtatatattttgaaatgatcgccacaataagtctggctaac 
ctgtatcaccgacatagGGCTCTTTTTAAATGTTTTATGTTCTTTTGCATGAAACAGTAATATTCTTTTGAATGCTCTTACTTTAGCTATGAATTGTTCC 
TTATGAAAACTAAGTAAGAGATCACTTTTTCCTTTCGATACTTAACCACTTAGTAGTATTACCCTTTGTGATTGCATTAATCCTTAACAAATGAGAACAT 
TAGTCACGGAAATGGTGAAGTGAAGAATGTAATTTTCAGTGTCTGAGGTCAAAAAAGATTAAATGTGTTCATGAAACATCTATTTAGTCTTTAACTTCat 
tgctcagctctgcctttgtagtgcagaaacagccggggacaatacataatgtaatgggtgtggggtggctgtgttccagtagatcttttacttaaaaata 
caggccgaaggccaggcagcagtttggcaatccctgGGGGAGATTATTGTACCTTTTTTTAATGTTAAATTATCCCTTTGAAGTTAGTCATGGTTATTTC 
ATTTAGTTTAGAATATAATGGTTAATACATAGTGTATGTACACCATGTGGAATTATTTTTTCCCATTTTGCATTTCTTCTtttgttgagatataattaac 
atagaacattatattagcttcaggtgtacagtgtaattatttgataattgtatatattgcagattgatcaccaccataagactagttaacatccatcacc 
acacatagttataaatttttttcttgtgatgagaacttttaaggtctattctcttagcaaccttcaaatatacaatacagtattattaattctagtcacc 
gtgctgtgtattatatcctcatgacccattTTATTATTTTGTTTCGAAAGGTATGGCTACCATATTACCAAAGCTTCATATTTTATCTGCTATGATCAAG 
ACACCATTAAAAAATTGTTTGAAAACCTTAGAAACTAC 

>PGM2_myoLuc Myotis lucifugus (microbat) -L1MA9 6174-6264 20% -MER58A 38-157 26% VISAELASFLATKNLSLSQQLKAIYVE YGYHITKASYFICHDQGTIKKLFENLRNY AAPE01636299 
GTCATAAGCGCAGAGCTGGCTAGCTTTCTTGCAACCAAAAATTTGTCTCTGTCTCAGCAGCTAAAGGCCATCTACGTTGAGTAAGTTTCTATTGATTATTG 
AATTGAAGTAATATAGTTTGATTAGTTTCATGTGTACAATGTAATGATTCAATATGTGTATATATTGGGACATGGTTGCCACAATAAGTCGTTAACATAC 
ATTACCACATGTGGCAATGTATTTTAAGTGTATTATGTTCTTGCGTATGAGATGCTAATGTTCTTTCCAAAGCTCTGACTTTAGTTATGAATTCTATTTC 
TTAAGAAAACGAAACGAGATTATCTTTTCCTTTTGATACTTACCATTTGTGATAGCACTAATCTTTACTAAATGAGAACATGACACAGAATGTGATTTTA 
AGTGTCTGATGCCAAAAAAGATTAAATGTGTTCATGAAACGTCTATTTAGTCTTTATAGCAGTTTCTCAACTCTTGCCTTTCTGATGCAAAAGGAGCCAG 
ACACAGTACATAATGCAATGGGCGTGGTATGGCTGTTCCAGTATAATTTTACTTACAAGTATAGGCTGAAGGCAAGGTAGCAGCTTGGTGAGCCCTCGGG 
TAAATTGTTGCACCTCCTTTTAATGCTAAATGATTGCTTTGAAGCTAGTCATGGTCATTTGTCTCATTACGTATTTGAGAATGTGCTGGTTGGTGCCCGT 
TCTGTATATGCTATGCATAATTATTTGTTCCTCATTTTGCATGTATTTGTATTTGTTTTGATAGGTATGGCTACCATATTACCAAAGCTTCATATTTTAT 
CTGCCATGATCAAGGAACCATTAAGAAATTATTTGAGAACCTTAGAAACTAT 

>PGM2_pteVam Pteropus vampyrus (macrobat) -L1MA9 6161-6291 25% -MER58A 35-145 29% VISAELASFLATKNLSLSQQLKAIYVE YGYHITKASYFICHDQGTIKKLFENLRNY 
GTCATAAGCGCGGAGTTGGCTAGCTTTTTAGCAACCAAGAATTTGTCTTTGTCTCAGCAGCTAAAGGCCATCTATGTTGAGTAAGTTTCTATTGACTCTA 
CATAACTGAAATAATATTTTTTATTAGTTTCAGGTGTACAGCACAGTGATTCGGTATATGTATATATTATGACATGATTGCTATAAGTCTATTGCATGCA 
TCAGTCTATTACTACATGCATCACCACACGTAGTAATATTTTTAAATGTATTATGTACTTGTGCACAAGATACTAATATTCTTTCCAATGCTCTTACTTT 
AGTTATGAATTCTATTTCTTATAAAAACCAAATAAGAAATTACCTTTTCCCTTTGATACTTAGCCATTTAATAGTAATTACCATTTGTGATGACAGTAAC 
CTTTACCAGATGAGACATTAGCCACAGAAACAGCTAAAGAATATGATTTTAAGTGTCCGATGTCAAAAGATTAAATGTGTTTATGAAACATCCTATTTAG 
TCTTTTTATAGCATTATTCAGCTGTGCCTTTGTAGTACAAAAGCAGCCAGACCCGATGCATATGTAATGGGTGCAGCGTGGCTACATTTCTGTAAAATTT 
TTACTTACAAATATAGGCTGAAGGCCAGGCAACAGTTTGGTGATCCCCTGAGTAAATTGTTATACTTCTTTCTTAATGCTGAACTATTCCTTTGAAGCTA 
GTCATGGTCATTTGTTTCATTAAGCGTTTTAGAATGTACTGGTTGATACATGTTCTGTGTACACTATGCAGAATGATTTGTTCCTTATTTTGCATGTGTT 
TGTATTTATTTTGATAGGTATGGCTACCATATTACCAAAGCTTCATATTTCATCTGCCATGATCAAGGCACCATCAAAAAATTATTTGAAAACCTTAGAAACTAT 

>PGM2_pipAbr Pipistrellus abramus (microbat) -L1MA9 6180-6301 25% -MER58A 38-157 24% AB258957 AIYVE YGYHITKASYFICHDQGTIKKLFENLRNY 
GGCCATCTATGTCGAGTAAGTTTCTATTGATTATTGAATTAAAGTAATATAATTTGATTAGATTCATGCGTACAGTGTAATGATTCAATACATGTATATA 
ATGGGACATGGTTGCCACAATAAGTCGTTAACATACATCACCACCTGTGGCAATATATTTTAGGTGTATTATGTTCTTTAGTATGAGACACTAGTACTAA 
TATTCTTTCCAAGGCTCTGACTTTAGTTATGAATTCTATTTCTTAAGAAAATGAAACGAGATTATCTTTTCCTTTGGATACTTACCATTTGTGATTGCAC 
TAATCTTGATTAAACGAGAACATTACACAGAATGTGATTTTAAGTGTCTGATGCCAAAAAAGATTACATGTGTTCATGAAACATCTATTTAGTCTTTATA 
GCAATTTCTCAACTCTTGCCTTTCTGGTGCAAAAGCAGCCTGACACAATACATAATGTAATCGGCGAGGGATGGCTGGTCCAATAAAACTGTACTTACCA 
ATGTAGGCTGAAGGCAAGGTAGCAGCGTGGTGTTCCCTCAGAATTATTTGTTCCTCATTTTGCACGTATTATTTGTTTTGATAGGTATGGCTACCATATT 
ACCAAAGCTTCATATTTTATCTGCCATGATCAAGGCACCATTAAGAAATTATTTGAAAACCTAAGAAACTACGATGGGAAGAATAATTAT 

>PGM2_bosTau Bos taurus (cow) -L1MA9 6155-6263 28% -MER58A 7-157 21% VITAELASFLATKNLSLSQQLKAIYVE  YGYHITRASYFICHDQETIKQLFENLRNY AB258958 [L1_Carn7] 
GTCATAACTGCAGAGTTGGCCAGCTTTCTAGCAACCAAGAATTTGTCTTTGTCTCAGCAGCTAAAAGCCATCTATGTTGAGTAAGTTTCTATTGACTATT 
TAATTGAAGTAATTTTTTTTTATCAGttcaggtatacaacacagtgattcagtgtatgtctatattgtgaaatgatcacagtggatacaattaacatgca 
tccccacacaggaatattttttaatgtTTTACTCTCTTCTTGTGCACCCGATACTCATATTCTTTCTGATGCTCTTGCTTTAGTTATGAATTCTATTTCG 
TATGAAAACTAAATAAGAGATCACCTTTTCCTTTTGCTACTTAAGCAGTTAATAGTAATTACCATTCATGATGACGTTAATCCTTAATAAATGAGAACGT 
TAGCTGCAGAAATGGCTAAGGGAAGAATGTGATTTTTTAAATGTCCAGTGTTGAAAAAGACTAAATGTGTTCATTAAACATCTATTTAgtctttgtagca 
attacttatttctgcctttctagtgcaaaagcaaccagacacaaggtaatgggcatgacgtggctgtattccaatgataaaacttttacttacaaacaga 
gactgagggccACACAGCAGGGCAGTGATTCCTGGTGTAGATTGTTGGACCTCTTTATTTAATGCTGAATTACTCCTTTGAAATTAGTCATGGTTGTTTG 
TTTTAGAATATACTGTTTGATAGATACATGTTCAGTGTACACTGTGCCCAATTATTTGTCCCTCATTTGCATGTAACCATGTTTGTATTGATAGGTATGG 
CTACCATATCACCAGAGCTTCGTATTTTATCTGCCATGATCAAGAAACTATTAAACAATTATTTGAAAACCTTAGAAACTAT 

>PGM2_turTru Tursiops truncatus (dolphin) -L1MA9 6155-6265 29% -MER58A 37-148 21% FISAEVGSFLAQNCLVSAAKAIYV YGYHITKASYFICHDQGTIKKLFENLRNY 
TTCATAAGTGCAGAGGTTGGCAGCTTTCTAGCACAGAATTGTCTTGTTTCAGCAGCTAAAGCCATCTATGTTGAGTAAGTTCTTCTATGACTGTTAAATG 
AGTAATGTTTTTTTTCATTTCAGTTGTGCAACACAATGATTCAATGTATATCTATTATTGTGAAATGATTGCAACAAATACAGTTTACATGTATCCCCAC 
ATGTAGTAATATTTTTTAATGTTTTACTCCGTTCTTATGCATGAGATACTAATATTCTTTCTGATGTCCTTACTTTGGCTATGAATTCTATTGCCTATAA 
AAACTAAATAAGGGATCACCTTTTCCTTTCGATATTTAACTACTTAATAGTAGTTACCCCTTCATGATGACATTGATTCTTAACAAATGAGAACATTAGT 
TGCAGAAATGGCTAAGGGAAGAATGTGATTTTTAAGTGTCCAATGTCAAAAAAGACACATGTGTTCACAAAACATGTTTAGCCTTTAAAGCAATTATTCA 
CCAGTGTCTTTGTAGTGCAAAAGCAGCCAGACACAATACATAAGGTAATGGGCATGGCATGGCTACGTTCCAATAGAGAAACTTTTACTTAGAAATACAG 
GCTGAGGGCCACAGAGCAGTTCAGCGATCCCTGGGGTAGATTGTTGGACCTCTTTTATAAAATTGGACCTCTTTTTTTTTTTTTTTTTTTTTGGCGGGGG 
GTACGTGGACCTCTCACTGTTGTGGCCTCTCCCGTTGCAGAGCACAGGCTCCAGACGCGCAGGCTCAGTGGCCATGGCTCGCGGGCCCAGCCGCTCCACG 
GCATGTGGGATCTTCCCAGACCGGGGCACGAACCCGTGTCCCCTGCGTCGGCAGGCGGACTCTCAACCACTGCGCCACCAGGGAAGCCCTGAACCTCTTT 
TTTAATGCTGAATTATTCCTTTGAAATTAGTCGCGGTTATTTGTTTTAGAATATACTGGTTGATACATGTTCAGTGTACACTGTGCAGAATTATTTGTTC 
CTCGTTTTGCATGTAATTGTGTTTGTATTGATAG GTATGGCTACCATATCACCAAGGCTTCGTATTTTATCTGCCACGATCAAGGCACTATTAAAAAATTATTTGAAAACCTTAGAAACTAC 

>PGM2_susScr Sus scrofa (pig) cdna + tiled -L1MA9 6159-6264 27% MER58 212-271 28% VISAELASFLATKNLSLSQQLNAIYVE YGYHVTKGTYFICHDQGNVKKLFENLRNY 
GTCATAAGCGCAGAGTTGGCCAGCTTTCTAGCAACCAAGAATTTGTCTTTGTCTCAGCAGCTAAATGCCATCTATGTTGA 
GTAAGTTTCTATTGACTGCATTTAATTGAAGTAATTTTTTTAATCAGTTTCGGGTGTACGACATAATGATTCAGTGTATATGTATTGTGAAATGATCCCAA 
TGAGTACAGCTAACATGCATCCCACACGTAATAATATTTTTTTTTCTTTCTTTTTCTTTTTTTAGGGCTACTCCTGTGGCATATGGAAGTTCCCAGGCTA 
AGGGTCGAATAGGATCCATAGCCGCTAGCCTAAGCCACAGCCACAGCAGCACGGAATTCGAGCCACATCTTTGACCTCCGCTACAGCTCATGGCAATGCC 
AGATCCTTAACCCACTGAGCAAAGCCAGGGATCAAACCCAACATCTCATGGATCCTAGTCGGGTTTGTTAACCCTTGAGCTGCAAAGGGAACTCCCATAA 
TAATCCTTTTAAATGTTTTACTCTGTTCTGATGCATGAGACTAATATTCTTTCTGATACTCTCATTTTAGCTATAAAGTTGATTTCTTATGAAAACTCAG 
TAAGAGATCACTCTTTCCTTTTGATATTTAACCCCTTAATAGTAATTACCATTCATGATGACATTAATCCATAACAGATGAGAACAGTAGTTGCAGAAATGGGTAAT 
GGAAGAATGTGATTTCAACTAAATGTCCAATATCAAAAAAGACTAAGTGTGTTCATGAAACATCTATTTACTATTTATAGCAGTTATTCAGCTCTGCCTT 
TGTAGTGGTAAAGTGGTCAGACACAATACTTAAGGTAAAAGTTTCCAGTTATGAAACTTTTACTTACAAATATGGGCTGAGACTGGGCAATAGTTCAGTG 
ATTCCTTGGGGTAGATTCTTGGACCTCTTTTTTTAAATGTTGGACCTCTTTTTTAATGCTAAGTTATTCCTTTGAAATTAGTCTTGCTTATTTGTGTCAT 
TTGTATTGAAGTATACTGGTGAATTACATGTTCTGTGTATGCTGTGTGGAATTATTTGTTCCTCATTTTGCATGTAATTGTATTTGTATTGATAGG 
TATGGCTACCATGTTACCAAAGGTACATATTTTATCTGCCATGATCAAGGCAATGTTAAAAAATTATTTGAAAACCTTAGAAACTACGATGGGAAGAATAATTAT 

>PGM2_vicVic Vicugna vicugna (vicugna) tiled -L1MA9 6162-6310 24% -MER58A 35-157 20% VITAELASFLATKNLSLSQQLKAIYVE YGYHITKASYFICHDQGTVKKLFENLRNY 
GTCATAACTGCAGAGTTGGCTAGCTTTCTAGCAACCAAGAATTTGTCTTTGTCTCAGCAGCTAAAGGCCATTTACGTTGAGTAAGTTTCTATTAATGCTG 
TTTAATTGGAGTAAGCTTTTTATCCATTTCAGATGTACCACATTATGACTCAGTATACGTCTACATTGTGAAATGATCACAATTAGTAAAGTTAACGTGT 
ATCATCACACATAGTAATATTTTATAATGCTTTACTCTGTTCTTGTGCATGGGACACTAATGTTCTTTCTGATGCTCTTTCTTTAGTTATGAATTCTGTT 
TCTTATGAGAACTAGATAAGAGATCATCTTTTCCTTTTGATACCTAATCACTTAATAGTAATTACCATTCATGATGACATTAATCCTTACAAATGAGAAA 
ATTAGTTGCAGAAATGGCTAATGGAAGAATGCGATTTTAAGTGTCTAATGTCAAAAAAGACTAAATGTGTTCATGAAACATCTGTTTAGTCTTTATAGCA 
ATTACTCAACTCTACCTTTGTAGTGCAGAAGCAGCCAGACTCAACACATAAGGTAATGATGTGGCTGTTCCACTAATAAAACTTTTACTCAAAAACACTG 
GCTGAGGGCCAGGCAACAGTTCAGCAATCCCTGGGGTAGATAGTTGGACCTCTTTTTTTTAATTCTAAATTATTCCTTTGAAACTCATCATGGTTATTTG 
TGTCATTTATTTTAGAGTATACTGGTTGATGACATGTTCAGTGTACACTGTGCAGAATTCTTTGTTCCTTGTTTGCATGTAATTGTATTTGTATTGATAG 
GTATGGCTACCATATTACCAAAGCTTCATATTTCATCTGTCACGATCAAGGCACTGTTAAAAAATTATTTGAAAACCTTAGAAACTAC 

>PGM2_ateAlb Atelerix albiventris (African hedgehog) No repetitive sequences [VISAELASFLATKNLSLSQQLKAIYVE] YGYHITKASYFICHDQVTIKKLFENLRNY AB258952  
TTAATGTGTTTGTTAAACATCTATTTATTCTTTACAGCTATCACTCAACTCTGACTTTGTAATACAAAATAGCCACACTTAGTCCATGAGGTCATGGACC 
TGATGTGACTGCCCCAATAAAACTTATACCTACAGATATAATCAAAATAAGATAAAATGGATGCTATCAATACTTAAGAATATTGGCTAAGTAAAAACAA 
AGAACTAGTTTAGAAACCTACAGGGGGTTATTGTTCTTCCTTTTTTTCATGCTATATTATTCCTTTGAAGCCAGTCATAGTTATTAGTCTCATTAACTTT 
ATAATATACTGGTTATATATGTTCTGTGTATACTAGGTAAAGTTATTTCTACCTAATTTTGCATACGTTTTATTTGTTTGCTAGGTATGGCTACCATATA 
ACCAAAGCTTCATATTTTATCTGCCATGATCAAGTCACCATTAAAAAATTATTTGAAAACCTTAGAAATTAT 

>PGM2_sorAra Sorex araneus (shrew) +SOR1_SINE +SOR1_SINE VISAELASFLATRNLSLSQQLKAIYVE YGYHITKASYFICHDQSIIKKLFENLRNY AALT01183695 AALT01470682 
GTCATTAGCGCGGAGCTGGCCAGCTTTCTCGCCACCAGGAACCTGAGTTTGTCCCAGCAGCTAAAGGCCATCTATGTGGAGTAAGTTCCCTACTGACTGT 
GCTTAATCAAAATAACCCGTATTTTTGGATCCATTTTTAACGGTTTATTATGCTCTTGTGTGTGTGATACTGATAGTCTCTCTAATGTCCTCACTTCAGT 
TATAAATCCTATTTCTTAAAAACATGAAGTTAAGGGGCTGAACCGATAGCACAGCGATAGCAAGGTTTGCCTTGCATGTGACCGATCTGGGTTCGATTCC 
CAGCATCCCATTTGGTCCCCTGAGCACTGCCAGGAGTAATTCCTGAGTGCATGAGTCAGGAGTAATCCCTGTGCATCGCTGGGTGTCACCAAAAAAAAAA 
AAACCATGAAGTTAAAAAATCACCTTTTGGGGGGGGTCGGAGAGATAGTGCAGCAGTGGGTAGGGAGCTTGAGTCATTCATGGGTCACCCAGCTTCAATC 
CCTGGCACGCCCTGTGGCCTCCCAAGTCCCGCCAGGAGTGATCCCTGAGCTCAGAACCATAAGCAAGCCCTGAGCACCATTGGTGTGGCCCCAGAATAAA 
TAAATTAGAGATAGAAATCACTTTTTCATGCTTAACTACTTAATAATACTTATGATTGCCATACTCCCTAATGAATGAGATCTAATCGCAGAACTAGTTA 
TTAGTTAAAAGTGTGAATTTAAATGTGTAGTGTCAAAAAAATG ACCAAGATAACCAGCTTATAACTTAGACTTATAAATGACTGCTTATCAATATATCT 
AAGGCCAGACAGCAGTTTACTTTAGCAGTTCCTAGGATAGGTTATTGTTCCTCTTTTTTTTTTCCCTTTATTTTTTGCCCCCTAGAGATCTACCTTTTAA 
AAAAATATTTTTTTAATTGAATCACAATGAGATACACAGTTACAAATTGTTTCTGATTTGATTTCAGTCAGACAATGTTCAAATATCTGTCCCTTTCACA 
GTGTACATTTCCCACCACCAGTGTCCCCACTTTCCTTCCTTGTTCCTCTTTTTTCATGCTCAGTGATTCCTTTGAAGCGAATTATGGTCATTCGCTTCAC 
TTGCTTAAAAGCAAATGAATCAGCGGCCGATTGATGTCCTGTGTTCGAAAGACAGAATTCTTTGTTCCTTATTTTGCGTGTATTTGTATTGATAGGTATG 
GCTACCATATAACCAAAGCTTCGTATTTTATCTGTCACGATCAAAGCATCATTAAAAAGTTGTTTGAAAACCTTAGAAATTAT


Analysis of L1MA9 retroposon INT283 within gene ZUBR1

This potentially informative retroposon insertion denoted INT283 conflicts with Pegasoferae topology. That is not a fatal flaw because a certain fraction of such events resolve anomalously via lineage-sorting after speciation.

Pegasoferae.png

Again, this presented a favorable annotation situation because the two flanking exons are well-conserved and the intonic distance is short at about 1500 bp. Using new genomic data, the species density can be brought up 10 Laurasiatheres, tiling traces in unassembled genomes as necessary. The conflict with Pegasoferae holds up even sampling at this greater taxonomic sampling depth: an orthologous L1MA9 is also missing in microbat, shrew, hedgehog but present with correct orientation and correct fragment coordinates in vicugna, pig, and dolphin.

It can always be asked whether this is the "same" L1MA9 in cetartiodactyls or merely a similar one from a separate insertion event of the active parental element. However pushing the putative event back to basal vicugna narrows the window for that. While this situation can be dismissed with an appeal to lineage-sorting (importantly 4 events support Pegasoferae versus this 1 conflict).

Deletion in bat could equally be argued, though located orthologous dna in macrobat now pushes that putative event back into the shorter stem window as well. Absence in bat is not especially informative given their genomes are greatly reduced in size relative to other placental mammals -- much of this loss would occur in intragenic dna which like much intergenic does not often experience selective pressure for retention. 

>ZUBR1_canFam Canis familiaris (dog)         2108 bp -L1MA9 6025-6299 25%
>ZUBR1_felCat Felis catus (cat)              1631 bp -L1MA9 5958-6299 30%
>ZUBR1_equCab Equus caballus (horse)         1667 bp -L1MA9 5959-6299 23%
>ZUBR1_myoLuc Myotis lucifugus (microbat)    1227 bp  no repeat detectable
>ZUBR1_pteVam Pteropus vampyrus (macrobat)   1388 bp  no repeat detectable
>ZUBR1_bosTau Bos taurus (cow)               1891 bp -L1MA9 5958-6302 24%  also -tRNA-Gly -tRNA-Glu SINEs
>ZUBR1_turTru Tursiops truncatus (dolphin)   1688 bp -L1MA9 5936-6312 21%
>ZUBR1_susScr Sus scrofa (pig) 1022bp        ---- bp -L1MA9 5958-6182 22%  not fully tileable
>ZUBR1_vicVic Vicugna vicugna (vicugna)      1525 bp -L1MA9 5937-6312 22%
>ZUBR1_eriEur Erinaceus europaeus (hedgehog) 1256 bp  no repeat detectable 
>ZUBR1_sorAra Sorex araneus (shrew)          1098 bp  no repeat detectable

Markup of exons and intronic retroposons of INT283 within ZUBR1:
  blue: coding exons
  magenta: L1MA9 INT391

>ZUBR1_canFam Canis familiaris (dog) 2108 bp -L1MA9 6025-6299 25% KKYLSQKNVVEKLNANVMHGK HVIVLECTCHIMSYLADVTNALSQSNGQGPSH
AAGAAATACCTATCACAGAAGAACGTGGTTGAAAAACTGAATGCCAATGTGATGCATGGAAAGGTAAGCGAAATGCACCTTGACAGCAGTCAGGAAGTGA
TGAGTCTTCTTTGTGGTCATGTAGAAGACTCTCCTTTTGACTGGTTCCTGGTCCTAGCCAGCCTGCCCACAATTTCAAAGCCCTGGGGGTGTGTAACATG
AACTACCTGCTCTCAGGCTTCTACTAGGTTATGAGGAATGATGAGGGGAGGGAAGGGGGAATACAAGACGATAGACAAAACATCCAACTGAATCCTTAAA
ACCTAGTAAATTCTTGCTATTTTTAGATTTTGTTATGTTGTGGAAAATTGTTCCCTGCTCCTGCATTGGAACTTTGTGCTCTGAGTATGTGTTTTAGGGG
GTTACCTACTGCCTTCTCAGCTCTAGTCCACTTGCTAGTATTGTTTACTGCTGAGAAAAAGGGTTTTTAAACTGACAGAAATCTTGCATTCAGGCATTTT
TCCTACTTGCCCTACCGTGAACTGGACATAAGTGGCTAAAAAGAGCTAACTGGCCTCTGAGACCTAGCACAGCACCGTTCATGTCTCCTTTCCTTTCTTT
CATGTTTCTTCTCTCAGCTCTGAACTGTCAGAGTGCAAAGGGAAGGAACTTAGAAATCTGAGGCCTTGACGCCAGGTGCTGGGATTTTAGGCAAACCTAA
GCTACTGGTAGTGGTTTGCTGGAAGACTTTTTGCTTGGTTTCTGAGGCTGTTCCTTTCTTATTGCATTAATTTAAAACCTGGTAATGTAAGTGTCTTTCA
CCAGTGGTTAAAAAAATACTGATGGTAGGAAAAAAGCCAATGAGAGCCCATTCATACTTTTAATCTAGTCttttttgttttcttttgttttttattttta
ttttttttttattttttatttttttaaagattttatttattcttgagagacacacacacacacacacagagatacagagatacaggcagagggagaagca
ggctccatgtagggagcctgatgtgggacttgatccccagactccaggatcaagccctgggccaaaggcaggtactaaaccgctgagccacccaggtgtc
cctcttttgttttttAAattgaggtatccttaacatgacactagattattttcaggtggacagcataatcattagatgtttgtgtaggctgtgaaatgat
cacagtaaggctagttaacatgtcttcatacatagttccaagatgtttttttctaataatgagggcttttaagatctattctcttagtgactttcaaata
tgcaatacagtatgttttttttttttttcagtatgttgttaactatagtccttatactgtctgtgtattatatccctgtgacttatttattttataactg
gaaggttgtaggtttttttttggtaaagatttttatttatttattcatgagacagagagaggcagagtcataggtaaagggagaagcaggctccctgcaa
ggagcctgatgcgggactcgattccaggaccctgggatcacgacccgagccaaaggcagatgctcaacccctgagtcacccaggcatcccaaggttgtag
cttttgaacccacttcatctgttctccactcaccccctccttctccctgcctctggcaactaccattctgttctctgTATCAGTCATCTTTTCTTGAATG
ATTTTTGCCTCCAGTTTTACCTGCTTTCCTGATTTCAGGTTTGCCTCATTTTATAGCATTTTGTGGAGAATGGTTTTTGTGCTTAAGAATGAAAGAATCA
CATTAATTCAGTACAGCATATTGACTGGCTACATGTGGTTACAGTGCTCAGAGCTGAGGAAATAGATAATGTAAACATGTTTTTTTGTCTGCTTTTAAAC
CATTTCTCTGATCTTCAGCTTTATTGGGAAAAGTTTGAGAAAACACAGTATATAATAATTAGGTATGGAGAAGCTAAGGTCTCTTTGGTATGATGGTGGT
CTTCTCTTCTAGCACGTGATAGTCCTGGAGTGCACGTGCCATATTATGTCTTACTTGGCTGATGTCACCAATGCCCTGAGCCAGAGTAATGGTCAAGGCC
CAAGTCAC

>ZUBR1_felCat Felis catus (cat) 1631bp -L1MA9 5958-6299 30% KKYLSQKNVVEKLNANVMHGK HVIVLECTCHIMSYLADVTNALSQSNGQGPSH
AAGAAATACCTGTCACAGAAGAATGTGGTTGAAAAACTGAATGCCAATGTAATGCATGGAAAGGTAAGCAAAATGCAGAGAGACAGCAGTCGGTGAGTGA
TGATCCTTACCTTTGTGGTCACATAGAAGGCTCTGCTTCTTACTGGCTTGTGTCCCTGGCCAGCCTGCCTGCAATTTCAAAGCCCTGGGAGTGTATAAAT
CCGAACTGTGTGCCCTTGGGCCTTTGCTGAGTGATGAGGAATGATAGGAGGGAAATAATATGGGAAACAGTATCCAACTGAATCCTTCATAAAACCTGGT
GGATTCTTGCTATTTTTAGCTATTGGTGTGCTGTGGAACTGGAGCTGTGTGCTCTGAGTAGGTGTTCTGTGCGGTTACAGACTCTGCCTTCTCAGCTCTA
GTCCAGTTGCTAGAATAGTTTAATTTACCTGAAGATTCAGGGCATCTCTGAGAAGGGTTTTGAACTGACAGAAAGTCCACGTTCAGTTGTTCGCCCGCCC
CACCACGGACCTGCCGTAGGTCACTGAGAGCGGGTAACCGGCCTCTGAGACCCAGCAGCATAGCGCTGTTTATTTCTCAGTAATGAGATGATTTAAATTT
CAGTAATTTCAGCCTTTCTTGCTCGTCTTTCTCCTCTGAGTCTGCACTGTCGCTGCAGAGTGAAGAGCTCAGAAGTCTGAGGCCTTGATGCCAGGCTGCT
GGGTCCTCAGGCAGGCATGAGCTGCTGGCAGCTGTTCGCTGGAAAGCTTGTGGCTTCATTTCCGAAGCTGTTCCTCTCTTACTGCTTTCGCTTAAAAGTC
TTTGGCTAATGGTTAGAAAAAATTGCTAATGGTAGGGAGAAAGCCAGCGAGAGCCTATTCATACTTTGAATCTAGTCTGTTTTTCCTTtcttcgtttaaa
ttgaggtatacttgacaggtaacactgtatccgtttcaggtgcacagcacagggattcactgtttgggcgtgttgtggagtgatccccacaataaggcta
gttgctgtctgtctccatatgtagttctaaaacgtgttttcctcgtaaggagtttagagatctgctcacttagcaactatcaacacgtcatacattgtta
gctgtagtcgccatgctgtgctttatttacacccctgtgacttatttattttataaccggaagtttgtgtcttttgaacctcattcatccattctccacc
cactgctcccctgactctggcaaccaccagtctcttctctgTATCATTTTCTTCTCTTTTTCTATTTTCCTGACGACAGTTTTACTTCATTTCATAATTT
GTAAAGGGTTGTCTTTGTGCTTAAGGATGAGTGAATCCCGTTAATTCAGTACCGTGTATTGACTGGCTACACGTGGCCATAGTGCTCAGAGTGAGGAAGT
AGATAATTGAAGCATGTGGATTTTCTTGTCTGCTTTTATACCATTTCTCTGATTGCGGGCTTTATTGGGAAAAGTCTGAGAATCGGATATGGAGAACCGA
AGTTTCTGTGACGGGGTAGTGGTCTTCTCTTCTAGCATGTGATAGTCCTGGAGTGCACGTGCCACATTATGTCTTACTTGGCTGATGTCACCAATGCCCT
GAGCCAGAGTAATGGTCAAGGCCCAAGTCAC

>ZUBR1_equCab Equus caballus (horse) 1667bp -L1MA9 5959-6299 23% KKYLSQKNVVEKLNANVMHGK HVMVLECTCHIMSYLADVTNALSQSNGQGPSH
AAGAAATACCTGTCACAGAAGAATGTGGTTGAAAAACTGAATGCCAATGTAATGCATGGAAAGGTAAGAGAAGTGAGGAGTGGCGACAGTCAGGGAGTGA
GGGTTCTTACCTTTGTGGTCAGGTGGAGGGCTCTCCTTCTCACTGGCTTCTGTCCCTGGCTGGCCTCCGGAGGATAAAGGCCTACGATCCCAAAGGCCTA
GAAGTGTGTAATTGCGAACTGCATGCCCTCAGGCCTCTTCTGGGTGGCAAGAAGTGATAGGAAGGAAATATTCTGGTAAGCAAATATCCAGCAGAATCCT
TTTTAAAACATAGTGAATTCCTGCTATTTTTAGATACTGGTATGCTATGGAAAATTCTCCCCTGCCCCTGCAGGGGAGCTTTGCTCTCTGAGCAGGTGCT
ATATGGGGTTACAGACTACCTTCTCAGCTCCAGTCCAGATGGTAGAATTGTTTACTTTACCTGAAGTTTCAGGTCACTGTGTTGAGAAAAAAGGGTTTGA
AACTGACAAGAGATCTTGCATTCAGGCATTTTTTCCCCCTACCCAACTCGTAAACCTGACAAAGGTGGCTAACAGCAGATAACTGGTCTCTGAGACCCAC
CACAGCCCCCTGTTTCTCCCTTCTTTCTTGCTAATCTTTATCCTTTCAGCACTCAGCTGTCAGAGTACAGAGTGAAGGAACTTAGCGATCTGAGGCTTTG
ATGCCAGACTGTTGGGTTTTTAAGGCAAGCATGAACTGCCTGCAGTAGTTTGCTGGAAAATTTTTCACTTGATCTCTGAAGCTATTCTGCTCTGCTGCAG
TAATTTAAAACCCAATAATTTAAATGTCTTTCACTACAGGTTAAAAAAAATGCTAATCGTAGAAAGTATGTCAGTGAGAGCCTATTCATACTTCTAATCT
AGTCTTTTTTTAAattgagatataattgacatattagtttcacatgtacaacatgatgattcaatgtttgtatatatcgtaaaatggtcaccacagtaat
tctagttaagatccatcatcaaacatagttacaaattttctttttaatgttgaggacttctaagctctactctcttagcagctttcaaatatgcaatata
atattagctgtattgaatgtaatgttgtacattccatctcatggcttatttattttataactggaagtttgtaccttttgaccccatttatccatttcat
ccactcctcccaccgcctctctctggcaaccactactctattgtctatcaatctagttttttcttGAATGATTTTTGTCTCTATTTTCACTCTATTTTCC
TGGGTTGAATTTTTTTACTTCATTTTACAGAGTTTTATGAAAAATTATCTTTGTGCTTAAGAATGAGTGAATCACACTAATTCAGTACAATTTATTGACT
GGCTACATGCAGTCATAGTGCTAAGAGCTGAAGAAATAGATAATTCAAATGTTTTTCTTTTCTGCTTTTATACCATCCCTCTGATCTTGAGCTTTATTGA
GAAAACAGTTTATGTAGTAATCAAATACAGAGATCTAAAACTTTCTGTGGTATGGTGGTCTTCTTTTGTAGCATGTGATGGTCCTGGAGTGCACATGCCA
TATTATGTCTTACTTGGCTGATGTCACCAATGCCCTGAGCCAGAGTAATGGTCAGGGCCCAAGTCAC

>ZUBR1_myoLuc Myotis lucifugus (microbat) 1227 bp No repetitive sequences were detected KKYLSQKNVVEKLNANVMHGK HVVVLECTCHIMSYLADVTNALSQSNGQGPSH AAPE01620425
AAGAAGTACCTGTCACAGAAGAATGTGGTTGAAAAACTGAATGCCAATGTAATGCATGGAAAGGTAAGAAAACTGAGGAGTGACAACAGTCAGCGAGTGA
TGATTCTCTGTCTGTGTCAGGTGGAAGTCTCTCCTCTCTGTTGGCTTCTGTCCCTGGCCAGCCTACAGAGGAAGAGGCTACAAGTTTCAAAGACCTAGAA
AAATGTAATTGCAAACTGCATGCCCTTTAACACCTTTTGGGTGGCAGAATCCTTAAAACATAATGAACTCCAGCTATTTTTAGATACTGCTATGCTGTGG
AACACTGTCTCCTGCTCCTACATTGCCCCCATCTGCTCTGAGGAGGTGTTATGTGGGGTTACAGACTATCTCTTCAGCTCCAGTCTAGATACTAGGATGG
TTTACTTTGCCTGAGGGTTCAGGTCACCGTGCTGAGAAAATGGTTTGAAACTGACAGAAATCTTACATTCAGGCATTCCCCAAACCCTCAGCCCTCAATT
CATGAACCTGGCATAGGAAGCTAATGGCCAACCACCACGACACCATTCCTTTCTCCCTCTTTTCTTGCTAATCTTTATCCTTTCAGCTCTGAACTGTCTG
TGCAGAGTGAGGAACTGAGAAATCTGAGGCTTTGATGCTAGACTGTTGAGTTTTTTAGGCAAGCAAGAACTACCTGCAAAGGGTTGCTGGAAATTTTTCA
CTTGATCTCTGAAGCTGTTTCTCCTCTACTGCATTGATTTAAAACCAGTAATTTAAGTGTCTTTTACTTATGGTTAAAAGATGCTAATGAGAACCTAGTC
ATACTTTTAATCTAATCTTTTCTTGAATATTTGTCTTCATTTTTCTCCCTTTTCCTTATTTCAGTTTTATTTCATTTTATAATATTTTGTAAAGACTCAT
CTTTGGGCTTAAGAATAAATGAATACACAGTAATTCAGTGCAATTTATTGACCAGCTACATGTGGTCATAGTGCTAAGAGTTGGGGAAATGGATAATTAA
AGTACTTTTTTTCTCTTATACCATTCCTCTGAAATTGAACTTTATTAGGAAAAGCTTGACAAAACATAGTTTACATAATAATGAAATATGGGGGACCAAG
GCTTCTATGGTGTGGTGTTCTTTTCTTGTAGCATGTGGTCGTCCTAGAGTGCACATGCCATATTATGTCTTACTTGGCTGATGTCACCAATGCACTGAGC
CAGAGTAACGGTCAAGGCCCAAGTCAC

>ZUBR1_pteVam Pteropus vampyrus (macrobat) 1388 bp tiled No repetitive sequences were detected KKYLSQKNVVEKLNANVMHGK HVVVLECTCHIMSYLADVTNALSQSNGQGPSH
AAGAAATACCTATCACAGAAGAATGTGGTTGAAAAACTGAATGCCAATGTAATGCATGGAAAGGTAAGAAAAGTGAGGCGTGACTACAGTGAGGGAGTGA
TGATTCTGTTTGTGGTCAGATGGAAGGCTCTCCTTTCCATTGGCTTCTGTCTCTGGCTGCTGTACGTTTTCAAAGACCTGACAGTGTGTCTTTGCTAACT
GCATGCCCTCAGGCGTCTTTTGGGTGGCAAGAGGTGATAGGAAGAAAACATTTTGGCAAACAAACATCCACCAGAATCCTTCTTAAAACATTGTGAATTC
CTGCTATTTTTAGATACCAATATGCTATGGAAAACTGCCCTCTGCTCTTGCATTGGAACTGTGCTCTCTTGAGTAGGTATTATATGGGGTTACAGACTAC
CTCTTCAGCACCAGTTTGGATACTAGAATTGTTTACCTTGCCTGAAGATTCAGGTCACTGTGCTGAGAAAAGGGATTCGAATCTGACAGAAATCTTGCAT
TGAGGCACAGCCCCTTCCTCCACCCCACCCCCACCCAACTCATATACCTGACAGAGATGGCTAAACAGATAACTCCTCTTTGAGACCCGCCACAGCACGG
ATTCATTTCTTTCTCTTTTGCTAATCTGTATCCTTTCAACTCTGAGCCGTAAAGGGAGGGCCTCAACTGCCAGGTAGTTCATCAACCCGCCACAGCACGG
ATTCATTTCTTTCTCTTTTGCTAATCTGTATCCTTTCAACTCTGAGCCGTCAGAATGCATAGTGAGGAACCAAGACATCTGCGGCTTTAATGCCAGACTG
TTGGGCATGAACTACCTGCAGTGGTTTGCTGGCAAGTTTTTCACTTATCTCTGAAGCTATTCCTCGTCTACTGCATTAATTCAAACCCAGTAATTTAAAT
GTCTTTCACTAATGGTTAAAAATGCTAATGATAGGAAAAATGCTAATGAGTGCTTATTCATGCTTTTAATCTAGACGCTTCTTGAATGATTTTTGTTTCC
ATTTTTACTCTATTTTCCTGGTTTTGATTTTATAATATAAAGAGTTACCTTTGTGCTTAAAAATAAATGAATATACAGTAATTCAGTACAATTTATTGAC
CGGCCTTATGTGGTCATAGTGCTGAGAGCTGGAGAAATAATTAGAACATGTTTTTGTGCTTTGTTTCATTTTTGCTTTTATACCATTCCTTTGAAATTGA
GCTTTATTGGGAAAAGCTTGAGAAAACAAGTTTACATATTAATGAAATACAAAGAACCGAGGTTTCAGTGGAATGGTGGTCTTCTTTTTTAGCATGTGGT
AGTCCTGGAGTGCACATGCCATATTATGTCTTACTTGGCTGATGTCACCAATGCCCTGAGCCAGAGTAACGGTCAAGGTCCAAGTCAC

>ZUBR1_bosTau Bos taurus (cow) 1891bp -L1MA9 5958-6302 24% -tRNA-Gly -tRNA-Glu KKYLSQKNVVEKLNANVMHGK HVMVLECTCHIMSYLADVTNALSQSNGQGPSH
AAGAAATATCTGTCACAGAAGAATGTGGTTGAAAAACTGAATGCCAATGTAATGCACGGAAAGGTAAGGAGAGTGAGGGGAGCGATGGGTCCTGTCTTGG
TGGCCGGGTGGAGGGAAGTCCCTTTCCTGTTGGTTTCTGTCCCTGGCTCCCCTGCAGAGGGGAAGGCCTAGGATCTCAAAGACCTCGAAGCGTGTCATCA
CCAAGTGCACGCCCACAGGCCTCTTCCTGGGGGCAAGAAGTGGTCTGGAGGAAATGTTCTGCGAAACAGACATCCAACAGAATCCTTCTGAAAACAGTGA
ATTACTGCTGTGTTTAGCTATTGGTATTCTCTGGGAAATTGTCTGCTGCTCCTGCATTGGGATTGTGTGCTCTGAGTGTCAGACACAGGTTCCCGTTTAC
TTCCTCAGCGCCAGTCCAGATGCTAGAATCGTTTATGTTATTTGGAGGTTCAGGCCACTGTGCTGAGAAAAAGGGTGGCAACTGGCAGAAATCTTGCATT
TGAACATTTTCTCCCTCTACCCAACCTGCGAGCCCGTCATTGTCGCTAATTTAAATGTTTTTCACTAATGGTTAAAAAAATGATTATGGCAGGGAAAAAA
GCCAATGAGAGGTTACTCATACTTTAATACAATCTTTTTATCTTTtttcttgaggtataattgacacagatattagtttcaggtttacagcatagtgatc
tgacatttgtctgtattgcaaaatgatcacagtctagttaatatccatcaccatacatagttaagttttttttcttgtaatgaggacttttaagacctgc
tctcttggcgactttcagatgtgcatacattagtattaactctggtcaccatgcttgacatttcatctccatggcttacttattttataagtggaagttt
gtatcttttgactcacatcacccacttcactgaatcaccctcctaccccctgcctctggtaccaccactctgttctctgtatcactctagttttttCTTG
AGTGATTTTTGTGTCTATCTCAACTTTATTTTCCTGGTTTACACTGTACTTCATTTTCTAAGGTTTTTAAATATATACACatttatttcgctgtgctggg
cccttgcagctgcttgggcgttctctcgtcactgcgagcaggggctgtgctctagtgccgttgggctctcttgttgtggaacctgggccccagggctcga
gctcttcagtaactgcagctcccaggctctagagcgcaggctcagtagttgtggcccatgggcttcattgccccgtggcttgtgggatcttcctggatca
gggatcaaacccacgtctgttgtgttggcaggtggattctttaccactgaaccaccagggaagcccTATTTTATGATTTTTTAAAGAGTTGTCTTTAAAG
GATGTCTTTAAAGTTGTGCTTAAAGGATGAATCATACTGATTCAGTACAGTTTCtttaatttttaaagtttttaaattttttGGTTACCCCATGCAGCAT
ATAGACTCTtagttccctgaccagagatcagacctgcatcctttgcattggaagtgctgaatcctaaaccactggcccccagggaAGTCCCCATGCAGTT
TATTGGCCAGCCACTTGCTGTTGTAGTGCGAAGAGCTAAGGAAATAGATAATTAAAACATGTTATTTTTCTTCTCTGCTTTTTGTGCTGTTCCTTTGATC
TTGAGCTTTATCGGAAAAAGCGTGAGAAAACACAATTTGCATGATAATGGAATGTGGAGAACTGACCTTTCATGGTGTGGTGGTCTTCTTTATAGCACGT
GATGGTCCTAGAGTGCACCTGCCATATTATGTCTTACTTGGCTGATGTCACCAATGCCCTGAGCCAGAGTAACGGGCAAGGCCCGAGTCAC

>ZUBR1_turTru Tursiops truncatus (dolphin) 1688 bp tiled -L1MA9 5936-6312 21% KKYLSQKNVVEKLNANVMHGK HVVVLECTCHVMSYLADVTNALSQSNGQGPSH
AAGAAATACCTGTCACAGAAGAATGTGGTCGAAAAACTGAATGCCAATGTAATGCATGGAAAGGTAAGACAAGTGAGGAGTGACGGCAGTCAGGGAGTGG
TGATTCTTATCTTTGTGGCCAGGTAGAAGTCTCCTTCCTGTTGGTTTCTGTCCCTGGCTAGCCTACAGAGGATAAGGCCTATAATCTCAAAGGCCTGGAA
GTGTGTAATTGCTAACTGCATGCCCTTAGGCCTCTTCTCGGTGGCAAGAAGTGATAGGAAGGAAATATTCTGGTAAGCAGACATCCAACAGAGTCCTTCT
TAAAACAGTGAATTCCTGCTATTTTTAGGTATTGGCATGCTCTGGAAAATTGTCCCCTGCTCCTGCATTGGAACTGTGTGCTCTGAGTGTTATACGGAGT
TACGGTCTCCCTCCTCAGCTCCAGTCCAGATGCTAGAATTGTTTACTTTACCTGAAAGTTCAGGTCACTGTGCTGAGAAAAAGGGTGGAAACTGGCAGAA
ATCTTGCATTCAGGCATTTTCTTCCCCCACCCAACCCATGAACTTGACATAGTGGCTAAGAGCAGATAACTGGCCTCTGACCCACCACAGCACCATTCAT
CTCTCCCTGCTTTCTTGCTGATCTTTATCCTTTCCACACTGAACTGTTAAGAGTGCAGAGTGAAGGAACTTAGAAATCTGAGGCTTTGATGCCAGACTTT
TGGGTTTTTTTAGGCAAGCACGAACTATCTGCAGTGATATGCTGGAAAAATTTTCCCTTGATCTCTGAAGCTATTCCTCCCTTACTGCATTAATTAAAAA
CCCAGTAATTTAAATATCTTCCACTAATGGTTAAAAAAAATGGTAACAGCAGGAAAAAAGCCAATGAGAGCTTATTCATACTTTTAATATAGCTTTTTTT
CTTTTTTCTTGAGGTGTAATTGACATAGAATATTATATTAGTTTCAGATGTACAACATAATGATTTGATATTTGTTTTTATTGCAGAATGATCACAGTAA
GTCTAGTTAATACATCACCATACGTAGTTAACAAAATTTGTTTTTTCTTGCAATGAGGACTTTTAAGACCTACTCTCTTCATAACTTTCAGATATGCATA
CAATAGTATTTATTAACTCTAGTCACTATGTTGGACATTACATCCCCATGACTTACTTATTTTATAACTGGAAGTTTGTACCTTTTGACCCCCATCACCC
ATTTCGCCCACCCTCCTACCCACTGCCTCTGGCACCACCAGTCTGTTCTTTGTATCAGTCTATTTTTTTCTTGAATGAGTTTTGTCTCCATTTTAACTTT
TTTTTCTTGATTTCCATCGTACTTCATTTTATAAAATTTTTTAAAGAGTTGTCTTTGTGCTTAAGAAAGAATGAATCACACTGATTCAGTACAGTTTATT
GACCAACTACATGTAGTCATAGTGCTACGAGCTGAGGAAATAGATAATTAAAACATGTTGTTTTTCTTCTCTGCTTTTATACTATTCCTTTGATATTGAG
CTTTATTGGAAAAAGCTTGAGAAAACACAGTTTACATAATAACCAAATATGGAGAACTGAGGTTTCCGTGGTGTGGTGGTCTTCTCTTACAGCATGTGGT
AGTCCTGGAGTGTACCTGCCATGTTATGTCTTACTTGGCTGATGTCACCAATGCCTTGAGCCAGAGTAACGGTCAAGGCCCAAGTCAC

>ZUBR1_susScr Sus scrofa (pig) 1022bp not fully tileable -L1MA9 5958-6182 22% KKYLSQKNVVEKLNANVMHGK HVIVLECTCHIMSYLADVTNALSQSNGQGPSH
AAGAAATACCTGTCACAGAAGAATGTGGTTGAAAAACTGAATGCTAATGTGATGCATGGAAAGGTAAGAAGAGTGAAGAGTGACAGCAGTCAGGGAGTGA
TGATTCTTATCTTTGTGGCCAGGTGGGAGTGTCTTTNCCCATGGCTTCTGTCCCTGGCTAGCCTGCAGAGGATAGGCCTATAACTCAAGGCCTCGAGTGT
GTAATGCTAATACTGCCTTAAGCCTCTCGGGGGCAGGATGATAGAAGAATATCTGTAACAACTCAGCATATCTCTGAACAGGATATGGATTTTAAGTGTG
TGTCGAAAGCCCCGCTGNATGGGGCCTGAGTAATGGGTAGTCATCCTATCAACGTGCGAAAATGACTGAAATG
CGAGGCATGCTAAACTGGACCGGTCTTTAAACCATACATAGTGGAATATCTTTTTTCGTGTGATGGCTGAAGACTTCCTCTCTTAGCAGCATGCACATAT
GCACTATAGTCACCCTGCTTGACAGTAGATCCCCATGACTTATGTTATAACTGAAAGTTTGTACCTTTTGACCTTCCCTTCACTCCTTTNGCCCATCCTC
CCACCCCTGCCTCTGGCACCACCAATATATTCTCTGTACCAACCTAGTTTTTTCTCGAACAGTTTTTGTTTCCACTTTAATTTTATTTTCCCGAGTTTAA
TTGTGTTTCATTTTACAAGATTTTAAAAGTGTTACCTTTTTGCTTAAGAACGAATGAATTTATTGACCAACTACATGTAGTCATAATAGTGTTAAGAGCT
GAGGGAATAGATAATTAACATGTTTTTCTTCTTTGCTTTTTATACCATTTCTTTGATCTTGAGCTTTATTGGAAAAAGCTTGAAAAACAGTTTACATAAT
AATTAAAATATGGAGGCAGCAGTTTCCACGGTGTGGTGGTCTTCTCTTTTAGCATGTGATAGTCCTGGAGTGCACCTGCCATATTATGTCTTACTTGGCC
GATGTCACCAATGCCCTGAGCCAGAGTAATGGTCAAGGCCCAAGTCACC

>ZUBR1_vicVic Vicugna vicugna (vicugna) 1525bp not fully tileable -L1MA9 5937-6312 22% KKYLSQKNVVEKLNANVMHGK HVVVLECTCHIMSYLADVTNALSQSNGQGPSH
AAGAAATACCTGTCACAAAAGAATGTGGTTGAAAAGCTGAATGCCAATGTAATGCATGGAAAGGTAAGAAAAGTGAGGAGTTGACAACAGTCAGGGAGTG
ATGATTTTTTTCTTTGTGGCCGGGTGGAATTCTCTTTCCTGTTGGTTTCTGTCCCTGGGAAACCTACAGAGGATGAGGCCTATAATCTCAGAGACCTAGA
AAGTAATTGCTAACTGCATGCCCTTGGGCCTCTTCTCGGTGGCGAGAAGTGATGGGAAGGAAATATTCTGGTAAACGAGCATCCATCAGAATCCTTCTTA
AAACAATGAATTACTGCTCTTTTTACATATTGGTATACTCTGGAAAATTGTCCCCTGCTCCTGCGTTGGAACTGTGCTCTGAGTGTTATTTGAGGTTACA
GTCTGCCTCCTCAACTCTAGTCCAGATGCTAAAATTGTTTCTTTACCTAAATGATCTGTCTGTGTGATGAGAAAAAGAGTTAACAGTGGCATAAGTCTTG
CATTCCCGCCTTTTCTCCCCTGACCCAACTCTGAACCTGACCTAGTGGTTAAGATGCAAATACTGGCCTCTGACTCCCGCATCTACAGTTGGCTCTCCTT
CCCTCCTTGCTAATCTTCATCTTAGCCCCTGATCTGTCAAGAGTGATGATGTACGGAGCTAGAATTCGGAGGCTTGAATGCCAGAGATTTTGAATTTTTTCAGGAAGCCGAAAACTATCTGG

GTCATCGCACTGTGGTGGATTCTCATACTTTTAATATAGTCTTTTTTCCTTCTTTATTGAGGTATAATTGACACAGAACATTAGTTTCAGGTGTACAACA
TAAAGATTTGATATTTGTATATACTGCAGAATGACTACAGTAAGTCTAGTTAATACCGTCACCATACAGTTAAAACTGTTTTTTCTTGTGGTGAGGACTT
TTAAGACCTACTCTCTTAGCAACTCTCAAATATACAGTACGATATTATTAACTATAGTCAGCATGTTTGACATTACATCCCCATGACTTACTGATTTTAT
AACTGGAAATTTATACCTTTTGATCCCTTTACCCATTTTGCCCACTTCCCGCCCCCTGCCTCTGGCATCACCAGTTCTGTTTTCTCTATCAGTGTAGTTT
TTTCTTGAATGATTTTTGTCTCCATTTTAACTTTACTGTCCTGATTTCAGTAGTAGATTTTTAAAGAGTTATCTTTGTGCTTAAGGATAAATGAATCACA
TTAGATCAGTACAGTGTATTGACCAACTGCATTTATCATAATGCTGAGAGCTGAGGAGGTAGATAATGAAAGCATGCTGTTTTTCTTCTCTGCTTTTATA
CCATTGCTTGATCTTAAACTTTATTGGAAAAAGCTTGAGAAAACACAGCTTCCATACTAATCAAATATGGAAAACTGAAGTTTCCTTGGTGTGGTCTTCT
CTTGTAGCATGTGGTAGTCCTCGAGTGCACATGCCATATTATGTCTTACTTGGCTGATGTCACCAATGCCCTGAGCCAGAGTAACGGTCAAGGCCCAAGTCAC

>ZUBR1_eriEur Erinaceus europaeus (hedgehog) 1256 bp tiled No repetitive sequences were detected KKYLSQKNVVEKLNAGVMHGK HVTVLECTCHIMSYLADVTNALSQSNGQGPSH 
AAGAAATACCTGTCACAGAAGAACGTGGTTGAAAAACTGAACGCCGGTGTAATGCATGGGAAGGTAAGGAGAGCAGAGTGGCAGAAGTAGGGGACGGCGA
TTCTTGACCCCGTGCCCTGGCAGAAGCCTCTCCTTCCTACTTGCCGCCTTCTGTCCAGAAGATAAGGCTTGAAATCTCCAGGGCCTTCAAGGGCGTCACT
GCTAACAGCATGCCCTCAAGCCTGCTCTGGGGGGGCTGCTAATTCCGAAATAGCACATTTCTGCTCATGTTTAAAAAGTGTTTGCGCGTGTGTTTGCATG
CGCGCCCTGCCCCGCTCTTGTTTGGGTAGGTGGCCCTCAGCTCTAGTATAGGCCTGGGCTCCTTCACTGTAGCGGAGACGTGCCACTAACTCCAGCAGCT
GCGCATCCTGGCAGCCTCTCTCTCTCTCTCTCGCCACATCACAACCCTGACGTAGGTGGCTGAGAGCAGACAGTTGACCTCTGAGACCCACCTCTCTCAC
TTTTCCCTCTGTTGCTGACTTGTATCCTTTCAGCTCTGACACTCAGTCAAGACACCTAGAAGCCGAAGACCTTAATGCCTGCAGTGGTTTTCTGGAAAAG
TCTTCAGTTCCTCTCTGGAACTGTTTCTCCCTGACTCAAACGCCTTTGACTAGTGGCTAAAAAACACCCCACTAGTTGTAGGACCAATGCGAATGAGAGC
GTGCTCGAGGCCCCAGCGGTTCCAGGTTCGATCCCCAAGCCACTGTAAGCCTAGGCTGACTAGTGCGCTGGTCCAGCGGAGCGGAGCGGAGCGCAGAGCA
GTGCTCTTACATCAGGCGGGGTCCTCTCTGATGGCAGGCCTCACGTGAGCGGGGGGTTGGCTCTGGCGCAGGGGGTGGAGCGAAGGGTGTGCTCGGTCGC
CTAGTTCCCTCTCTGGTACACAGTAGTTTTGAATGATTTTTGTTGCGTTTTACTGTTTTCCCTGGTTTCATTTCTCTTCCTCTTAGGAGATCTTGTAAAG
AATCACCTTGGTACTTAGGATGGGTGTGTACTTACTCAGTACATTTACTGAGTGGCTCCATGAGATGAGCGGGGGACATAAGATAGTTCAGTCACACTGC
TTTTCTGTCATTCCTGTGACTGGAGCTGCATTGGAAAACACTTGCCTTCTCCTCTTGTAGCACGTGACAGTCCTGGAGTGCACATGCCACATCATGTCGT
ACTTGGCTGATGTCACCAATGCCTTGAGCCAGAGCAACGGTCAAGGTCCAAGTCAC

>ZUBR1_sorAra Sorex araneus (shrew) 1098bp No repetitive sequences were detected KKYLSQKNVVEKLNANVMHGK HVIVLECTCHIMSYLADVTNALSQSNGQGPSH AALT01499066
AAGAAATACCTGTCACAGAAGAATGTGGTTGAAAAACTGAATGCCAATGTAATGCATGGAAAGGTAAGAGGAATGAGCGGTGATGATGCCATGGGGTGGT
GATTCCTACCCCTGTGACCTCTTTCTTAAAGCCTTGTGACCTGGCCACCCTGTCTAAGATCGGGTGTACACACCTCAGAGTTATAGTGCAAATCTCAACC
CCCTTTGGACAGTTAGGAAGATATAGGCAGGAAATACTGTGGGAAATACATACCCAGTAGCATCTTTCTGAAGATACATTAAATTTCTGCTATTTTAATA
TACTGCTATATGTTGTAACACTGGCATGCACTGCTGCTTTGTAACTGTACTCACTGTGCTGGTAAGAGGGGTCGACGCTGCTAGAAGTCTCACATTTCAA
CATTTTCCCAAGACCTGTCTCAAGCCTCTGACATTGGTGGCTAGAGCAGATAACTGGCCTCTAAGGCCTACCACCTTCAGGTCTTTTTTTTTTTTTTTTT
TGCTAATCTTTATCCTTTTGGCACTGAGCTGTCAGAATGCAGAGTGAAGGTATTAAGAAATCTGAAGCTTTGATGCCAGACTGTTTATTTTTACCAAGCA
TGAGCTACCTGTAGTGATATGCGGCAAAAGTTGTCATTTAGTCTCTGAGGTTAGTCCTTCCCTACTGAACTAATTTAAAACTCAGCAATTTAAAAGTTTC
ACGCTTTCATTTACATATAGATAATATGTCTTTTGGGGCCTTGGGCCAAAGGTCAAAAATACTGAAAGAGTAAAAGTTTGCAACTTACAGTGAATGACTA
TGCTCTCCATATTATTTCCTGACTTGCTGAATATGGTTATATTGTGGAAAGTTAAGGAAACAGATAATTAAAACCTGTGTTTATCCTTTGTTCTAATAAC
ATCCCTTGGCTTTATTAGTAGAAACTTGAGAAACCAGTCAGATAATAAATTATGAGTTGTGGAGAAATGACTCTCCTGTGGTATGGTATTCTTCTCTTGT
AGCACGTGATAGTCCTGGAGTGTACCTGCCATATTATGTCTTACCTGGCTGATGTCACCAATGCTCTGAGCCAGAGTAATGGTCAGGGCCCAAGTCAC

Analysis of L1MA9 retroposon INT391

Extended validation of this L1MA9 insertion, which occurs in a short intron of the gene ACSL5, is feasible in May 2008 because of newly available genomes. elements. The basic technique consists of first establishing the comparative genomics of the two outside coding exons. These are needed to reliably probe contig assemblies and trace archives with tblastn and blastn respectively. A complete intron can often be obtained by tiling out to the center from the two ends. It is imperative to avoid paralogous exons in doing so.

Pegasoferae.png

In the case of INT391, dog, cat, horse, microbat, macrobat had the retroposon judging by location, fragment coordinates relative to the full length retroposon, and strand orientation relative to the coding exons (minus strand here). Cow, dolphin, pig, vicugna, and shrew did not have it. Since cetartiodacytl L1MA9s might have been interrupted by a later retroposon breaking the L1MA9 into two unrecognizable shorter pieces, it is necessary to remove other repeats and re-run RepeatMasker.

Despite more intensive phylogenetic sampling, INT391 continues to support Pegasoferae as Nishijimi et al originally stated. It should be noted that the MER-class retroposon, while not at issue here, exhibits the type of homoplasy that makes retroposons dicey as tree topology markers. Introns are often susceptible to multiple insertions of similar retroposons as well as to complicated patterns of micro deletions that prevent their recognition even if they aren't fully deleted. 

Summary of the phylogenetic distribution of the L1MA9 retroposon INT391:

>INT391_ACSL5_Peg_canFam +MER91 85-140 23%9 -L1MA9 6082-6298 24% span 762bp
>INT391_ACSL5_Peg_felCat -MER91C 97-140 27% -L1MA9 6082-6301 22%
>INT391_ACSL5_Peg_equCab -MER91B 62-128 26% -L1MA9 6082-6302 21%
>INT391_ACSL5_Peg_myoLuc  no MER            -L1MA9 6079-6277 23%
>INT391_ACSL5_Peg_pteVam -MER91B 8-62 24%   -L1MA9 6060-6302 25% 

>INT391_ACSL5_Peg_bosTau -MER91C 55 -85 28%  No L1MA9
>INT391_ACSL5_Peg_turTru -MER91 261-311 22%  No L1MA9
>INT391_ACSL5_Peg_susScr -MER91 257-306  8%  No L1MA9 
>INT391_ACSL5_Peg_vicVic -MER91 284-337 24%  No L1MA9  
>INT391_ACSL5_Peg_sorAra  no MER91           No L1MA9

Markup of exons and intronic retroposons of INT391 within ACSL5:
  blue: coding exons
  magenta: L1MA9 INT391
  red: MER91 retroposon

>INT391_ACSL5_Peg_canFam +MER91 85-140 23% -L1MA9 6082-6298 24% span 762bp GDPKGAMLTHQNIISNVSSFLKCME YTFKPTPEDVTISYLPLAHMFERIVQ
ACAGGTGACCCTAAAGGAGCCATGCTGACCCATCAAAATATTATTTCAAATGTTTCTTCTTTCCTCAAATGTATGGAGGTCAGTGGTCAATTGTCAAGGA
GGTCTTCATTAAAATGTAAATCTGTCATAAGATTTTAATCCTGATGTAAGAGGAGTCAGAGACTAACACAAAACAAAACAAAAACAAAACTCATGATAAA
GGCCTGAAGAAGGGACAAATAGTGGTGTCTCTTTGTCCAGAGGACTGTGCATTTTCAAGCCTTGGCCTTTTAGAATCACTGCACATCTCTACACTCAGTG
AAATTAAGGggcacctctcagagttatacagtgcaccacctgtacaactgggtgtggcagtcctgGGAAGGAGCAGTTTTTTTTAAATTAAAGAAAAAAT
Tttgagatacaattaacataacactatattaatttcagatacacaacataatgatttcatatatatgttgcaaaatggttcccacaataaatctaacatc
cattatcacacatagctatagtttctttttcttgtgatgagaatttttaagatctgctcacttactaacttgcagatatgcaatacagtattattaacta
tagttaACGGGAGTTACTTTTAAGTCTCCTTCGGAAGAGAAAGTTGGCATTAACACAATGTCTCCTCCTTGTTCTAATCTACAGTATACTTTCAAGCCCA
CCCCTGAAGATGTGACCATATCCTACCTGCCCTTGGCTCATATGTTTGAGAGGATTGTACAG

>INT391_ACSL5_Peg_felCat -MER91C 97-140 27% -L1MA9 6082-6301 22% GDPKGAMLTHENIVANSSAFLKCME CIFKPTTEDVSISYLPLAHMFERIVQ
GGTGACCCTAAAGGAGCCATGTTGACCCATGAAAATATTGTTGCAAACAGTTCTGCTTTTCTCAAATGTATGGAGGTCAGTGGTCAATTTAAAAAGAGGT
AGTCATTAAAATGTAAATCCATCATAAGATTTTGATCTTGATGTCAGAGGAGGCAGAGACAAAAAACAAAACAAAACCAAAAGCCACGTTAAAGGCCTGA
CAATGAATCAGTGTGGACAAATACTGGTGCATCTTTGTCCAGAGGACTGTGCATTTTCCAGCCTTGGTCTCTTAGAATCACTGCATGTATCTACACTCAG
TGAAGTTAAGGAGCACCTTAACTTCagtcatacagtgcaaaacctgtgcaactatgtgtggcaatcctgGCAATTTCTTTAAAAGTAAAGAAAAAAAttt
gttgagatattattgacgtattaatttcaggtgtacaacgtgattccatatatgtatgtactgcaaaatggtccctgtgataaattccaagtccatcaac
acacataattttttttcttgtgatgagaacttttcagatctactcacttaacaactttcaaatctgcaacacagcattattaactgtagttaATAGGAGC
TGCTTTTAAATCTCCTTTAGAATAGAAAGTTAGCACTAATCCAATGGTGTCTCTTTCTTGTTCTGGTCTATAGTGTATTTTCAAGCCCACCACTGAGGAT
GTGTCCATTTCCTACCTCCCCTTGGCTCATATGTTTGAGAGGATTGTACAG

>INT391_ACSL5_Peg_equCab -MER91B 62-128 26% -L1MA9 6082-6302 21% GDPKGAMITHQNITSNTAAFLRSME GTFEINLEDVTISYLPLAHMFERVVQ
GGTGACCCCAAAGGAGCCATGATAACCCATCAAAATATTACTTCAAATACTGCTGCTTTTCTTAGATCTATGGAGGTCAGTGATCAATTGAAAAAGAGGA
ATTCCTAATTAAATTTCAATTGAAAATTCCTAATTAAAATAGGAATCTGCCATAAGATTTTAATCTTGAAATTAGAGAAGGCATAGAGGAAAAAAATAGG
TTTAAGGCCTAAGTATGCACACATATCAGTGCCTCTTTGTCCAGAGGACTGTGCATTTTCACGTCTTGGTCTTTTAGGATCACTGCAGAGCTCTACACTC
TGTGCAgttaagggtacctcttacagttgtacagtacatcacctgcacaaccatatgtggcagttctgGGAAGGAGTAGttttttaaaaattaaaaaaat
attttattgagatatgattgacatataacattatgctagtttcagatgtacaacataatgatttgaggtttgggtatattgcaaaatgatccccacaata
agtctagttaacatccatcaccacgcatagttacaaattttttcttgtgatgaaaacgtttaagatctactctcttagcaaatttctaatatataataca
gtattactaactagaattaATAGTAGTTTTTAAATCTCCTTCGAAGAGAAAGTTGGATTAATACAATGTTGTCTCCTCTTTGTTCCCTGATCTGTAGGGT
ACTTTTGAGATCAACCTTGAGGATGTGACCATATCCTACCTCCCCTTGGCTCATATGTTTGAAAGGGTTGTACAG

>INT391_ACSL5_Peg_myoLuc no MER -L1MA9 6079-6277 23% GDPKGAMLTHQNVVSNASAFLRCVE ESFAPTPEDVSISYLPLAHMFERVVQ AAPE01034117
GGTGACCCCAAAGGAGCCATGCTAACCCATCAAAATGTTGTTTCAAATGCTTCAGCTTTCCTCAGATGCGTGGAGGTTAGTGGTAGCTTGAAAAAGAGGT
CTTCGTTAGAATGTGACTCTGTCATAAGATTTTAATCTTGAAGCTAGAGGAGGCAGAGAAGAAAAAAACCAAAACAGGTTAAGGGCCTGAGTGTGGACAA
ACACATGTGCATCTTTGTGTGGAGGGCTGTGCATTTTCAAGCCGTGATCTTTGAGGATCCCTGCAGACCTCTACTCCAGCGCAGTCCAGGGCACCTCTCC
CAGTTCTTCAGGGCACCCCCTGCATGACTGTATGGGGCACTCATGGAAGGAAATAGTTAAAAAAAAATTTAAATTTTAAATGAGATGTAACGATGCCTaa
cattataatagtttcaggtgtgcaacataatgattcaatatttatatgtattgcaaaatgatcctcatagtaagtgtagttaatatccatcactgcacac
agttacaaattctttgttcttgtgatcagaacttctaagatcaactctctcagcaactttcgaatatacaatagagtgttattaactatagttaacaAGG
GTAGTTCTTAAATCTCTTTGGTAAAGAAGGTTGGCATTAATCCGATTTTGTCTCCTCCCCCTTCCCGATCTGTAGGAAAGCTTTGCACCCACCCCCGAGG
ATGTGAGCATATCCTACCTCCCCTTGGCTCATATGTTTGAGAGGGTTGTACAG

>INT391_ACSL5_Peg_pteVam -MER91B 8-62 24% -L1MA9 6060-6302 25% GEPKGAVLTHQNVISNAAAFLKLLEVS DSFQVTPKDVTISYLPLAHMFERIVQ ti|1386642117 ti|1371644127
GGTGAGCCCAAAGGGGCCGTGCTAACCCATCAAAATGTCATTTCAAATGCTGCTGCTTTTCTCAAACTTTTGGAGGTCAGTCGATCAAATGAAAAAGAAG
TCCTGATCAAAATGTGAATTTGTCATAAGATTTTAATCTTGAAGTCAGAGGAGGCAGAGAGGGGGAAAAAAAACAGGTTAAGGGCCTGAATGTGGGCAAA
TATTTGTGCATCTTTGTCTGGAGGACTGTGCATTTTCAAGCCTTGGTCTTTTAGGATCACTGCAGACCTTTGTACTCAGTTAAGGGCACCTCTTAGAGTG
ATGCAGTGTACCGCCCGCACAACTGTATGTGGCCCACCTAGAAAGAAGTAGCTTAAATTTTTTAAAAATTTTAATTGAGATATAATTGATATCTAACATT
GCCTTAGTTTCAGGTGTACAATGTAATGATTCAATATTTGTATATGTTGCTAAACGATCCTCAAAATAAGTCTAGCTAAGAAAGATCACCACACTTAGAT
AAAAACTCTTTTTTTGTGTGTGACAAGAACTTTTAGCAACTTTCATTATTAACTGTCGTTAACAGGGTAGTTCTTAAATCTCCTTTGGAAGAGAAAGTTG
GCATTAATCCAATGTCATTTCCTCTTTGTTCTTTATCTATAGGACAGCTTCCAGGTCACTCCCAAGGATGTGACCATATCCTACCTCCCCTTGGCTCATA
TGTTTGAGAGGATTGTACAGGTGAGT

>INT391_ACSL5_Peg_bosTau -tRNA-GluSine -MER91C 55-85 28% No L1MA9 GDPKGAMLTHANIVSNASGFLKCME GVFEPNPEDVCISYLPLAHMFERIVQ
GGTGATCCCAAAGGAGCCATGTTAACCCATGCAAATATTGTTTCCAATGCTTCTGGTTTTCTCAAATGTATGGAGGTCAGTGGTCAATTGAAAACAAGGC
CCTCATTAAAATGTAAATCTGTCGTAAGATTTTAATCTTAAAGTGAGAGGAGGCAGAGAGGGAAAAAACTGATTGAAGGCCTGAGTGTGGATGAATACCA
GTACATCTTTGTCTGGAGTTTTGCCCTTTTATTTATTTATTAatatatatatatatatatatatatTTTTTAATCTGGACCATTTTTAAAGTTTTTATCG
AATGTGTTATAGTATTGGTTCTGTTTTATGTTTTGATTTTTGGGGGGCTACAAGgtacatgggatctcagctccctgaccaggggtagaactcacaccct
ctgcattggaaggtgaagtcttaaccactggacctctggggaagtccCATAGAGTTTTGCTGTGTTAGGGTCACTGCAGATCTCCACACTCAATGCAGTT
AGAgcagcccttagatttacacagggcacatctgcacagctgtatgcagcagtcctAGAAAGAAGTGTTTAAATCCTCTTTGGAAGAGGAAATTGACATT
AACCCATTGTTGTCTCTTTTCCATTTCCTGATCTCTAGGGTGTTTTTGAGCCCAATCCTGAGGACGTGTGTATATCCTACCTCCCCTTGGCTCATATGTT
TGAAAGGATTGTACAG

>INT391_ACSL5_Peg_turTru -MER91 261-311 22% No L1MA9 GDPKGAMLTHENIVSNAAAFLKCVE HTFEPSSEDVTISYLPLAHMFERVVQ
GGTGACCCCAAAGGAGCCATGTTAACCCATGAAAATATCGTTTCAAATGCTGCTGCTTTTCTCAAATGTGTGGAGGTCAGTGGTCAATTGAAAAGGAGGC
CCTCGTTAAAATGGGAATCTGTCATAAGATTTTAAAGTTAGAGGAGGCAGAGGGGGAAGAAACAGGTTGAAGGCCTGAGTGTGGACAAATACTGGTGCAT
CTTTGTCTAGAGTTTTGCTCTTTTAGGGTCACTGCAGATCTCTGCACTCAGTGCAGTTAGGGCACCCCTTAGGGCACAGTGCACACCTGTACAACTGTAT
GCAGCAGTCCTAGAAAGAAGAAGTGTTTAAATCTTCTTTGGAAGAGAAAGTTGGCATTAATCCACTGTTGTCTCCTTTCCATTTCCTGATCTATAGCATA
CTTTTGAGCCCAGTTCTGAGGACGTGACCATATCCTACCTCCCCTTGGCTCATATGTTTGAGAGGGTTGTACAG

>INT391_ACSL5_Peg_susScr -MER91 257-306 8% No L1MA9 GDPKGAMITHQNIVSNVASFLKRLE YTFQPTPEDVSISYLPLAHMFDRIVQ ti|2023263948
GGTGACCCCAAAGGAGCCATGATAACCCATCAAAATATTGTTTCAAATGTTGCTTCTTTTCTCAAACGTCTGGAGGTCAGTGGTCGACTGAAAAAGAAGC
CCCTGTTGAAATGTGAATCTGTTATAAGATTTTAAAGTTAGAGGAGGCAGAGAGGAAAGAACCAGGTCAAAGCCCCAAGTATGGGAAAATACTAGTGCAT
CTTTGGAGTTTTGCTCTTCTAGGGTCACTATAGATCTCTACACTCAGTGTAATTAGGGCACCCCCCAGAGTTGTGCAGTGCACACCTGCACAACTGTATG
TGGCAGTACTAGAAAGTAGTGTTTAAATCTTCTTTGGAGGAAAAAGTTGGCATTAATCCATTGTTGTCTCCTTTCCCTTTCCTGATCTACAGTACACTTT
TCAGCCCACCCCTGAGGACGTGTCCATATCCTACCTCCCCTTGGCTCATATGTTTGATAGGATCGTACAG

>INT391_ACSL5_Peg_vicVic -MER91 284-337 24% No L1MA9 GDPKGAMITHENVVSNVAAFLKFME YSFEPTPEDVAISYLPLAHMFERVVQ ti|1970855441 
GGTGACCCCAAAGGAGCCATGATAACCCATGAAAATGTTGTTTCAAATGTTGCTGCTTTTCTCAAATTTATGGAGGTCAGTGATCAACTGAAAAAGACAC
CCTCGTTAAAATGTGAATCTGTCATAAGACTTTAATCTTCAGGTTAGAGGAGGCAGAGAGGGAAAATGACAGGTTTAAAGCCTGAGGGTTGACAAAGACT
GGTGCATCTTTGTCTGGAGGACTGTGCGTTTCCAAGTTTTACTCTTAAGAATCACTGCCGGTCTCTCCACCCAGTGCAGTTAGGGCATCTCTTAGATTTG
CGCAGTGCACACTTGTGCAACTGTATGTGGCGGTCCTAGAAAGAAGTAGTGCTTAAATCTTCTTTGGAAGAGAAAGTTGGCATTAATCGAATGTTGTCTT
CCTCCCATTCCCTGATCTCTAGTATTCTTTCGAGCCCACCCCTGAGGATGTGGCCATATCCTACCTCCCCTTGGCTCATATGTTTGAGAGGGTTGTACAG

>INT391_ACSL5_Peg_sorAra -SOR1SINE No L1MA9 WGPKGAKITHEILSSKAZAFLNSVE YAFEPTPEDVSISYLPLAHMFERVVQ AALT01576933
GGGCCTAAGTGGTGCTGAGGATGGAACCCAGGCCTTCTGCAGCTCCAACCCCCTGGGCCAGCTCTCCAGCTCTAAAGTGCCCCTAATGTAAGGGGAT
GCAGGAAATATGGCAGAGCTGAAGTCATGAACCCAGAAACAACAGGAGGAGGTGATGGGCTTTTCTTTGTAACTGCATCTGTGATTGTGGTCTTGTGGAA
TGTCGCTGCACATTGCAAAGCCAAAGACGGGCTGTGTGCTTTATAAAGGGTCTTTCTCTCCACCTCTTGTCTCCTCCAGGTGACCCCAAAGGAGCCATGA
TCACGCATGAAAATATTGTTTCAAACGCCTCTGCTTTCCTCAAGTGTGTGGAGGTCAGTGGATGTGGGAAAAGAGGTCCTAGCAAAAGGGTGGATGCCAC
AAAGTTCAGAAGTGGAAGTTAGAGCAGCAGCAGGGCTGGAGGGTGGCGTTCAAAGGGCTGTGTGTGTGCAGATGCCCCGACAGCTTGGGACATCAGTGTT
ATCATTATCATTATTATTATTACCATTTTGGTTTTTGGGGTACACTTGGGAATGGACAGGGGGCACTTCTGGCTTATGCACTCAGGAATTACTCCTGGTG
GTGCTCAGGGAACCATGTGGGATGCTGGGAATCAAGCCACATGCAAGGCAAATGCCCTACCCACTGTGCTATTGCTCCAGTCTCATCAGTGTTTTAGGAA
GCTGTGTATGTTGCTGCCTTGATATCCAGCACCTCTCTGCTCTCGGCGTGTAACAGCGCCCCTCAGAGCTCCACGGGGGGTCTAGCCTGCACACCCAGGT
GTGGCCCTGCTGGAAATGCCTGGTCTTTAGGTCTTCTTTGTCTGGGGAAATTTGGCATTGATCGATGGTCTCTTTCCTCTGTGCCCTGATCTGTAGTATG
CGTTCGAGCCCACGCCTGAGGATGTGAGCATCTCCTACCTCCCCTTGGCACACATGTTTGAGAGGGTCGTGCAG


Phylogenetically informative coding insertions and deletions

Mammalian genomes contain about 20,000 genes comprised of some 190,000 exons. Insertions and deletions (indels) accrue slowly in these exons over time as species diverge from one another. These supplement information that can be derived from amino acid substitution analysis. In some instances, the initial indel occurs and is fixed across a stem population (a stem is an interval of evolutionary time not giving rise to lineages surviving to the present day).

Such rare genomic events can be phylogenetically informative. However they are potentially subject to re-occurence and reversion in some descendent clades which could confuse the issue. For this reason, it is imperative to screen out indels in regions of dna prone to this type of event by virtue of their repetitive nature (conducive to repeated replication slippage) or compositional simplicity.

Lineage-sorting is another issue but provided the stem persisted long enough for informative indels to arise in adequate numbers, those of the true topology should significantly outnumber anomalies arising from the two alleles exisitng at the time of speciation sorting out differently in descendent clades. However in the situation when several mammalian orders arise over a very short period of time (in effect a polytomy) or when the speciation process itself is blurred by millions of years of hybridization or genetic mixing at population boundaries, the whole concept of discrete topological tree branching may be inapplicable.


Analysis of a potentially informative indel in CHML

A loss of one amino acid can be observed within an exon of the gene CHML in carnivores, bats, and horse but not in other Laurasiatheres (or other placental mammals. This gene is similar enough to a second gene CHM that it too needed full-on phylogenetic annotation -- it has no indel in any species so must not be cross-annotated for CHML in species without assemblies. The key to that is including upstream amino acids where sufficient divergence between the two genes resides.

The background story here is a common one in gene dosage compensation. In the amniote ancestor and birds and lizards today there is but one multi-exonic gene CHM. In mammals, as the sex chromosomes underwent upheaval, the ortholog ended up on chrX which has implications for reduced levels of expression compared to an autosomal gene. That may have favored persistence of a retroprocessed (intronless) copy on chr1. In marsupials, the two copies remained quite similar. In placentals, the second gene CHML diverged extensively from the first while remaining well conserved within its orthology class.

Pegasoferae.png

The one-residue indel appears cleanly restricted to Pegasoferae. There are 5 Laurasiatheres with it and 5 without it, which needs further buttressing by PCR (adding more basal species has the effect of localizing the event farther back on the stem). The parental gene did not develop the indel in any bioinformatically accessible species.

Interestingly, the retrogene CHML landed within intron 1 of encephalopsin OPN3 with the same direction of transcription. This raises some questions about how CHML is translated (as it would apparently be spliced out). Encephalopsin has an interesting history in mammals involving multiple independent losses.

The region annotated below corresponds to a known domain called GDI (for GDP dissociation inhibitor: pfam00996). The 3D structure of this region is available in the parent gene in rat, PDB 1LTX so the structural location of the indel could be determined. Very likely it lies within a loop and has minimal functional impact. 

CHML chr1:239,864,567-239,864,746                              gene_genSpp
AFRQCSFSEYLKTKKLTPNLQHFVLHSIAMTSESSCTTIDGLNATKNFLQCLGRFGNTPF   CHML_homSap Homo sapiens (human)
AFRQCSFSEYLKTKKLTPNLQHFVLHSIAMTSESSCTTIDGLNATKNFLQCLGRFGNTPF   CHML_panTro Pan troglodytes (chimp)
AFRQCSFSEYLKTKKLTPNLQHFVLHSIAMTSESSCTTIDGLNATKNFLQCLGRFGNTPF   CHML_ponPyg Pongo pygmaeus (orang_sumatran)
AFRQCSFSEYLKTKKLTPNLQHFVLHSIAMTSESSCTTIDGLNAIKNFLQCLGRFGNTPF   CHML_macMul Macaca mulatta (rhesus)
AFRQCSFSEYLKTKKLTPNLQHFVLHSIAMTSESSCTTIDGLNATKNFLQCLGRFGNTPF   CHML_calJac Callithrix jacchus (marmoset)
AFEQCLFSEYLKTKKLTPNLQHFILHSIAMTSESSCTTIDGLKATKNFLQCLGRFGNTPF   CHML_otoGar Otolemur garnettii (bushbaby)
AFKQCSFSEYLKTKKLTPNLQHFVLHSIAMTSESSCTTVDGLKATKNFLQCLGRFGDTPF   CHML_micMur Microcebus murinus (mouse_lemur)
AFEQCLFSEYLKTKKLTPNLRHFILHSIAMTSESSCSTLDGLKATKTFLQCLGRFGNTPF   CHML_tupBel Tupaia belangeri (tree_shrew)
DFKQCSFSDYLKTKKLTPNLQHFILHSIAMTSESSCTTLDGLQATKTFLQCLGRFGNTPF   CHML_musMus Mus musculus (mouse)
DFKQCSFSDYLKTKKLTPNLQHFILHSIAMSSDSSCTTLDGLQATKNFLRCLGRFGNTPF   CHML_ratNor Rattus norvegicus (rat)
DFQQCLFSEYLKTKRLTPNLQHFILHSIAMTSESSCTTLDGLKATKNFLQCLGRFGNTPF   CHML_cavPor Cavia porcellus (guinea_pig)
DFKQCSFSEYLKAKKLTPNLQHFVLHSIAMTSETSCTTLDGLKATKIFLQCLGRFGNTPF   CHML_oryCun Oryctolagus cuniculus (rabbit)
DFKQCSFSEYLKTKKLTPNLQHFILHSIAMTSESSCTTLDGLRATKNFLQCLGRFGNTPF   CHML_ochPri Ochotona princeps (pika)
AFVHCSFSDYLKTKKLTPNLQHFVLHSIAMT-ESSCTTIDGLKATKNFLRCLGRFGNTPF   CHML_canFam Canis familiaris (dog)
AFMQCSFSEYLKTKKLTPNLQHFVLHSIAMT-ESSCTTIDGLKATKNFLQCLGRFGNTPF   CHML_felCat Felis catus (cat)
AFMQCSFSEYLKTKKLTPNLQHFVLHSIAMT-ESSCTTIDGLKATKNFLQCLGRFGNTPF   CHML_equCab Equus caballus (horse)
DFTQRPFSEYLKTQKLTPNLQHFILHSIAMT-EPSCLTVDGLKATKHFLQCLGRYGNTPF   CHML_myoLuc Myotis lucifugus (microbat)
DFTQCSFSEYLKTKKLTPNLQHFVLYSIAMT-ESSCTTVDGLKAAKNFLRCLGRFGNTPF   CHML_pteVam Pteropus vampyrus (macrobat)
AFTQCSFSEYLKTKNLTPSLQHFILHSIAMMSESSCTTVDGLKATKTFLQCLGRFGNTPF   CHML_bosTau Bos taurus (cow)
AFTQCSFSEYLKTKKLTPSLQHFVLHSIAMMSESSCTTIEGLKATKNFLQCLGKFGNTPF   CHML_turTru Tursiops truncatus (dolphin)
DFMQCSFSEYLKAKKLTPSLQHFVLHSIAMTSESSCTTIDGLKATKNFLQCLGRFGNTPF   CHML_susScr Sus scrofa (pig)
AFVQSSFSEYLKTKKLTPNLQHFVLHSIAMMSESPCTTIDGLKATKNFLQCLGRFGNTPF   CHML_vicVic Vicugna vicugna (vicugna)
AFVQSSFSEYLKTKKLTPNLQHYILHSISMTSESSCTTLDGLKATKKFLQCLGRFGNTPF   CHML_eriEur Erinaceus europaeus (hedgehog)
AFIQCSFSDYLKTKKLTPNLQHFILHSIAMTPEASCSTVDGLKATKIFLQCLGRFGNTPF   CHML_sorAra Sorex araneus (shrew)
TFKQCSFSEYLKTKRLTPNIHHFVLHSIAITSQSSCTIIDGLKATKTFLWCLGWFSKNPF   CHML_dasNov Dasypus novemcinctus (armadillo)
AFEQCSFSEYLKTKKLTPNLQHFILHSIAMTSQSSCTTLDGLKATKNFLQCLGRFGNTPF   CHML_choHof Choloepus hoffmanni (sloth)
AFKQCSFSEYLKTKKLTPNLQHFVLHSIAMTSESSCTTIDGLKATKNFLQCLGRFGNTPF   CHML_loxAfr Loxodonta africana (elephant)
AFKHCSFSEYLKTKKLTPNLQHFVLHSIAMTSESSCTTIDGLKATKTFLQCLGRFGNTPF   CHML_proCap Procavia capensis (hyrax)
...                                                            CHML_echTel Echinops telfairi (tenrec)
AYEESTFSEYLKTQKLTPILRHFVLHSIAMASETSTSTLDGLRGTKNFLQCLGRYGNTPF   CHML_monDom Monodelphis domestica (opossum)
...                                                            CHML_ornAna Ornithorhynchus anatinus (platypus)
AQKECTFSDYLKTQKLTPNLQHFILHSIAMVSEVNCCTIDGLKATQRFLQCLGRYGNTPF   CHML_anoCar Anolis carolinensis (lizard)
NYKNSTFAQFLKTRKLTPSLQHFILHSIAMVSEKDCNTLEGLQATRKFLQCLGRYGNTPF   CHML_galGal Gallus gallus (chicken)



CHM chrX:85,097,861-85,098,040   genSpp
GYEEITFYEYLKTQKLTPNLQYIVMHSIAMTSETASSTIDGLKATKNFLHCLGRYGNTPF   CHM_homSap Homo sapiens (human)
GYEEITFYEYLKTQKLTPNLQYIVMHSIAMTSETASSTIDGLKATKNFLHCLGRYGNTPF   CHM_panTro Pan troglodytes (chimp)
GYEEITFYEYLKTQKLTPNLQYIVLHSIAMTSETTSSTMDGLKATKNFLHCLGRYGNTPF   CHM_ponPyg Pongo pygmaeus (orang_sumatran)
GYEDITFYEYLKTQKLTPNLQYIVLHSIAMTSETASSTIDGLKATRNFLHCLGRYGNTPF   CHM_macMul Macaca mulatta (rhesus)
GYEEITFCEYLKTQKLTPNLQYIVLHSIAMTSQTASSTIDGLKATKNFLHCLGRYGNTPF   CHM_calJac Callithrix jacchus (marmoset)
...                                                            CHM_otoGar Otolemur garnettii (bushbaby)
...                                                            CHM_micMur Microcebus murinus (mouse_lemur)
AYEEITFSEYLKTQKLTPNLQYFVLHSIAMTSELASSTLDGLKATKNFLRCLGRYGNTPF   CHM_tupBel Tupaia belangeri (tree_shrew)
AYEETTFSEYLKTQKLTPNLQYFVLHSIAMTSETTSSTVDGLKATKKFLQCLGRYGNTPF   CHM_musMus Mus musculus (mouse)
AYEGTTFSEYLKTQKLTPNLQYFVLHSIAMTSETTSCTVDGLKATKKFLQCLGRYGNTPF   CHM_ratNor Rattus norvegicus (rat)
AYETITFSEFLKTQKLTPNLQYFVLHSIAMTSETTSSTIDGLKATKNFLHCLGRYGNTPF   CHM_cavPor Cavia porcellus (guinea_pig)
GYEEIAFSEYLKTQKLTPNLQYFVLHSIAMTSETTTTTLDGLKATKNFLHCLGRYGNTPF   CHM_oryCun Oryctolagus cuniculus (rabbit)
...                                                            CHM_ochPri Ochotona princeps (pika)
AYEEITFSEYLKTQKLTPNLQYFVLHSIAMTSETASNTIDGLKATKNFLHCLGRYGNTPF   CHM_canFam Canis familiaris (dog)
...                                                            CHM_felCat Felis catus (cat)
AYEEITFSEYLKTQKLTPNLQYFVLHSIAMTSETASSTIDGLKATKNFLHCLGRYGNTPF   CHM_equCab Equus caballus (horse)
AYEDITFSEYLKTQKLTPNLQHFVLHSIAMTSKTTSSTIDGLKATRKFLHCLGRYGNTPF   CHM_myoLuc Myotis lucifugus (microbat)
AYEEITFSEYLKTQKLTPNLQYFVLHSIAMISERASSTIDGLKATKNFLCCLGRYGNTPF   CHM_pteVam Pteropus vampyrus (macrobat)
AYEEITFSEYLKTQKLTPNLQYFVLHSMAMTSETGSSTIDGLKATKNFLHSLGRYGNTPF   CHM_bosTau Bos taurus (cow)
AYEEITFSEYLKTQKLTPNLQYFVLHSIAMTSETASSTIDGLRATKNFLHCLGRYGNTPF   CHM_turTru Tursiops truncatus (dolphin)
...                                                            CHM_susScr Sus scrofa (pig)
AYEEISFSEYLKTQKLTPNLQYFVLHSIAMTSETASSTIDGLKATRNFLHCLGRYGNTPF   CHM_vicVic Vicugna vicugna (vicugna)
...                                                            CHM_eriEur Erinaceus europaeus (hedgehog)
AYEKMTFSEYLKTQNLTPNLQYFVLHSIAMASETGSSTIDGLKATKNFLQCLGRYGNTPF   CHM_sorAra Sorex araneus (shrew)
...                                                            CHM_dasNov Dasypus novemcinctus (armadillo)
...                                                            CHM_choHof Choloepus hoffmanni (sloth)
...                                                            CHM_loxAfr Loxodonta africana (elephant)
...                                                            CHM_proCap Procavia capensis (hyrax)
AYEEITFSEYLKMRKLTPNLQYFVLHSIAMTSETTSTTIDGLKATRNFLHCLGRYGNSPF   CHM_echTel Echinops telfairi (tenrec)
AYEDCTFSEYLKTQRLTPNLQHFVLHSIAMVSETSTSTLDGLRETRNFLQCLGRYGNTPF   CHM_monDom Monodelphis domestica (opossum)
...                                                            CHM_ornAna Ornithorhynchus anatinus (platypus)
AQKECTFSDYLKTQKLTPNLQHFILHSIAMVSEVNCCTIDGLKATQRFLQCLGRYGNTPF   CHM_anoCar Anolis carolinensis (lizard)
NYKNSTFAQFLKTRKLTPSLQHFILHSIAMVSEKDCNTLEGLQATRKFLQCLGRYGNTPF   CHM_galGal Gallus gallus (chicken)


Analysis of a five residue deletion in DIO1

The five amino acid deletion here occurs in first exon of iodothyronine deiodinase, a much-studied gene. A consistent picture is seen in dog, bears, cat, horse, macrobat, and microbat with artiodactyls (cow, dolphin, pig, vicuna) and eulipotyphlya (hedgehog and shrew) lacking the deletion, which is evidently the ancestral condition judging by marsupials, more basal Atlantogenata, and Euarchontoglires.

Pegasoferae.png

This event supports -- but does not by itself establish -- the topology ((((dog horse) bat) cow) eulipotyphla) at the expensive of ((((dog horse) cow) bat) eulipotyphla). It does not speak to various possible internal resolutions of ((dog horse) bat). Longer indels are uncommon however so it is difficult to avoid the conclusion that artiodactyls are an outgroup (without invoking lineage-sorting).

Mammals have two other iodothyronine deiodinase paralogs but these are sufficiently diverged at this exon to prevent any annotational confusion. They too are full-length in this region, suggesting that length is a very ancient character indeed. No 3D structure is available for any member of the family but they can be supposed to have the basic ferredoxin fold (like many other selenoproteins).

Note two species within Afrothera have an 8 residue deletion in a similar region of the protein, suggesting it is a loop region inessential to protein function. No data is available for tenrec or other species in this clade, so it cannot be more precisely dated without PCR of additional species. However armadillo and sloth lack the deletion, bounding its timeframe somewhat.

The alignment below shows the deletion in 'difference' mode relative to human. Here dots mean the residue matches human. This mode of display results in less visual clutter while emphasizing degree of conservation, which is an important quality parameter for phylogeneticall informative indels. 

DIO1_homSa  MGLPQPGLWLKRLWVLLEVAVHVVVGKVLLILFPDRVKRNILAMGEKTGMTRNPHFSHDNWIPTFFSTQYFWFVLKVRWQRLEDTTELGGLAPNCPVVRLSGQRCNIWEFMQ
DIO1_panTr  ..................................................................................................H.............
DIO1_macMu  .....S...V.K................................................................................................D...
DIO1_calJa  ....G..................A......T.......K......D........N...........................................H.........D...
DIO1_otoGa  ....R..........F.......A...M..........SQ.....QQ.V.AK.............LQHPV.LVCPEGPL.....M..R.........SAS...K....D...
DIO1_musMu  .....LW......VIF.Q..LE.A.....MT...G...QS.....Q....A...R.AP...V.....I................RA.F.......T..C....K....D.I.
DIOI_ratNo  ...S.LW......VIF.Q..LE.AT....MT...E...Q......Q........R.AP...V.....I................RA.Y.......T.......K..V.D.I.
DIO1_oryCu  ....R...........VQ...E.A.....MT...E...Q......Q...IAQ..N.AQ.S........................A..P.......S.......Q.S..D..R
DIOI_cavPo  ...TW...........VQ...E.AM....MT...E.I.KS..............Q..................I.........E.A.......D.S..C...EKRT..D..H
DIO1_canFa  ....R.V...R......Q...Q.A....F.K...A...QH.V..NGN-----K....Y...A..LY.M.........Q......R..P....................D...
DIO1_ursAr  ....R.V...R......Q..M..A..........E...QQV...NK.-----.....Y...L...Y.M................R..P....................D... 
DIO1_felCa  ...S.L....R.....FQ..LQ.A....F.....S...QH.V..NR.-----.....Y...A..LY.V................R..P.................S..D..K
DIO1_equCa  ....RA...........Q..LQ.A......T.......QH.V..NQ.-----.....Y...V..LY...........H........KR......S.............D...
DIO1_myoLu  ..............I..Q..L..TL...Q.K...R...QH....NR.-----.....Y...A..L...P....I..........K..E.S...............H..D...
DIO1_pteVa  .E..W..R.........Q..L..A....Q.T...R...Q..V..NR.-----.....F...L..L...............Q.....KE..........C.........D...
DIO1_bosTa  ....S...........FQ..L..AI.....T...R...Q...................E..............I..........M..Q..............E..S..D...
DIO1_turTr  ....L...........FQ.GL..AM.....T...R...Q.....S.....AK.....YE........A.....I..........M..Q..R.................D...
DIO1_susSc  .E..L...........FQ..L..AM....MT...G...QD....SQ....AK......E........A................K..E..........S......H..D...
DIO1_vicVi  ...SL...........FQ.VL..AL.....T...G...QD....SQR...AQ.....YE..............I.............Q.....D....C..-D.VH..D...
DIO1_eriEu  ....S...........FQ..L..AI.....T...R...Q...................E..............I..........M..Q..............E..S..D...
DIO1_sunMu  ....GL..L...FG..VR..LK.A......T.W.SAIRPHL...S.....AK..R.TYED.A...............N..Q...R.KQ.DI..DS...H.....ARL.D...
DIO1_dasNo  ...S..........I.FQ..L..A...T..T...G...Q....KSQ.SHKAE....PY...G....N......L..IG......K..Q..........H.........D...
DIO1_choHo  ...SW............Q..L..AM..I..T...G...Q.....SRRANN.KD.Q.PY...G....N.................K..Q..........H..R......D...
DIO1_loxAf  ..............IF.K..L..AM.........G...K....Q--------....AY.M.GS.L..IP....I...Y......K..E..P..D....C........SD...
DIO1_proCa  ......V..........R..L..AM.....A...G...K....Q--------....AY.M.CS.L..VP........Y......K..E..........H.....R...D...
DIO1_monDo  .LRLWLW.........Q.VG..LM..LMKM.S...M.QH..G..Q.SSIFQ..N.KYE..G....TLP..L...R........QALQ..P..D....S.R..PRRL.D..HA
DIO1_triVu  .  AG.L..VR.F.A..Q..F......L.KT...NMM.KH..SL.QRSSISQ.TQ.AYE..G.....I...F............QALQ......P...T.K.ESRH..D..H
DIO1_anoCa  .  FKA.RLVLKT.L..Q.CLSTA...LFM....ATA..Y..KQS.RSS.G...N.VYE..G.....F..LL.....K.K....KALQ.CP...T...DFD.KIHH.LD...

Possibly informative whole gene duplication in bat opsin

An apparental functional duplication of a visual opsin gene has been reported previously in the megabat Haplonycteris fischeri that is missing in Pteropus and Myotis. This is another form of rare genomic event, a large insertion indel since most mammals have but two imaging opsins.

This gene duplication might simply be restricted to this one genus (or even this one species). Alternatively it might have greater phylogenetic depth and be somewhat informative in resolving intra-bat taxonomy. This would require PCR of many additional bat species since no further genomic work is anticipated any time soon. It is not relevent to Pegasoferae per se since bats are clearly monophyletic overall, even as the macro/micro distinction remains equivocal as a taxonomic character.

The key paragraph in the article:

"When we sequenced the region from exon 4 to exon 5 of the M/L opsin gene in an individual from H. fischeri, an additional copy was found. While exons 4 and 5 of the two copies were identical at nonsynonymous sites, the two copies of intron 4 differed by 20 nucleotides and 11 indels, including one large indel of ~750 bp and involving a total of 794 sites. These differences appeared to be too large to represent two alleles of the same locus, indicating the possibility of two duplicate genes. Indeed, the sequence data from intron 5 revealed three different sequences, denoted as 5–1, 5–2, and 5–3 (fig. 4). Whereas introns 5–1 and 5–2 may represent two polymorphic alleles from the same locus, intron 5–3 differs from intron 5–1 at 10 sites and should represent another locus. (Because a locus can have at most only two different sequences, the presence of three sequences should indicate a gene duplication.)"

Possibly informative indel in OPN4 bat melanopsin

Another potentially informative indel for bats -- a one residue deletion -- separates Myotis from everything else. Its phylogenetic depth can only be determined by sequencing additional species of bats. It might contribute to establishing microbates are polyphyletic (or it could simply be an idiosyncracy of the genus Myotis). The indel occurs in a well-understood region of melanopsin, the only rhabdomeric opsin that has persisted into mammals. This gene is not directly involved in imaging vision but the structural/functional implications of the indel still might be determinable. 

Melanopsin OPN4 chr10:88,408,220-88,408,423 indel in cytoplasmic loop between transmembrane segments 3 and 4
.....FYAFCGALFGISSMITLTAIA.......................FVLLGVWLYALAWSLPPFFGW
2 GCEFYAFCGALFGISSMITLTAIALDRYLVITRPLATFGVASKRRAAFVLLGVWLYALAWSLPPFFGW 1   MEL1_homSap Homo sapiens (human) melanopsin OPN4 
2 GCEFYAFCGALFGISSMITLTAIALDRYLVITRPLATFGVASKRRAAFVLLGVWLYALAWSLPPFFGW 1   MEL1_panTro Pan troglodytes (chimp)
2 GCEFYAFCGALFGISSMITLTAIALDRYLVITRPLATIGVASKRRAAFVLLGVWLYALAWSLPPFFGW 1   MEL1_ponpyg Pongo pygmaeus (orang_sumatran)
2 GCEFYAFCGALFGISSMITLTAIALDRYLVITRPLATIGVASKRRAAFVLLGVWLYALAWSLPPFFGW 1   MEL1_macMul Macaca mulatta (rhesus) 
2 GCEFYAFCGALFGISSMITLTAIALDRYLVITRPLTTVGVASKRRAALVLLGVWLYSLAWSLPPFFGW 1   MEL1_otoGar Otolemur garnettii (bushbaby)
2 GCEFYAFCGALFGISSMITLTAIALDRYLVITRPLASVGTASKRRAGLVLLGVWLYALAWSLPPFFGW 1   MEL1_micMar Microcebus murinus (mouse_lemur)
2 GCEFYAFCGAVFGITSMITLTAIAMDRYLVITRPLATIGRGSKRRTALVLLGVWLYALAWSLPPFFGW 1   MEL1_musMus Mus musculus (mouse)
2 GCKFYAFCGAVFGIVSMITLTAIAMDRYLVITRPLATIGMRSKRRTALVLLGVWLYALAWSLPPFFGW 1   MEL1_ratNor Rattus norvegicus (rat) 
2 GCEFYAFCGAVLGITSMITLTAIALDRYLVITRPLATIGMGSKRRTALVLLGIWLYALAWSLPPFFGW 1   MEL1_phoSun Phodopus sungorus (hamster)
2 GCEFYAFCGAVFGISSMITLTAIALDRYLVITRPLATIGMASKKRAAFFLLGVWFYALAWSLPPFFGW 1   MEL1_speTri Spermophilus tridecemlineatus (squirrel)
2 GCEFYAFCGAVSGITSMTTLTAIALDRYLVITRPLATIGVASKRRTALVLLGVWLYALAWSLPPFFGW 1   MEL1_nanSpa Nannospalax ehrenbergi (mole-rat)
2 GCEFYAFCGALFGITSMITLTAITLDRYLVITRPLATIGVASKRQAALVLLGVWLYALAWSLPPFFGW 1   MEL1_cavPor Cavia porcellus (guinea_pig)
2 GCEFYAFCGALFGISSMITLTAIALDRYLVITRPLAAVGMVSKKRAGLVLLGVWLYALAWSLPPLFGW 1   MEL1_oryCun Oryctolagus cuniculus (rabbit) 
2 GCEFYAFCGALFGISSMITLTAIALDRYLVITRPLAAVGMVSKRRTGLVLLGVWLYSLACSLPPLFGw 1   MEL1_ochPri Ochotona princeps (pika)
2 GCEFYAFCGALFGITSMITLTAIALDRYLVITHPLAAVGVVSKRRAALVLLGVWLYALAWSLPPFFGW 1   MEL1_canfam Canis familiaris (dog)
2 GCEFYAFCGALFGITSMITLMAIALDRYLVITHPLATIGVVSKRRAALVLLGVWLYALAWSLPPFFGW 1   MEL1_felCat Felis catus (cat)
2 GCEFYAFCGALFGITSMITLTAIALDRYLVITRPLATVGVVSKRWAALVLLGIWLYALAWSLPPFFGW 1   MEL1_equCab Equus caballus (horse)
2 GCEFYAFCGALFGITSMITLTAIALDRYLVITRPLA-IGVVSKRRAALVLLGVWLYALAWSLPPFFGW 1   MEL1_myoLuc Myotis lucifugus (microbat)  7/7 traces
2 GCEFYAFCGALFGITSMITLTAIALDRYLVITRPLAAIGVVSKRRAALVLLGVWLYALAWSLPPFFGW 1   MEL1_pteVam Pteropus vampyrus (macrobat) 3/3 traces
2 GCEFYAFCGALFGITSMITLTAIALDRYLVITRPLATVGMVSKRRAALVLLGVWLYALAWSLPPFFGW 1   MEL1_bosTau Bos taurus (cow)
2 GCEFYAFCGAVFGITSMITLTAIALDRYLVITRPLATVGMVSKRRAALVLLGVWLYALAWSLPPFFGW 1   MEL1_turTru Tursiops truncatus (dolphin)
2 GCEFYAFCGAVFGITSMITLTAIALDRYLVITYPLATVGMVSKRRAALVLLGVWLYALAWSLPPFFGW 1   MEL1_susScr Sus scrofa (pig) VPT
2 GCEFYAFCGALFGITSMITLTAIALDRYLVITRPLATIGVVSKRRVALVLLGVWLYSLAWSLPPFFGW 1   MEL1_eriEur Erinaceus europaeus (hedgehog)
2 GCEFYAFCGALFGITSMMTLTAIALDRYLVITRPLASIGVVSKRRAALVLLGVWLYALAWSLPPFFGW 1   MEL1_sorAra Sorex araneus (shrew)
2 GCKFYAFCGALFGITSMITLTAIALDRYLVITRPLATIGVVSKRRAALVLLGIWLYALAWSLPPFFGW 1   MEL1_loxAfr Loxodonta africana (elephant)
2 GCEFYAFCGALFGITSMITLTAIALDRYLVITRPLATIGVVSKRRAALVLLVIWLYALAWSLPPFFGW 1   MEL1_echTel Echinops telfairi (tenrec)
2 GCEFYAFCGALFGITSMITLTAIALDRYLVITRPLATIGVVSKRRTALVLLGTWLYALAWSLPPFFGW 1   MEL1_proCap Procavia_capensis (hyrax)
2 GCEIYAFCGALFGIASMMTLLAISLDRYLVITRPLAATGVVSRRRALLALPGIWLYALAwSLPPFFGW 1   MEL1_dasNov Dasypus novemcinctus (armadillo)
2 ACEFYAFCGALFGITSMITLMAIALDRYFVITRPLASIGVISKKKTGFILLGVWLYSLAWSLPPFFGW 1   MEL1_monDom Monodelphis domestica (opossum) 
2 GCEFYAFCGALFGITSMITLMVIALDRYFVITRPLASIGMISKKKTGLILLGVWLYSLAWSLPPFFGW 1   MEL1_smiCra Sminthopsis crassicaudata (fat-tailed dunnart) 
2 GCEFYAFCGALFGITSMITLMVIALDRYFVITRPLASIGVVSKKKTGLILLGVWLYSLAWSLPPFFGW 1   MEL1_macEug Macropus eugenii (wallaby) 
2 GCEFYAFCGALFGITSMITLMVIALDRYFVITRPLASIGMISKKKTGLILLGVWLYSLAWSLPPFFGW 1   MEL1_smiCra Sminthopsis crassicaudata (dunnart)
2 GCQLYAFCGALFGITSMITLTVIALDRYFVITRPLASIGVISKKRALLILTGVWFYSLAWSLPPFFGW 1   MEL1_ornAna Ornithorhynchus anatinus (platypus) 
2 GCELYAFCGALFGITSMITLMVIALDRYFVITKPLASVRVMSKKKALIILVGVWLYSLAWSLPPFFGW 1   MEL1_galGal Gallus gallus (chicken)
2 GCELYAFCGALFGITSMITLMVIALDRYFVITKPLASVGVTSKKKALIILVGVWLYSLAWSLPPFFGW 1   MEL1_taeGut Taeniopygia guttata (finch)
2 GCELYAFCGALFGIASMITLTVIALDRYFVITRPLASIGAMSTKKALLILSGVWLYSLAWSLPPFFGW 1   MEL1_anoCar Anolis carolinensis (lizard)
2 GCELYAFCGALFGITSMITLMVIAVDRYFVITRPLTSIGVMSKKRAVLILSGVWLYSLAWSLPPFFGW 1   MEL1_xenTro Xenopus tropicalis (frog)  

These sequences may be relevent to primer design:

>MEL1_myoLuc Myotis lucifugus (microbat)
aggctgtgagttctatgccttctgtggggctctctttggcatcacctccatgatcaccctgacggccattgccctggaccgctacctggtgatcacgcgccctctggc catcggg
gtggtgtccaaaaggcgggcggccctcgtcctgctgggcgtctggctctacgccctggcctggagt 

>MEL1_pteVam Pteropus vampyrus (macrobat)
aggctgcgagttctatgccttctgtggtgctctctttggcatcacctccatgattaccctgacggctatcgccctggaccgctacctggtgatcacacgcccactggctgccatcggg
gtggtgtccaagaggcgggcagcgcttgttctgctgggtgtctggctctacgccctggcctggagtctgccacccttctttggctggag

Possibly informative indel in SS18L1 supporting chiroptera + artiodactyl

SS18L1 peg.png

This autosomal indel, at face value, groups artiodactyls and bats to the exclusion of dog, horse, shrew, and hedgehog. Note the ambient gene SS18L1 has rather anomalous composition in its distal half and the exon containing the indel falls under standard masking filters such as seg. It is anomalous in the mammalian proteomewide context in glutamine and tyrosine, no doubt because the dna composition of the exon exhibits very high GC, 32A 18T 58C 57G. The exon has some self-similarity upon blast to a distal region of the gene: 

SNPPSQQGSSQQYLGQEEYYGEQYSHSQGAAEPMGQQ
S+  S QG SQ Y GQ          SQG++  MGQ+
SHYSSAQGGSQHYQGQSSI-AMMGQGSQGSSM-MGQR

The alignment shows the indel phylo-consistently in 3/3 available artiodactyls and 2/2 available bats but not in 4/4 other Laurasiatheres or other vertebrates. The percent identity of human to artiodactyls fallsoff fairly dramatically relative to percent identity to horse and dog (or even marsupial and platypus). It's most unusual for a human/cow ortholog to be more diverged than human/lizard. Some Atlantogenata also appear to be diverging rapidly but without the indel. This cannot be attributed to misalignment or paralog/pseudogene confusion.

In summary, this indel demonstrates some of the subtle issues in using rare genomic events in phylogeny. The indel supports cow + bat topology but not so strongly given the compositional propensity to homoplasy in the context of rapid sequence divergence in some clades. 


SMMQQQAATSHYSSAQGGSQHYQGQSSIAMMGQGSQGSSMMGQRPMAPYRPSQQ Homo sapiens
SMMQQQAATSHYSSAQGGSQHYQGQSSIAMMGQGSQGSSMMGQRPMAPYRPSQQ Pan troglodytes 100%
SMMQQQAATSHYSSAQGGSQHYQGQSSIAMMGQGSQGSSMMGQRPMAPYRPSQQ Macaca mulatta 100%
SMMHQQAATSHYNSAQGGSQHYQGQAPIAMMGQGGQGGSMMGQRPMAPYRPSQQ Mus musculus 88%
SMMHQQAATSHYNSAQGGSQHYQGQAPIAMMGQGGQGGSMMGQRPMAPYRPSQQ Rattus rattus 88%
SMMHQQAASSHYNSAQGGSQHYQGQSSIAMMGQSGQGSSMMGQRPMAPYRPSQQ Canis familiaris 90%
SMMHQQAASSHYNSAQGGSQHYQGQSSIAMMGQSGQGSSMMGQRPMAPYRPSQQ Equus caballus 90%
SMMHQQAASSHYNSAQGGSQHYQGQP-IAMMGQSGQGSSMMGQRPMAPYRPSQQ Myotis lucifugus 87%
SMMHQQAASSHYASAQGGSQHYQGQP-IAMMGQSGQGSSMMGPRPLAPYRPSQQ Pteropus vampyrus 83%
SMMHQQAASSHYSAAQGGSQHYQGQS-MAMMGQSGQGGGVMGQRPMAPYRPSQQ Bos taurus 81%
SMMHQQAASSHYSAAQGGAQHYQGQS-MAMMGQSGQGSGMIGQRPMAPYRPSQQ Sus scrofa 81%
SMMHQQAASSHYSAAQGGSQHYQGQS-MAMMGQSGQAGSMMGQRPMAPYRPSQQ Tursiops truncatus 83%
SMMHQQAASSHYNSAQGGSQHYQGQSSIAMMGPSGQGNSMMGQRPLAPYRPSQQ Erinaceus europaeus 85%
SMMHQQAASSHYSSAQGGG.HYQNQLALAMMGSGGQGSSLMSQRLLALYWPSQQ Sorex araneus 70% poor quality traces
SMMHQPSATPHYSSAPGGGPHYQGQASLAAMGQGTQGSSMMGQRPMAPYRSSQQ Dasypus novemcinctus 77%
SMMHQQTATSHYSSTQSGSQHYQGQSSIAMMGQSGQGSSLMGQR           Loxodonta africana
SIMHPQEAQTHFSSVQGGSQHYQGPSPVAMMGQGGQGGGLMGQRPMAPYRASQQ Procavia capensis
SMMHQQAATSHYSSAQGGSQHYQGQSSIAMMGQGGQGSGLMGQRPMAPYRASQQ Echinops telfairi 90%
SMMHQQAATSHYNSAQGGSQHYQGQSSIAMMSQSNQGSSMMGQRPMGPYRPSQQ Monodelphis domestica 88%
SMMHQQAATSHYNSAQGGTQHYQGQSSIAMMSQSNQGNSMMGQRPMGPYRPSQQ Ornithorhynchus anatinus 85%
SMMHQQAATSHYNSAQAGTQHYQGQSSIAMMSQSNQGNSMMGQRPMGPYRPSQQ Anolis carolinensis  83%
SMMHQQAATSHYNSAQGGSQHYQGQSSIAMMSQSNQGNSMMGQRPMGPYRASQQ Gallus gallus 85%
SMMHQQATGSHYTSAQAGSQHYQGQPSISMMNQSSQGSGMIGQRPLGPYRPSQQ Xenopus tropicalis 75%
not available                                          Felis catus
not available                                          Vicugna vicugna
not available                                          Choloepus hoffmanni

Possibly informative indel in ZNF622 supporting chiroptera + artiodactyl

This 3 residue deletion in exon 1 of ZNF622 seems informative but has some troubling side issues. First, two species seem to have a second somewhat diverged copy, rat and mouse lemur. With rat, it is on another chromosome but mouse has no counterpart. If this gene is prone to duplication, it becomes difficult in species without global assemblies (ie bats) to establish orthology.

Second, only dog is available for carnivores and its sequence is disturbingly diverged in percent identity -- 72% in a gene where cow is 82% with the 3 residue indel and 88% if the indel is filled by consensus sequence. The dog gene is in syntenic position with human. Meanwhile earlier diverged and usually fast evolving species like armadillo and rabbit are over 98% identical to human. Horse at 94% is about what is expected. Third, horse dna exhibits slight tandem repeat at both dna and protein level at the site of the indel that might be conducive to repeated replication slippage events. 

horse  8 bp tandem repeat in indel region
aaggccgtgcaggccgtgagc
    A  V  Q  A  V  S

This indel would benefit from PCR of additional carnivores, pangolin, perissodactyl, and bat species to expand representation of those divisions. It is necessary to develop an understanding on when and why the carnivore gene began to diverge anomalously. It is unusual to see 3 aa deletion in a gene that is fairly well conserved to depth but it may be no coincidence that laurasiatheres other than horse have both rapid divergence and the indel in some species. 


SKKFASFNAYENHLKSRRHVELEKKAVQAVNRKVEMMNEKNLEKGLGVDSV ZNF622_homSap Homo sapiens (human)
SKKFASFNAYENHLKSRRHVELEKKAVQAVNRKVEMMNEKNLEKGLGVDSV ZNF622_panTro Pan troglodytes (chimp) 100%
SKKFASFNAYENHLKSRRHVELEKKAVQAVNRKVEMMNEKNLEKGLGVDSV ZNF622_ponPyg Pongo pygmaeus (orang_sumatran) 100%
SKKFASFNAYENHLKSRRHVELEKKAVQAVNRKVEMMNEKNLEKGLGLDSV ZNF622_macMul Macaca mulatta (rhesus) 100%
SKKFASFNAYENHLKSRRHAELEKKAVQAVNRKVEMMNEKNLEKGLGVDGV ZNF622_calJac Callithrix jacchus (marmoset)
SKKFASFNAYENHLKSRRHVELEKKAVQAVNRKVEMMNEKNLEKGLGGDSL ZNF622_otoGar Otolemur garnettii (bushbaby) 96%
SKKFASFNAYENHLKSRRHVELEKKAVQAVNRKVEMMNEKNLEKGLGVDSV ZNF622_micMur Microcebus murinus (mouse_lemur) 100% ABDC01026332
NKKFASFNAYENHLKSWRHIDLEKKVVQAVNRKVEMMNEKNLEKILGMDSV ZNF622_micMur Microcebus murinus (mouse_lemur)  86% ABDC01455616
SKKFASFNAYENHLKSRRHVKLEKKAVQAVNRKVEMMNEKNLQKGLGVESV ZNF622_tupBel Tupaia belangeri (tree_shrew) weak trace
GKKFATFNAYENHLGSRRHAELERKAVRAASRRVELLNAKNLEKGLGADGV ZNF622_musMus Mus musculus (mouse) 74%
SKKFATFNAYENHLKSRRHVELEKKAVQAVSRQVEMMNEKNLEKGLGVDSV ZNF622_ratNor Rattus norvegicus (rat) 94% AAHX01014435 chr2  ++   77572184  77572336
SKKFATFNAYENYLKSRLHVELEKKTVQAVSRQVEMMNEKNLEKGLGVDSV ZNF622_ratNor Rattus norvegicus (rat) 88% AAHX01059254 chr9  +-   31986229  31986381    153
SKKFASFNAYENHLKSRRHVELEKKAVQAVNRKVEMMNEKNLEKGLDVDSV ZNF622_speTri Spermophilus tridecemlineatus (squirrel)
SKKFASFNAYENHLKSRRHVELEKKAVQAVNRKVEMMNEKNLEKGLGVDSV ZNF622_cavPor Cavia porcellus (guinea_pig)
SKKFASFNAYENHLKSRRHVELEKRAVQAVNRKVELMNEKNLEKGLGVDSV ZNF622_oryCun Oryctolagus cuniculus (rabbit) 100%
.KKFASLNAYENHLRSRRHLELEKKAVQAVNRQVELMNEKNLEKGLGADGV ZNF622_ochPri Ochotona princeps (pika) 86%
GKRFASFNAYENHLQSRRHAELERAAVRAVSRQVQLRNAKNLEKGLGADGV ZNF622_canFam Canis familiaris (dog) 72%
SKKFASFNAYENHLKSRRHVELEKKAVQAVSRKVEVMNEKNLEKGLSVDSV ZNF622_equCab Equus caballus (horse) 94%
SKKFACANAYENHLRSRRHVELERK---AVSRRVEMMNEKNLEKGLGVDRV ZNF622_myoLuc Myotis lucifugus (microbat) 80%/86%
SKKFACFNAYENHLKSRRHMELEKK---AVNRKVEMMNEKNLEKGLGVDSL ZNF622_pteVam Pteropus vampyrus (macrobat) 88%/94%
SKKFASFKAYENHLRSRRHVELEKQ---AVSRKVALMNEKNLEKGLGVDSV ZNF622_bosTau Bos taurus (cow) 82%/88%
SKKFASFKAYENHLRSRRHVELEKQ---AVSRKVALMNEKNLEKGLGVDSV ZNF622_oviAri Ovis aries (sheep) 84%
SKKFASFKAYENHLKSRRHVELEKR---AVSRKVAILNEKNLEKGLGVDSV ZNF622_susScr Sus scrofa (pig) 82%
SKKFASFKAYENHLKSRRHVELEKK---AVSRKVAIMNEKNLEKGLGVDSV ZNF622_vicVic Vicugna vicugna (vicugna) 86%/92%
GKRFASLNAFENHLRSRRHLELEKKAVQAASRRVQMLNAKNLEKGLAADGL ZNF622_eriEur Erinaceus europaeus (hedgehog)
...FASFNAYDNHLRSRRHVELEARAVQAVSRRVQRLNEKNLEKGL..... ZNF622_sorAra Sorex araneus (shrew)
SKKFASFNAYENHLKSRRHVELEKKAVQAVNRKVEMMNEKNLEKGLGADSV ZNF622_dasNov Dasypus novemcinctus (armadillo) 98%
SKKFASFNAYENHLKSRRHVELEKKAVQAVNRKVEMMNEKNLEKGLGADSV ZNF622_choHof Choloepus hoffmanni (sloth)
............HLKSRRHVELEKKAVQAVSRRVEMMNEKNLEKGLGADGV ZNF622_loxAfr Loxodonta africana (elephant)
SKKFASFNAYENHLKSRRHVELEKKAVQAVSRRVEMMNEKNLEKGLDAGGV ZNF622_proCap Procavia capensis (hyrax)
SKKFASFNAYENHLQSRRHVELEKKAVQAVNRRVERMNEKNLEKGLDADNV ZNF622_echTel Echinops telfairi (tenrec) 88%
SKKFATFNAYENHLKSRRHLELEKKAVQAVSRKVEMLNEKNLEKGLAPDGL ZNF622_monDom Monodelphis domestica (opossum) 84%
SKRFSTFNAYENHLKSKKHLELEKKAVQAVSKKVKILNEKNLEKGLAVESV ZNF622_galGal Gallus gallus (chicken)
SKRFSNFNAYENHLKSKKHLELEKKAVQAVSKKVELMNEKNLEKGLAQESV ZNF622_anoCar Anolis carolinensis (lizard)

not available ZNF622_felCat Felis catus (cat)
not available ZNF622_turTru Tursiops truncatus (dolphin)
not available ZNF622_ornAna Ornithorhynchus anatinus (platypus)

>homSap
cagtaagaagtttgcctctttcaacgcctacgagaaccacctcaagtcccggcgtcacgttgagctggagaagaaggccgtgcaggcagtgaatcggaaagtggagatgatgaatgaaaagaacttggagaaaggactgggcgtggacagtgtgga
>uc003jfq.1_hg18_1_6 208 0 1 chr5:16518150-16518774 - ZNF622
MATYTCITCRVAFRDADMQRAHYKTDWHRYNLRRKVASMAPVTAEGFQERVRAQRAVAEEESKGSATYCTVCSKKFASFNAYENHLKSRRHVELEKKAVQAVNRKVEMMNEKNLEKGLGVDSVDKDAMNAAIQQAIKAQPSMSPKKAPPAPAKEARNV
VAVGTGGRGTHDRDPSEKPPRLQWFEQQAKKLAKQQEEDSEEEEEDLDGD


Two residue insert in cow and bat CD5 illustrates homoplasy

Exon 5 of gene CD5 exhibts a two residue insertion in cow, sheep, and bat relative to other placental mammals. However, the insertion is not found in other artiodactyls (dolphin, pig, and vicugna) and so is homoplasic. Grouping bovids with microbats to the exclusion of other even-hoofed animals is a ridiculous concept.

Macrobat has no available data but this locus is unsuitable as a phylogenetic marker within bats. It is not so clear from dna alignement that the insertion occurs in quite the same spot in cows and microbat. This cell surface receptor CD5 is evolving too fast for all but the narrowest phylogenetic purposes -- the percent identity within Laurasiatheres is 70% relative to dog, far too low for an informative rare genomic event. 

human chr11 60645699 60645759 6
human AGCATCTGTGAAGGCACCGTGGAGGTGCGC------CAGGGGGCTCAGTGGGCAGCCCTGTGTGAC
...cow GACGTGTGCGAAGGCTCCGTGGAAGTGCGCAGTGGGAAGGGCCAGAAGTGGGACACGCTATGTGAC

human AGCATCTGTGAAGGCACCGTGGAGGTGCGCCAGGG----GGCT--CAGTGGGCAGCCCTGTGTGACA
mcbat AGCGTGTGCGCGGGCTCCGTGGAGGTGCGCCAGGGCCAGGGCCGGCAGTGGGAAGCCCTGTGCCACA



FQPKVQSRLVGGSSICEGTVEVR--QGAQWAALCDSSSARSSLRWEEVCREQQCGSVNSYRV  CD5_homSap Homo sapiens (human)
FQPKVQSRLVGGSSICEGTVEVR--QGAQWAALCDSSSARSSLRWEEVCREQQCGSVNSYRV  CD5_panTro Pan troglodytes (chimp)
FQPKVQSRLVGGSSICEGTVEVR--QGAQWAALCDSSSFRSSLRWEEVCREQQCGGVNSYRV  CD5_ponPyg Pongo pygmaeus (orang_sumatran)
FQPKVQSRLVGGSSICEGTVEVR--QGAQWAALCDSSSAKSSLRWEEVCREQQCGSFNSYQA  CD5_macMul Macaca mulatta (rhesus)
FQPKVQSRLVGGSSMCEGTVEVR--QGAQWAALCDSSSARSPLRWEEVCQEQRCGGVNSYRV  CD5_calJac Callithrix jacchus (marmoset)
FQPKVQSRLVGGSGMCEGTVEVR--QSTQWAPLCDSSPLKGTARWEEVCQEQQCGSVNSYHM  CD5_otoGar Otolemur garnettii (bushbaby)
FQPKVQSRLVGGSSVCEGSVEVR--QGTQWAALCDSSPAKGTARWEEVCQEQQCGSVNSYHV  CD5_micMur Microcebus murinus (mouse_lemur)
FQPKVQSRLVRGSGVCEGAVEVR--QGLQWAALCDSSGARRMERWNEVCQEQQCGNASSYRL  CD5_tupBel Tupaia belangeri (tree_shrew)
FQPKVQSRLVGGSSVCEGIAEVR--QRSQWEALCDSSAARGRGRWEELCREQQCGDLISFHT  CD5_musMus Mus musculus (mouse)
FQPKVQSRLVGGSSVCEGIAEVR--QRSQWAALCDSSAARGPGRWEELCQEQQCGNLISFHV  CD5_ratNor Rattus norvegicus (rat)
FQPKVQSRLVGGGSTCQGTVEVR--QGGPEAQWVALCHSTRSSARWEALCQEQQCGRFLTYH. CD5_cavPor Cavia porcellus (guinea_pig)
FQPKVQSRLVGGGSVCKGTVEVR--QATQWAALCDSHVSRGPARWAELCQEQKCNGLVSYH.  CD5_speTri Spermophilus tridecemlineatus (squirrel)
FQPKVQSRLVGGSSMCEGTAEVR--QGPRWAALCHNSSAKGTARWEELCQEQQCGIVNSYYV  CD5_oryCun Oryctolagus cuniculus (rabbit)
FQPKVQSRLVGGSGTCEGTVEVR--QRTQWAALCHSAPAKGMVRWEELCQEQQCGRVSSYHL  CD5_ochPri Ochotona princeps (pika)
FQPKVQSRLVGGSGLCEGSVEVR--QGRQWEVLCDVPRAKGTARWEEVCQEQRCGKLNSFRV  CD5_canFam Canis familiaris (dog)
FQPKVQSRLVGRRSLCEGSVEVR--QGKQWEVLCDSPRPKGTARWEEVCQELQCGSVASYRV  CD5_felCat Felis catus (cat)
FQPKVQSRLVGGSSLCEGSVEVR--QGKQWKTLCDIPSPKGAVRWEEVCQEQQCGKVNSYVH  CD5_equCab Equus caballus (horse) 79% to dog
FQPQVQSRLVGGSSVCAGSVEVRQGQGRQWEALCHSPWAKSMARWAEVCREQQCGPANSYQV  CD5_myoLuc Myotis lucifugus (microbat) 69% to dog
FQPKVQSRLVGGSDVCEGSVEVRSGKGQKWDTLCDDSWAKGTARWEEVCREQQCGNVSSYRG  CD5_bosTau Bos taurus (cow)
FQPKVQSRLVGGSDMCEGSVEVRSGKGQQWDTLCDSSWAKGTARWEEVCREQQCGNVSFYQ.  CD5_oviAri Ovis aries (sheep) 68% to dog
FQPKVQSRLVGGSGTCEGSVEVR--QGKQWDALCDSSSAKGMARWEDVCREQQCGNVSSYQL  CD5_turTru Tursiops truncatus (dolphin)
FQPKVQSRLVGHSGTCEGSVEVR--QGKQWDTLCDSSSAKSMARWEEVCREQQCGNVSSYQI  CD5_susScr Sus scrofa (pig) AK239283 transcript 70% to dog
FQPKVQSRLVGGSSSCEGAVEVR--HGKQWDPLCDSSSAKGAAARWEEVCQEQQCGNVSSYQ  CD5_vicVic Vicugna vicugna (vicugna)
SQPKVQSRLVGSSDPCAGTVEVR--QDGQWATLCSSNSAKSRALWEEVCHEQQCGRLSSYRE  CD5_sorAra Sorex araneus (shrew)
FQPKVRSRLAGGSSMCEGTVEVR--QGKQWGALCSSSLAKGMAPWEEVCQEQQCGHVRSYHM  CD5_dasNov Dasypus novemcinctus (armadillo)
FQPKVQSRLVGGRSMCEGTVEVR--QGGQWAALCDTSPAGTTARWEEVCQEQQCGGVSAYRV  CD5_proCap Procavia capensis (hyrax)
FQPKVQSRLVEGHSLCEGVVEVR--QGGRWAALCHNSMAT..ARWNEVCQEQQCGSVVTYGK  CD5_echTel Echinops telfairi (tenrec)
FQPKVRSRLKGGSHACAGTVEVN--FEGQWRALCS...QKN...WEEVCHEQHCGRLLT...  CD5_monDom Monodelphis domestica (opossum)
FQPEVKSRLTGGTSHCSGVVEVF--HKSNWKTLG....LNGASLWADVCQRQECGALISQKT  CD5_ornAna Ornithorhynchus anatinus (platypus)

not available                                                   CD5_pteVam Pteropus vampyrus (macrobat)


Deletion in SLC44A1 in bat and cow again homoplasic

This loss of one amino acid in the conserved transport gene SLC44A1 is limited to cow, sheep, and microbat. It is absent in dog, cat, horse, pig, vicugna, and macrobat. A moderately close paralog (at least in this exon) SLC44A3 is not an actual source of confusion; it has no indel in any species. This rare genomic event is not suited for within-bat or within-artiodactyl tree refinement because of this homoplasy, as well as an unrelated 3 aa loss in guinea pig. 

SALCSYNLKPSEYTTSPKSSVLCPKLPVPA  SLC44A1_homSap Homo sapiens (human) SFLCVYSLNSFNYTHSPKADSLCPRLPVP SLC44A3
SALCSYNLKPSEYTTSPKSSVLCPKLPVPA  SLC44A1_panTro Pan troglodytes (chimp)
SALCSYNLKPSEYTTSPKSSVLCPKLPVPA  SLC44A1_ponPyg Pongo pygmaeus (orang_sumatran)
SALCSYNLKPSEYTTSPKSSVLCPKLPVPA  SLC44A1_macMul Macaca mulatta (rhesus)
SALCSYNLKPSEYTTSSKSSVLCPKLPVPA  SLC44A1_otoGar Otolemur garnettii (bushbaby)
SALCSYNLKPSEYTTSSKSSVLCPKLPVPA  SLC44A1_micMur Microcebus murinus (mouse_lemur)
SALCSYNLKPSEYTTSSKSSVLCPKLPVPA  SLC44A1_tupBel Tupaia belangeri (tree_shrew)
SALCSYNIKPSEYTLTSKSSGFCPKLPVPA  SLC44A1_musMus Mus musculus (mouse)
SALCSYNIKPSEYTLTAKSSAFCPKLPVPA  SLC44A1_ratNor Rattus norvegicus (rat)
SALCSYHIKPSEYT---KSSDFCPKLPVPA  SLC44A1_cavPor Cavia porcellus (guinea_pig)
SALCSYDLKPSEYTTSPKSSVLCPKLPVPA  SLC44A1_oryCun Oryctolagus cuniculus (rabbit)
SALCSYNLKPSEYTTSSKASVLCPKLPVPA  SLC44A1_canFam Canis familiaris (dog)
SALCTYDLKPSEYTTSSKASALCPKLPVPA  SLC44A1_equCab Equus caballus (horse)
SALCSYNLKHSEYTTSSKASVLCPKLPVPA  SLC44A1_felCat Felis catus (cat)
SALCSYTLKPSEYTIPSKASGVCPKLPVPA  SLC44A1_pteVam Pteropus vampyrus (macrobat)
SALCHYKLKPSEYTSS-KASSLCPKLPVPA  SLC44A1_myoLuc Myotis lucifugus (microbat)
SALCSYDLKPSEYASS-KAKGLCPKLPVPA  SLC44A1_bosTau Bos taurus (cow) SFLCVYNLNSFNYTQIPNADLLCPRLPVP SLC44A3
SALCSYDLKPSEYASS-KAKGLCPKLPVPA  SLC44A1_oviAri Ovis aries (sheep)
SALCSYSLKPSEYTTSSKAPVLCPKLPVPA  SLC44A1_susScr Sus scrofa (pig)
SALCSYDLKPSEYTTSSKASVLCPKLPVPA  SLC44A1_vicVic Vicugna vicugna (vicugna)
SLLCSYNLKPSEYTTSSKASVLCPKLPVPA  SLC44A1_eriEur Erinaceus europaeus (hedgehog)
SALCSYNLKPSEYTTSSKASVLCPKLPVPA  SLC44A1_sorAra Sorex araneus (shrew)
SALCNYNLKPSEYTTSSKASALCPKLPVPA  SLC44A1_dasNov Dasypus novemcinctus (armadillo)
SALCSYNLKPSEYTTSSKASVLCPKLPVPA  SLC44A1_loxAfr Loxodonta africana (elephant)
SALCTYNLKPSEYVTHSKASVFCPKLPVP.  SLC44A1_echTel Echinops telfairi (tenrec)
SALCTYNLKPSEYVTHSKASVFCPKLPVP.  SLC44A1_monDom Monodelphis domestica (opossum)
SALCVYDLKPSEYSTHPKASVRCPKLPVP.  SLC44A1_triVul Trichosurus vulpecula (possum)
SALCSYHISPSAYTSDPSASKLCPKLPVP.  SLC44A1_ornAna Ornithorhynchus anatinus (platypus)

not available                   SLC44A1_turTru Tursiops truncatus (dolphin)

chr9 107150470 107150533 -3
human TGTAGCTACAACCTAAAGCCTTCTGAATACACTACATCTCCAAAATCTTCTGTTCTCTGCCCC
..cow TGCAGCTATGACCTAAAGCCTTCTGAATAT---GCATCATCAAAAGCAAAAGGTCTTTGCCCC

human TGTAGCTACAACCTAAAGCCTTCTGAATACACTACATCTCCAAAATCTTCTGTTCTCTGCCCCA
mcbat TGTCACTACAAGCTAAAGCCTTCTGAATACAC---ATCTTCAAAAGCGTCTTCTCTTTGCCCCA


Deletion in MLL3 in bat and cow not strongly informative

The very large gene MLL3 (4911 aa) is not strongly informative because the lack of conservation around the site of the one residue deletion seen in cow, dolphin, and pig makes comparison to bats too difficult. Both micro and macrobats have a similarly sited deletion but one that nucleotide-based alignment places somewhat offset. The site is also quasi-homoplasous in mouse lemur and nearby deletions are seen in pig and marsupial. The protein is too diverged in eulipotyphyla to allow meaningful comparison. Here again Laurasiatheres are anomalously non-conserved within amniotes suggesting a lack of selective pressure which is conducive to rapid change including in length and so homoplasy. 

NSRPPSPMDPYAKMVGTPRPPPVGHSFSRRNSAAPVENCTPLSSVSRPLQMNETTANRPS MLL3_homSap Homo sapiens (human)
NSRPPSPMDPYAKMVGTPRPPPVGHSFSRRNSAAPVENCTPLSSVSRPLQMNETTANRPS MLL3_panTro Pan troglodytes (chimp)
NSRPPSPVDPYAKMVGTPRPPPVGHSFSRRNSAAPVENCTPLSSVSRPLQMNETTANRPS MLL3_ponPyg Pongo pygmaeus (orang_sumatran)
NSRPPSPMDPYAKMVGTPRPPPVGHSFSRRNSAAPVENCTPLSSVSRPLQMNETTANRPS MLL3_macMul Macaca mulatta (rhesus)
NSRPPSPMDPYAKMVGTPRPPPGGHSFPRRNS-APMENCTPLSSVTRPIQMNETTANRPS MLL3_micMur Microcebus murinus (mouse_lemur)
NSRPPSPADPYAKMVGTPRPPPGGHSFSRRNSVAPMENCAPLSSVSRPVQMSETAAGRPS MLL3_tupBel Tupaia belangeri (tree_shrew)
HSRPPSPVDPYAKMVGTPRPPPGGHSFPRRNSVTPVENCVPLSSVPRPIHMNETSATRPS MLL3_musMus Mus musculus (mouse)
HSRPPSPVDPYAKMVGTPRPPPVGHSFPRRNSVTPVENCVPLSSVPRPIHMNETSATRPS MLL3_ratNor Rattus norvegicus (rat)
NSRPPSPIDPYAKMVGTPRPPPGGHSFCRRNSVAPVENCVPLSSVPRPIQMSETPANRPS MLL3_cavPor Cavia porcellus (guinea_pig)
.SRPPSPMDPYAKMVGTPRPPPGGHSFPRRNSVAQVENCTPLSSVSRPIQMNETTTNRPS MLL3_oryCun Oryctolagus cuniculus (rabbit)
NSRPPSPVDPYAKMVGTPRPPPVGHSFPRRNSVPPVENCAPLSSVSRPMQVNETTTNRPS MLL3_ochPri Ochotona princeps (pika)
HSRPPSPMDPYAKMVGTPRPAPGGHSFSRRNSAAPADSCTPLPSVSRPAQMTDTTANRPS MLL3_canFam Canis familiaris (dog)
HSRPPSPVDPYAKMVGTPRPPPGGHGFSRRNSTALVENCAPLPPVPRPAPVSEATANRPS MLL3_felCat Felis catus (cat)
NSRPPSPVDPYAKMVGTPRPPPGAHCFSRRNSAALVENCAPLSSVSRPAQMSETTANRPS MLL3_equCab Equus caballus (horse)
NSRPPSPVDPYAKMVGTPRPPPGGHSFSRRN-SALVESCVSLSSAPRPPQMGEGTANRPS MLL3_myoLuc Myotis lucifugus (microbat)
.SRPPSPMDPYAKMVGTPRPPPGGHSFPRRT-SALAETRVPLPPAPRPTQTSEATANRPS MLL3_pteVam Pteropus vampyrus (macrobat)
NSRPPSPMDPYAKMVGTPRPPPGGHSFPRRN-AALAESCGPLPSGSRPPQMGEAAANRPS MLL3_bosTau Bos taurus (cow)
NSRPPSPADPYAKMVGTPRPPAGGHGFSRRN-SALVENCAPLPSVSRPTQMSETTASRPS MLL3_turTru Tursiops truncatus (dolphin)
NPRPPSPVDPYAKMVGTPRPPPGGHGFSRRN-SALVETSAPLSSVSRP--MSETPASRPS MLL3_susScr Sus scrofa (pig)
NSRPPSPMDPYAKMVGTPRPPPEVHSFSRRNSVASVENCAPLSSVSRSIQISETAANRPS MLL3_dasNov Dasypus novemcinctus (armadillo)
NSRPPSPVDPYAKMVGTPRPSAAGHSFPRRNSVTPVENCAPLSSVSRPIQISETTANRPS MLL3_loxAfr Loxodonta africana (elephant)
NSRSPSPMDPYAKMVGTPRPPAGGHSFPRRNSVAPGENCTSLSSASRPIQISETATNRPS MLL3_echTel Echinops telfairi (tenrec)
SSRPPSPVDPYAKMVGTPRPLPAGPNFPRRNSVGPVETCT---TPSRSIQVTETTASRLS MLL3_monDom Monodelphis domestica (opossum)
.SRPPSPLDPYAKMVGTPRPPPVGANFARRNSIAPLESCGPPPSAARPVPSPETTGRRPS MLL3_ornAna Ornithorhynchus anatinus (platypus)
NTRPPSPMDPYAKMVGTPRPAPTNQNFVRRGSIAPLDTCAPQSSISRPVQVTEPSGSRPS MLL3_galGal Gallus gallus (chicken)
SARPPSPIDPYAKMVGTPRPLPVNQNYIRRNSVPSVDFCPPPSPISRPAQAPEIAGKRPS MLL3_anoCar Anolis carolinensis (lizard)

not available                                                MLL3_vicVic Vicugna vicugna (vicugna)
not available                                                MLL3_eriEur Erinaceus europaeus (hedgehog)
not available                                                MLL3_sorAra Sorex araneus (shrew)


chr7 151510091 151510154 -3
human AAAGGTGTACAGTTTTCCACTGGTGCAGCAGAATTTCTTCTGGAAAAACTATGGCCCACAGGA
cow AGTGGCCCACAGCTCTCCGCCAGTGCAGCG---TTTCTTCTGGGAAAGCTGTGGCCCCCGGGA

human AAAGGTGTACAGTTTTCCACTGGTGCAGCAGAATTTCTTCTGGAAAAACTATGGCCCACAGGAG
mibat AAAGATACACAGCTTTCCACCAGT---GCAGAATTCCTTCTGGAAAAGCTGTGGCCCCCAGGAG

Deletion in KIAA0240 in bat and cow is terminal-leaf homoplasic

The deletion here is found solely in cow and microbat. It is lacking in dolphin, pig, and vicugna as well as macrobat. The gene KIAA0240 is otherwise well-suited for phylogeny. This is an example of where the screen worked but a genuine case of terminal leaf homoplasy occured. 

LSPGQSSVSQGRPGFATMPSVTSMSGPSRFPAVSSASTAHPSLGSAVQSGSSGSNFTGDQ KIAA0240_homSap Homo sapiens (human)
LSPGQSSVSQGRPGFATMPSVTSMSGPSRFPAVSSASTAHPSLGSAVQSGSSGSNFTGDQ KIAA0240_panTro Pan troglodytes (chimp)
LSPGQSSVSQGRPGFTTMPSVTSMSGPSRFPAVSSASTAHPSLGSAVQSGSSGSNFTGDQ KIAA0240_ponPyg Pongo pygmaeus (orang_sumatran)
LSPGQSSVSQGRPGFTTMPSVTSMSGPSRFPAVSSASTAHPSLGSAVQSGSSGSNFTGDQ KIAA0240_macMul Macaca mulatta (rhesus)
LSPGQSSVSQGRPGFTTMPSVTSMSGPSRFPAVSSASTAHPSLGSAVQSGSSGSNFTGDQ KIAA0240_calJac Callithrix jacchus (marmoset)
LSPGQSSVSQGRPGFTAMPSVTSMSGPSRFPAVSSTSTAHPSLGSVVQSGASGSNFTGDQ KIAA0240_otoGar Otolemur garnettii (bushbaby)
LSPGQSSVSQGRPGFTAMPSVTSMSGPSRFPAVSSASTAHPSLGSVVQSGASGSNFTGDQ KIAA0240_micMur Microcebus murinus (mouse_lemur)
LSPGQSSVSQGRPVFTPMSSVTSMSGPSRFPAVSSASTAHPSLGSAVQSGASGSNFTGEQ KIAA0240_tupBel Tupaia belangeri (tree_shrew)
LSPGQSSVSQGRPGFATMPAVSGMAGPARFPAVSSASTAHPTLGPTVQSGAPGSNFTGDQ KIAA0240_musMus Mus musculus (mouse)
LSPGQSSVSQGRPGFATMASVSSMSGPARFPAVSSASTAHPTLGPAVQSGASGSNFTGDQ KIAA0240_ratNor Rattus norvegicus (rat)
LSPGQSSVSQGRPGFTTMPSVTSMAGPSRFPAASSASTAHPSLGPAAQSGPSGANFTGDQ KIAA0240_cavPor Cavia porcellus (guinea_pig)
LSPGQSSVSQGRPGFTTMPSATSMSGPSRFPAVSSGNTAHPSLGSVVQSGASGSNFTGD. KIAA0240_speTri Spermophilus tridecemlineatus (squirrel)
LSPGQSSVSQGRPAFTTMPSATSLSGPSRFPAVSSASTAHPSLGSAVQSAASGSNFAGDQ KIAA0240_oryCun Oryctolagus cuniculus (rabbit)
LSPGQSNVSQGRPGFTTMASATSMSGPSRFPAVSSASTAHPSVGSAVQSAASGSNFTGDQ KIAA0240_ochPri Ochotona princeps (pika)
LSPGQSNVSQGRPGFTTMPSVTSMSGPSRFPSVSSSSTAHPSLGSVVQSGASGSNFTGDQ KIAA0240_canFam Canis familiaris (dog)
LSPGQSSVSQGRPGFTTMPSVTNMSGPSRFPVVSSSSTAHPSLGSAVQSGASGSNFTGDQ KIAA0240_felCat Felis catus (cat)
LSPGQSSVSQGRPGFTTMPSVTSMAGPSRFPVVSSTSTAHPSLGSAVQSGASGSNFTGDQ KIAA0240_equCab Equus caballus (horse)
LSPGQSNVSQGRPGFTTVPSVTSMSGPSRFPVVSSSSTAHPSLGSAVQSGASGSNFAGD. KIAA0240_pteVam Pteropus vampyrus (macrobat)
LSPGQSSVSQGRPGFTPMPSVTSMSGPSRFP-VSSSSTVHPSLGSAVQSGASGSNFTGDQ KIAA0240_myoLuc Myotis lucifugus (microbat)
LSPGQSSVSQGRPGFTTMPSVTSMAGPSRFP-VSSSSTAHPSLGSAVQSGASGSNFTGDQ KIAA0240_bosTau Bos taurus (cow)
LSPGQSSVSQGRPGFTTMPSVTSMSGPSRFPAVSSSSTAHPSLGSAVQSGASGSNFTGDQ KIAA0240_susScr Sus scrofa (pig)
LSPGQGSVSQGRPGFAAMPSVTSMSGPSRFPVVSSSSTAHPSLGAAVQSGASGSNFTGDQ KIAA0240_turTru Tursiops truncatus (dolphin)
LSPGQSSVSQGRPGFTTMPSVTSMSGPSRFPVVSSSSTAHPSLGSAVQSGATGSNFTGDQ KIAA0240_vicVic Vicugna vicugna (vicugna)
LSPGQSSVSQGRPGFTTMPSVTSMSGSNRFPAVSSSSTAHPSLGSSVQSGASGSNFMGDQ KIAA0240_eriEur Erinaceus europaeus (hedgehog)
LSPGQGSVSQGRPGFAAMPSVPSMSGPSRFPAVSSSGTAHQNLGSATQAGAPGSSFTPDQ KIAA0240_sorAra Sorex araneus (shrew)
LSPGQSSVSQGRPGFTTMPSVTSMSGPSRFPNVSSSSTAHPSLGSAVQSGASGSNFTGDQ KIAA0240_dasNov Dasypus novemcinctus (armadillo)
LSPGQSSVSQGRPGFTTMPSVTNMSGPSRFPNVSSSSTAHPSLGSAVQSGMSGSNFTGDQ KIAA0240_choHof Choloepus hoffmanni (sloth)
LLPGQSGISQGRPGVTTMPSVIPMSEPSQFLAVNSPKTAHPRLGSAPQSGALGSKFPGD. KIAA0240_loxAfr Loxodonta africana (elephant)
LSPGZNVLTRGKPGFTTMPSVTSMAGPSRFPVVSSSSTAHPSLGSTVQAGVSGSNFPGDQ KIAA0240_echTel Echinops telfairi (tenrec)
LSPGQSSVSQGRPGFPGQSAVTSVSAPGRFTVVSSSSTALPNLGPSVQSATSATNFNGDQ KIAA0240_monDom Monodelphis domestica (opossum)
LSPGQTGVSQGRPGFTSMPAVANVSVPNRFTVVSSSATVHPSPGSAVQSVASGSNFTGDQ KIAA0240_ornAna Ornithorhynchus anatinus (platypus)
LSPSQANASQGRSSFTTMSTVSNMSASNRFAVVSSSGSVHPSLGPSVQSVASGGNFTGDQ KIAA0240_galGal Gallus gallus (chicken)
LSPSQGNISQSRTSFSTMSSSSNMSSNSRFTAVSSSAVVHPSIGPSAQSVASGGSFAGDQ KIAA0240_anoCar Anolis carolinensis (lizard)

not available KIAA0240_oviAri Ovis aries (sheep)

not sought KIAA0240_tarSyr Tarsius syrichta (tarsier)
not sought KIAA0240_proCap Procavia capensis (hyrax)
not sought KIAA0240_macEug Macropus eugenii (wallaby)
not sought KIAA0240_taeGut Taeniopygia guttata (finch)

chr6 42905641 42905704 -3
human GACAAGCATGTCAGGACCTAGTCGGTTCCCTGCTGTCAGCTCAGCCAGCACTGCCCATCCTAG
  cow GACAAGCATGGCAGGACCTAGTCGGTTCCC---TGTTAGTTCATCCAGCACTGCCCATCCTAG

human GACAAGCATGTCAGGACCTAGTCGGTTCCCTGCTGTCAGCTCAGCCAGCACTGCCCATCCTAGT
mibat GACAAGCATGTCAGGACCTAGTCGGTTCC---CTGTTAGCTCGTCCAGCACTGTCCATCCTAGT

Insertion in NEK11 in bat, cow, and sheep not shared by pig or dolphin

EIPEDPLVAEEYYADAFDSYCEESDEEEEE-IALERPEKEIRNEGSQPAYRTNQQ  NEK11_homSap Homo sapiens (human)
EIPEDPLVAEEYYADAFDSYCEESDEEEEE-IALERPEKEIRNEGSQPAYRTNQQ  NEK11_panTro Pan troglodytes (chimp)
EIPEDPLVAEEYYADAFDSYCEESDEEEEE-IVLAGPEKEIKNEGSQPTYRTNQQ  NEK11_ponPyg Pongo pygmaeus (orang_sumatran)
EIPEDPLVAEEYYADAFDSYCEESDEEEEE-IVLAGPEKEIKNEGSQPTYRTNQQ  NEK11_macMul Macaca mulatta (rhesus)
EIPEDPLVAEEYYADTFDSYCEESDEEEEG-TVLSGPEKEIKKES-QPAYRTNQQ  NEK11_calJac Callithrix jacchus (marmoset)
EIPEDPLVAEEYYADVFDS-CSE-EEEEEE-IVFSASEGEVKDEGPQPPYRTHQQ  NEK11_otoGar Otolemur garnettii (bushbaby)
EIPEDPLVAEQYYSDVFDSCSEDSEEQEEE-MIFSEAGGDTKEEESPSVYRTNQQ  NEK11_musMus Mus musculus (mouse)
EIPEDPLVAEQYYADVFDSCSEDSGEQEEE-MAFSEAGGDMREEGSPPTYRTNQQ  NEK11_ratNor Rattus norvegicus (rat)
EIPEDPLVAEVYYADAFDSCSEDSEEQEGE-TGSLGPEVEAQDEGSQPTSRTNHQ  NEK11_cavPor Cavia porcellus (guinea_pig)
.IPEDPFVAEEYYADVFDSCSEESEEQEEE-ILFSGPEREVKD------YRTNQQ  NEK11_oryCun Oryctolagus cuniculus (rabbit)
EIPEDPLVAEEYYTDVFDSCSEESEEQEED-TLFSGPDRETKD-----GNRINQQ  NEK11_ochPri Ochotona princeps (pika)
EIPEDPLVAEEYYADAFDSCSEESEEEEEE-IMFSAPEEEVKDEGPRPAHRIFQQ  NEK11_canFam Canis familiaris (dog)
DIPEDPIVAEEYYADAFDSCSEESEEEEEE-IVFSGPEEEVKDEGPQPAYRTIQQ  NEK11_felCat Felis catus (cat)
EIPEDPLVAEEYYADAFDSCSEESEDEEEE-IVFSGPEEEVKDEVQQPAYRTNQQ  NEK11_equCab Equus caballus (horse)
.IPEDPRVAEEYYADTFDSCSEESEEEEEEEMVLAGLEAEVRDKGPQPDCRANQQ  NEK11_myoLuc Myotis lucifugus (microbat)
EIPEDPLVAEEYYADVFDSCSEESEESEEGKTVFSVKDEEVEDEGPQPVYRTNQQ  NEK11_bosTau Bos taurus (cow)
EIPADPLVAEEYYADVFDSCSEESEESEEEKTVFSVKDEEVEDEGPQPVYRTNQQ  NEK11_oviAri Ovis aries (sheep)
EIPEDPLVAEEYYTDAFDSCSEESEEEEEN-MVFSAGEEEVQDEGSQPAYRTNQQ  NEK11_susScr Sus scrofa (pig)
EIPEDPLVAEEYYADAFDSCSEESEEEEEN-TVFSAGEEEVKDEEPQPAYRTNQQ  NEK11_vicVic Vicugna vicugna (vicugna)
EIPEDPLKAEEYYADVFDSCSEESEEEGEE-TVFSGSE-EVSDDGLQPAHRTNQQ  NEK11_eriEur Erinaceus europaeus (hedgehog)
EIPEDPLVAEEYYADAFDSCSEESEDRGEE-ALFSGSGEDCEEEEPQLSYRTNQQ  NEK11_sorAra Sorex araneus (shrew)
EIPEDPLVAEEYYADVFDSCSEESEEEEEE-TVFSGPEEKAKDEGPQPVYRTNQQ  NEK11_choHof Choloepus hoffmanni (sloth)
EIPEDPLVAEEYYADTFDSCSEESEEEEEE-IVFSGPEEEVKDKEPQPAYRTNQ.  NEK11_loxAfr Loxodonta africana (elephant)
EIPEDPLVAEEYYADTFDSCSEESEEEEDE-TVFSGPGEEVKDEESQPASRTDQQ  NEK11_echTel Echinops telfairi (tenrec)
EIPEDPLVAEEYYDDVFDSCSEESEEEAEE-----KSEEMVEYETSQTVVKTNQQ  NEK11_ornAna Ornithorhynchus anatinus (platypus)
.IPEDPLIAEEYYNDVFDSCSETSEDQEEE-VVEADEVKEDEEEDTLFTYTTNQQ  NEK11_anoCar Anolis carolinensis (lizard)
 
not available NEK11_micMur Microcebus murinus (mouse_lemur)
not available NEK11_tupBel Tupaia belangeri (tree_shrew)
not available NEK11_speTri Spermophilus tridecemlineatus (squirrel)
not available NEK11_pteVam Pteropus vampyrus (macrobat)
not available NEK11_turTru Tursiops truncatus (dolphin)
not available NEK11_dasNov Dasypus novemcinctus (armadillo)
not available NEK11_monDom Monodelphis domestica (opossum)
 
not sought    NEK11_tarSyr Tarsius syrichta (tarsier)
not sought    NEK11_proCap Procavia capensis (hyrax)
not sought    NEK11_macEug Macropus eugenii (wallaby)
not sought    NEK11_galGal Gallus gallus (chicken)
not sought    NEK11_taeGut Taeniopygia guttata (finch)

Query:    13 EIPEDPLVAEEYYADAFDSYCEESDEEEEEIALERPEKEIRNEGSQPAYRTNQQ genome
            EIPEDPLVAEEYYADAFDSYC ESDEEEEEIALERPEKEIRNEGSQPAYRTNQQ
Sbjct:   467 EIPEDPLVAEEYYADAFDSYCVESDEEEEEIALERPEKEIRNEGSQPAYRTNQQ webb

chr3 132430108 132430168 3
human TTTGATTCCTATTGTGAAGAGAGTGATGAG---GAGGAAGAAGAAATAGCGTTAGAAAGACCA
  cow TTTGATTCCTGTTCTGAAGAAAGTGAGGAGAGTGAGGAAGGAAAAACAGTATTCTCAGTCAAG
 
human TTTGATTCCTATTGTGAAGAGAGT---GATGAGGAGGAAGAAGAAATAGCGTTAGAAAGACCAG
mibat TTTGACTCCTGTTCTGAAGAGAGTGAGGAGGAGGAGGAGGAAGAAATGGTGTTGGCAGGACTGG

Deletion in ENAM in microbat and horse not shared by macrobat

This one-residue deletion in horse and microbat lies in a very important gene for dentition, enamalin. This particular region of the protein is quite prone to indels with at least 6 other events (at other sites) in 32 other placental mammals. It is not taxonomically informative because macrobat lacks the indel. 


PNIRNFPSGRQWYFTGTVMGHRQNRPFY RNQQVQRGPRWN FFAWERKQVAR PGNPVYH   ENAM_homSap Homo sapiens (human)
PNVRNFPSGRQWYFTGTVMGHRQNRPFY RNQQVQRGPRWN SFAWEGKQVAR PGNPVYH   ENAM_panTro Pan troglodytes (chimp)
PNIRNFPSGTQWYFTGTVMGHRQNRPFY RNQQVQRGPRWN SFAWERKQVAR PGNPVYH   ENAM_gorGor Gorilla gorilla (gorilla)
PNIRKFPSGRQWYLTGTVTGHRRNGPFY RNQQVQRGPRWN FFAWEGKQVAR PGNPVYH   ENAM_ponPyg Pongo pygmaeus (orang_sumatran)
PNIRNFPSGRRWYPTGTAMGHRQNGPFY RNRQVQRGPQWN SFAWEGKQVVR PGNPVYH   ENAM_macMul Macaca mulatta (rhesus)
PNIRNFPSGRRWYPTGTAMGHRQNGPFY RNRQVQRGPQWN SFAWEGKQVVR PGNPVYH   ENAM_papAnu Papio anubis (baboon)
PNIRNFPSGRQWYFTGTVMGHRQNRPFY RNQQVPRGPRWN SFAWEGKQVAR PGNPVYH   ENAM_nasLar Nasalis larvatus (proboscis monkey)
PNIRSFPSGRQWYPT--TMGHRQNGPFY RNRQVQRGLRWN SFPWEGKQVAR PRNPVYH   ENAM_calJac Callithrix jacchus (marmoset)
PNVRRFPSGRQWYPTGTAMGHRQTGPFY RNQQFQRGPRWN SFV----QVAR AGNPTYH   ENAM_otoGar Otolemur garnettii (bushbaby)
PNARNVPWVRQWYPAGTAVGRRQNGPLY RSQQFQRVPRWH SFALESKQVAR PVNPPYR   ENAM_micMur Microcebus murinus (mouse_lemur)
PNIRNFPSGRQWHSTGTAMGNRQTRPFY RNQQVQRGPSWN SFALESKQAAH PRTPTYR   ENAM_tupBel Tupaia belangeri (tree_shrew)
YPYPNYPSERQWQTTGT-QGPRQNGPGY RNPQVERGPQWN SFAWEGKQATR PGNPTYG   ENAM_musMus Mus musculus (mouse)
YPYPNYPSERQWQTTDT-QGPKQNGPGY QNPQIQRGPQWN SFAWEGKQATTHPGNPTYH   ENAM_ratNor Rattus norvegicus (rat)
PNIRNSPSGRQSNPTHTATGQRPPGPSY RNQPGQWDAQGN SFAWEGKQAAG PKNPTYH   ENAM_cavPor Cavia porcellus (guinea_pig)
PNIRNPPTGRQWHPTGTAMGHRQYGPLY RNQQVQRGPRWN SLAWEGKQATR PGNPTYR   ENAM_speTri Spermophilus tridecemlineatus (squirrel)
.NTRNFPSERQWHHTGTAVGHRPNGPFY RNQQVQRGTQWN SFAWESKQATR PENPTYR   ENAM_oryCun Oryctolagus cuniculus (rabbit)
.NTRNFPSGRQWHQTGTAVGQRPNGPFY RNQQVQKNSQWN SFAWENKQATN PGNPASH   ENAM_ochPri Ochotona princeps (pika)
PNIRNFPAGRQWRPTGTFMGHRQNGPFY RNQQVQRGPRWN SFALERKQAMR PGNPIYR   ENAM_canFam Canis familiaris (dog)
PNIRNFPAGRQWRPTGTIMGRRQNGPFY RNQQVQRGPRWN SFALEGKQAFR SGNPIYR   ENAM_felCat Felis catus (cat)
PNIRNFPARRQWRPTGTATGNRQNGPFY RNQ-VQRDPQWN SFAWEGKRTVH PGNPIYR   ENAM_equCab Equus caballus (horse)
.NFPSFPVGRQWRPTGTTVGHRQNGPFY RNP-VQRGPRWN SYAWEGKQAVR PGNPIYH   ENAM_myoLuc Myotis lucifugus (microbat)
PNLQSFPVGRQWRPTGTAMGHGQNGPFY RNQQVQRGPRWN SFALEDRQTVR PGNPIYR   ENAM_pteVam Pteropus vampyrus (macrobat)
PNIRNFPAGRQWHPTGTSMGNRRNGPFY RNQQIQRAPRWN SFVLEGKQAIRLGYPIYRR   ENAM_bosTau Bos taurus (cow)
PNIRNFPAGRQWHPTGTFMGHRRNGPFY RNQQIQRGPRWN SFVLEGKQVIRPGYPIYRR   ENAM_oviAri Ovis aries (sheep) whRQWHpt insert
PNIRGFPARRQWRPPGPAMGHRRNGPFY RNQQIQRGPRWN SFTLEGKQAVRPGYPTYRR   ENAM_susScr Sus scrofa (pig)
PNIRSFPAGRQWRPTGTATGHKRNGPFY RNQQIQRGPRWN SFVLEGKQAVRPGYPIYRR   ENAM_turTru Tursiops truncatus (dolphin)
PNIRSFPARRQWRPTGTAMGHRQNGPFY RNQQIQRG.... ...................   ENAM_vicVic Vicugna vicugna (vicugna)
PNIRNYPAGRQWRPTGTILGHRQNWPFY RTQQVQGSPRWH SFALENKQALRPGTPFYRK   ENAM_eriEur Erinaceus europaeus (hedgehog)
PNVRNVPAGRQWRPTGTDTWQRQNVPFY RNQLYQRGPRWN SFTLENKQAIRPGIPFYSK   ENAM_sorAra Sorex araneus (shrew)
PNIRDFPARRPWHPSGNVMGHRENGPFY RN-QVQRGPRWN SFALESKKAVLLGNPAYHK   ENAM_dasNov Dasypus novemcinctus (armadillo)
PSVRGFPTGRQWRPTGTAMGHRQNGPFY RNQQVQRGARWN SFTLEGKQAARPGNPAYRK   ENAM_loxAfr Loxodonta africana (elephant)
PGAQGSPIARQWRPIGTAMGHRQNGPLY RNQQVQRGPRWN SFTLEGKPAARPGNPAYQK   ENAM_proCap Procavia capensis (hyrax)
PNIRGFPARRQWCPTGTTMGHRQNGPYY -QNQVQRGPWWK SFAL...............   ENAM_choHof Choloepus hoffmanni (sloth)

too diverged                                                    ENAM_monDom Monodelphis domestica (opossum)
too diverged                                                    ENAM_macEug Macropus eugenii (wallaby)
too diverged                                                    ENAM_ornAna Ornithorhynchus anatinus (platypus)
not available                                                   ENAM_echTel Echinops telfairi (tenrec)

chr4 71727036 71727099 -3
human AGACAGAATAGGCCTTTTTACAGAAATCAACAAGTTCAAAGGGGTCCTCGGTGGAACTTCTTT
horse AGACAGAATGGGCCTTTCTACCGAAATCAA---GTTCAAAGGGATCCTCAGTGGAACTCCTTT

human AGACAGAATAGGCCTTTTTACAGAAATCAACAAGTTCAAAGGGGTCCTCGGTGGAACTTCTTTG
mibat AGACAGAATGGGCCTTTTTACCGAAATCCA---GTCCAAAGGGGTCCTCGGTGGAACTCCTATG

Deletion in CDCP1 in microbat and horse shared by macrobat but homoplasic in rabbit

This one-residue deletion in exon 7 of CDCP1 occurs in horse and microbat and also macrobat but also at the same spot in rabbit but not pika. The deletion does not occur in cat, dog, or the 5 artiodactyls. Precise location of the indel is problematic because it occurs in a short EEE repeat (variations have D). Recall glu and asp have but two codons each. Otherwise this is a very well conserved region of the protein. This indel by itself is neither a throwaway nor a showstopper. It would benefit from PCR of additional perissodactyls (rhino etc) to isolate horse or push the event further up the stem. 


ERSGVVCQTGRAFMIIQEQRTRAEEIFSLDEDVLPKPSFHHHSFWVNISNCSPTSGKQLD CDCP1_homSap Homo sapiens (human)
ERSGVVCQTGRAFMIIQEQRTRAEEIFSLDEDVLPKPSFHHHSFWVNISNCSPTSGKQLD CDCP1_panTro Pan troglodytes (chimp)
ERTSVVCQTGRAFMIIQEQRTRAEEIFSLDEDVLPKPSFHHHSFWVNISNCSPASGKQLD CDCP1_ponPyg Pongo pygmaeus (orang_sumatran)
ERTGVVCQTGRAFMIIQEQRTRAEEIFSLDEDALPKPRFHHHSFWVNISNCSPASGKQLD CDCP1_macMul Macaca mulatta (rhesus)
ERTGVVCQTGRAFMIIQEQRTRAEEIFSLDEDVLPKPSFHHHSFWVNISNCSPASGKQLD CDCP1_calJac Callithrix jacchus (marmoset)
ERTGVVCQTGRAFMIIQEQHTRAEEIFSLEEEVLPKPSFHHHSFWVNISNCSPASGKQLD CDCP1_otoGar Otolemur garnettii (bushbaby)
ERTGVVCQTGRAFMVLQEQRTRVEEIFSLEEEALPQAKLHHHSFWVNISNCSPASGKQLD CDCP1_tarSyr Tarsius syrichta (tarsier) bad trace
ERTGVVCQTGRAFMVLQEQRTRVEEIFSLEEEALPQAKLLHHSFWVNISNCSPASGKQLD CDCP1_micMur Microcebus murinus (mouse_lemur) bad trace
...GVVCQTGRAFLIIKEQRTRAEEIFSLEEEALPKPSFRHHSFWLNISNCSPASGKQLD CDCP1_tupBel Tupaia belangeri (tree_shrew)
ERSGLACQSGRAFMIIQEQQSRAEEIFSLEEEVLPKPSFHHHSFWVNISNCSPMNGKQLD CDCP1_musMus Mus musculus (mouse)
ERSGLACQSGRAFMIIQEQQTRAEEIFSLEEEVLPKPSFHHHSFWVNISNCSPMNGKQLD CDCP1_ratNor Rattus norvegicus (rat)
ERSGVVCQSGRAYMIIQEQQSQAEEIFSLEDDILPKPRCYHHSFWVNISNCSPASSKQ.. CDCP1_dipOrd Dipodomys ordii (kangaroo_rat)
ERTGVVCQSERAFMIIQEQRTRAEEIFSLEDDRLPKPSFHRHSFWVNISNCSPASGKQLD CDCP1_cavPor Cavia porcellus (guinea_pig)
ERIGVACQTGWALMIIQEQRSQPEEIFNLEEVMLPKPSFHYHNFWVNISNCSPVSGKQLD CDCP1_speTri Spermophilus tridecemlineatus (squirrel)
ERMGVVCQTGRAFMIIQEQQTRAKEIFSLEE-VLPEPRVRRRSFWVNVSNCSPASGKQLD CDCP1_oryCun Oryctolagus cuniculus (rabbit)
ERTGVVCQTGRAFMIIQEQRSRVEEIFSLEEEVLPKPRVHRHSFWVNVSNCSPASGKQLD CDCP1_ochPri Ochotona princeps (pika)
ERTGVVCQTGRAFMIIQEQRSKAEEIFSLEDEVLPKPSFHHHSFWVNISNCSPVSGKQLD CDCP1_canFam Canis familiaris (dog)
ERTGVVCQTGRAFMIIQEQRTKAEEIFSLEDEVLPKPSFHHHSFWVNISNCSPVSGKQLD CDCP1_felCat Felis catus (cat)
ERTGLVCQTGRAFMIIQEQRMRAEEIFSLEE-VLPKPRFHHHSFWVNISNCSPVSGKQLD CDCP1_equCab Equus caballus (horse)
ERTGLVCQTGRAFMIIQEQLTKAEQIFSLEE-VLPKSSSHHHNFWVNISNCSPVRGKQLD CDCP1_myoLuc Myotis lucifugus (microbat)
EQTGLVCQTGRAFMIVQEQRTRAEEIFSLEE-VLPKPGFRHHSFWVNISNCSPLSGKQLD CDCP1_pteVam Pteropus vampyrus (macrobat)
ERTGVVCQTGRAFMIIQEQRAHAEEIFSLEEEVLPKPSFRYHSFWVNISNCSPMSGKQLD CDCP1_bosTau Bos taurus (cow)
ERTGVVCQTGRAFMIIQEQRARAEEIFSLEEEVLPKPSFHHHSFWVNISNCSPASGKQLD CDCP1_susScr Sus scrofa (pig)
ERTGVVCQTGRAFMIIQEQRAHTEEIFSLEEEVLPKPSFRYHSFWVNISNCSPMSKKQLD CDCP1_turTru Tursiops truncatus (dolphin)
ERTGVVCQTGRAFMIIQEQRSHAEEIFSLEEEVLPKPSFRHHSFWVNISNCSPVSGKQL. CDCP1_vicVic Vicugna vicugna (vicugna)
EKSGVVCQTGRAFMILQDQQHHSEEIFSLEDEVLPKPRFHRHSFWVNISNCSPASGKQLD CDCP1_eriEur Erinaceus europaeus (hedgehog)
ERTGVVCHTGRAFMIIQEQQTHVEEIFSLEEDVLPKPSFYHHSFWVNISNCSPVSGKQLD CDCP1_sorAra Sorex araneus (shrew)
EQTGVVCQTGRAFMIIQEQRTRAEEIFSLEEEVLPKPSFRRHSFWVNISNCSPVSGKQLD CDCP1_dasNov Dasypus novemcinctus (armadillo)
ERTSLVCQTGRAFMIIQEQQTNAEEIFSLEEDMLPKPSFRHHSFWVNISNCSPMSGKQLD CDCP1_choHof Choloepus hoffmanni (sloth)
ERTGVVCQTGRAFMIIQEQQSNAEEIFNLEDQVLPKPRFHHHSFWVNISNCSPMSGKQLD CDCP1_loxAfr Loxodonta africana (elephant)
ERTGVVCQTGRAFMIIQEQQSHAEEIFNLEDQVLPKPRFHHHSFWVNISNCSPMSGKQLD CDCP1_proCap Procavia capensis (hyrax)
ERTGVVCQTGRAFMIIQEQRAHAEEIFNLEDEVLPKPSFRHHSFWVNISNCSPVSGKQFE CDCP1_echTel Echinops telfairi (tenrec)
DRMGVSCETGRAFMIIQEQKAKAEEIVSRDDEPLPKPKDLHHNFWVNISNCSPMNGKQLD CDCP1_monDom Monodelphis domestica (opossum)
ERMGVACETGRAYMIIREQIPKAEEMVTREDELLPKPQVLHHSFWVNVSNCSPMKGKQLD CDCP1_ornAna Ornithorhynchus anatinus (platypus)
DRMGITCETGRAYVNIKEQMPGAEETVRREDELLPQPRNMHYNFWVNISNCKPVDPMQLS CDCP1_galGal Gallus gallus (chicken)
EWMGVTCEENRAHIYIREHNPGAKEMVCRDDEKLPRTLEMHDHFWVNITNCKPAAGKLLS CDCP1_anoCar Anolis carolinensis (lizard)
DRMDIMCETGRAFINIKEQKSWADIVLK-DYDTFPSSINLFYPFWFNITNCKPKSRQKLQ CDCP1_xenTro Xenopus tropicalis (frog) 

not available CDCP1_oviAri Ovis aries (sheep)
not sought CDCP1_macEug Macropus eugenii (wallaby)
not sought CDCP1_taeGut Taeniopygia guttata (finch)

Insertion in IRS1 in microbat and horse shared by macrobat but quasi-homoplasic in lemur

A one-residue insertion occurs in IRS1 in horse, microbat, and macrobat relative to other placentals but also is found at a similar site in lemur but not bushbaby. Close examination of lemur suggests its insertion comes at a slightly further downstream, ie AHHHQ vs AHHQ in bushbaby. That insertion is supported by 3 traces that agree on the location of the insertion: ti|1550444960, 1559993096, and 1569281779. Three traces also support no comparable insertion in bushbaby.

For unknown reasons, this region is poorly represented in trace archives, being missing in 8 genome project mammals including several with very high coverage. The insertion is located near a somewhat repetitive area of histidines and glutamines (which have two codons each and differ only in third codon position). Armadillo has a separate 4 amino acid deletion upsteam. Opossum is already rather diverged and chicken/lizard proteins are irrelevent.

Overall, while homoplasy in lemur can be argued away, the region is somewhat prone to indels. Additional species from PCR within Laurasiatheres could strengthen this candidate considerably. 

ADDSSSSTSSDSLGGGYCGARLEPSLPH-PHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_homSap Homo sapiens (human)
ADDSSSSTSSDSLGGGYCGARLEPSLPH-PHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_panTro Pan troglodytes (chimp)
ADDSSSSTSSDSLGGGYCGARLEPSLPH-PHHQVLQPHLPRKVDTAAQTNSRLARPTLL IRS1_ponPyg Pongo pygmaeus (orang_sumatran)
VDDSSSSTSSDSLGGGYCGARLEPSLPH-PHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_macMul Macaca mulatta (rhesus)
ADDSSSSTSSDSLGGGYCGARLEPSLPH-PHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_papAnu Papio anubis (baboon)
ADDSSSSTSSDSLGGGYCGARLEPSLPH-PHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_cerAet Cercopithecus aethiops
VEDSSSSTSSDSLGGGYCGARMEPSLSH-SHHQVLQLHLPRKVDSAAQTNSRLARPTRL IRS1_calJac Callithrix jacchus (marmoset)
AEDSSSSTSSDSLGGGYCGARPEPGLPH-PHHQILQSHLPRKVDTAAQTNSRLVRPTRL IRS1_tarSyr Tarsius syrichta (tarsier) bad trace
AEDSSSSTSSDSLGGGYCGARQEPGLPH-AHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_otoGar Otolemur garnettii (bushbaby)
AEDSSSSTSSDSLGGGYCGARLEPGLPHAHHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_micMur Microcebus murinus (mouse_lemur) bad trace
AEDSSSSTSSDSLGGGYCGARPESGLPH-LHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_tupBel Tupaia belangeri (tree_shrew)
AEDSSSSTSSDSLGGGYCGARPESSLTH-PHHHVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_musMus Mus musculus (mouse)
AEDSSSSTSSDSLGGGYCGARPESSVTH-PHHHALQPHLPRKVDTAAQTNSRLARPTRL IRS1_ratNor Rattus norvegicus (rat)
AEDSSSSTSSDSLGGGYCGARPEPGLPH-PHHHILQPRLPRKVDTAAQTNSRLARPTRL IRS1_cavPor Cavia porcellus (guinea_pig)
AEDSSSSTSSDSLGGGYCGARPEPGLPH-PHHHVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_oryCun Oryctolagus cuniculus (rabbit)
AEDSSSSTSSDSLGGGYCGVRPDPGLPH-IHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_canFam Canis familiaris (dog)
AEDSSSSTSSDSLGGGYCGVRPDSGLPH-IHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_felCat Felis catus (cat)
AEDSSSSTSSDSLGGGYCGARSEPGLPHHLHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_equCab Equus caballus (horse)
AEDSSSSTSNDSLGGGYCGVRPEPSLPQHLHHQVLQSHLPRKVDSAAQTNSRLARPTRL IRS1_myoLuc Myotis lucifugus (microbat)
AEDSSSSTSSDSLGGGHCGARPEPGLPHHLHHQVLQSHLPRKVDTAAQTNSRLARPTRL IRS1_pteVam Pteropus vampyrus (macrobat)
AEDSSSSTSSDSLGGGYCGARPEPGLPH-LHHQVLQAHLPRKVDTAAQTNNRLARPTRL IRS1_bosTau Bos taurus (cow)
.....SSTSSDSLGGGYCGARPEPGLPH-LHHQVLQPHLPRKVDTAAQTNNRLARPTRL IRS1_susScr Sus scrofa (pig)
ADDSSSSTSSDSLGGGYCGGRPEPGLPH-LHHQVLQPHLPRKVDTAAQTNRRLTRPTKL IRS1_eriEur Erinaceus europaeus (hedgehog)
AEDSSSSTSSDSLGGGYCAARPEPGLPP-LHHQVLQPHLPRKVDTAAQTHSRLTRPTRL IRS1_sorAra Sorex araneus (shrew)
AEDSSSSTSSDSLGGGYCGVRPE----H-LHHQVLQPHLPRKVDTAAQTNSRLARPTRL IRS1_dasNov Dasypus novemcinctus (armadillo)
AEDSSSSTSSDSLGGGYCGPRPEPGHPH-LHHQVLQPHLPRKVDTAAQTNSRLTRPTRL IRS1_proCap Procavia capensis (hyrax)
AEDSSSSTSSDSLGGGYCGPRPEPGHPP-LHHQVLQPHLPRKVDMAAQTNSRLARPTRL IRS1_echTel Echinops telfairi (tenrec)
AEDSSSSASSDSLGGG--GGQ-EGVHGH-LHHQALHQHLPRKMDLVAQTKSRLTRPTRL IRS1_monDom Monodelphis domestica (opossum)

not available  IRS1_speTri Spermophilus tridecemlineatus (squirrel)
not available  IRS1_dipOrd Dipodomys ordii (kangaroo_rat)
not available  IRS1_ochPri Ochotona princeps (pika)
not available  IRS1_oviAri Ovis aries (sheep)
not available  IRS1_turTru Tursiops truncatus (dolphin)
not available  IRS1_vicVic Vicugna vicugna (vicugna)
not available  IRS1_choHof Choloepus hoffmanni (sloth)
not available  IRS1_loxAfr Loxodonta africana (elephant)
not available  IRS1_ornAna Ornithorhynchus anatinus (platypus)
not available  IRS1_xenTro Xenopus tropicalis (frog)

not sought     IRS1_macEug Macropus eugenii (wallaby)
not sought     IRS1_taeGut Taeniopygia guttata (finch)

too diverged   IRS1_galGal Gallus gallus (chicken)
too diverged   IRS1_anoCar Anolis carolinensis (lizard)

Deletion in KIAA1009 of microbat and horse not shared by macrobat; rabbit indel not shared by pika

The one-residue deletion found in horse and microbat is not found in macrobat and so is not informative. They do not appear to be located quite orthologously. A five-residue deletion in rabbit is not supported in pika. This illustrates not that terminal leaf indels are common but rather they do exist and the selection algorithm can find them. 

DDIKEAHQITVRNLEAEIDVLKHQNAELDVKKNDKDDEDFQSIEFQVEQAHAKAKLVRLN KIAA1009_homSap Homo sapiens (human)
DDIKEAHQITVRNLEAEIDVLKHQNAELDVKKNDKDDKDFQSIEFQVEQAHAKAKLVRLN KIAA1009_panTro Pan troglodytes (chimp)
DDIKEAHQITVRKLEAEIDVLKHQNAELDVKKNDKDDKDFQSIEFQVEQAHAKAKLVRLN KIAA1009_ponPyg Pongo pygmaeus (orang_sumatran)
DDIKEAHQITVRNLEAEIDILKHQNAELDVKKNDKDDKDFQSIEFQVEQAHAKAKLVRLN KIAA1009_macMul Macaca mulatta (rhesus)
DDTKEAHQITVRKLEAEIDVLKHQNAELDVKKSGKVDKDFQSIEFQVEQAHAKAKLVRLN KIAA1009_calJac Callithrix jacchus (marmoset)
GDIKEAHQITVRKLEAEIDVLKHQNADLEHKKNDKGDQGLQSIEFQVEQAQARAKLARLN KIAA1009_musMus Mus musculus (mouse)
GGIKEAHQITVRKLEAEIDVLKHQNAHLEHKKNDKEDQDLQSIEFQVEQAQARAKLARLN KIAA1009_ratNor Rattus norvegicus (rat)
.DIKETHQTIVRDLEAEIDVLKRQNAELELKKNGTDDKDFQSIELQVEQAHAKAKLVRLN KIAA1009_cavPor Cavia porcellus (guinea_pig)
xxx KIAA1009_speTri Spermophilus tridecemlineatus (squirrel)
.DIKEAHLTTVRNLETEIDLLKHRNTELKHKKNDRDGKDLQSIELQVEQAHAKAKLVRL. KIAA1009_dipOrd Dipodomys ordii (kangaroo_rat)
DDIKEAHQITVRNLEAEIVVLKQRSAELELKKNGKDD-----IEFQVEQAHAKAKLVRLN KIAA1009_oryCun Oryctolagus cuniculus (rabbit)
..IKETHEIAVRNLEAEIDGLKQRNAELELKKNDKDGKDFQSIEFQVEQAHAKAKLVRL. KIAA1009_ochPri Ochotona princeps (pika)
SDIKEAHQITVRNLEAEINILKHQNAELECKKNDKDDKDFQSIEFQVEQAHAKAKLVRLN KIAA1009_canFam Canis familiaris (dog)
SDLKEAHQLTVRNLEAEIDVLKHRNAELELK-NDKDDQDFQSLEFQVEQAHAKAKLVRLN KIAA1009_equCab Equus caballus (horse)
.DIKEAHEITVRNLEAEIDTFKQQNAELELKKN-RDDKDFQSIEFQVEQAHAKAKLARLN KIAA1009_myoLuc Myotis lucifugus (microbat)
DDIKEAHQITVRNLEAEIDTLKHQNAELELKKDDKDDKDFQSIEFQVEQAHAKAKLVRLN KIAA1009_pteVam Pteropus vampyrus (macrobat)
DDVKEAHQITIRNLEAEIDVLKHQNAELELRKTEKDDKDFQSIEFQVEQAHSKAKLVRLN KIAA1009_bosTau Bos taurus (cow)
...KESHQSTVRNLEAEIDVLKHQNAELELKKNDKDDKDFQSIEFQVeQAHSKAKLVRLN KIAA1009_susScr Sus scrofa (pig)
DDVKEAHQITVGNLEAEIDVLKHQNAEWELKKDDKDDQDFQSIEFQVEQAHSKAKLVRL. KIAA1009_turTru Tursiops truncatus (dolphin)
NDLKEAHQITIRNLEAEIDILKNQNADLEHKKNDKDDKDFQSIEFQVEQAHAKAKLVRLN KIAA1009_eriEur Erinaceus europaeus (hedgehog)
.EIKEAHQITVKNLEAEIDVLKHQNAKLELKKNSKDNKDFQSIEFRVEQAHAKAKLVRLN KIAA1009_sorAra Sorex araneus (shrew)
.DLTGAHQITVRNLEAEIDVLKHQNAELELKKNDKHDKDFHSIEFQVEQAHAKAKLVRLN KIAA1009_choHof Choloepus hoffmanni (sloth)
.DIKEAHQITVRNLEAEIDMLKHQNAELELKKNDKDDKDFQSLEFQVEQAHAKAKLVRLN KIAA1009_loxAfr Loxodonta africana (elephant)
.DMKDVHLATVKTLEAEIESLKSQNAQLELKKNEKDDNDFQSLEFQVEQAHTKARLVRLN KIAA1009_monDom Monodelphis domestica (opossum)
.DVKEAHQVTVRNLEAEIEALKKQNAQLELQKSERGDQDFQAIEFQVEQAHTKARLARLN KIAA1009_ornAna Ornithorhynchus anatinus (platypus)
.NLKTTHQITVENLKTEIENLKSQNSQLKLRSK-KDNKDLQSTDWQMKQGKTKEKLLKLN KIAA1009_galGal Gallus gallus (chicken)
.NVNEAHQMTVNNLQAEIDSLRSQIGELERQKNATDNAELQSLEHQVEQAHAKAKMVRLN KIAA1009_anoCar Anolis carolinensis (lizard)

not available KIAA1009_felCat Felis catus (cat)
not available KIAA1009_oviAri Ovis aries (sheep)
not available KIAA1009_vicVic Vicugna vicugna (vicugna)

not sought    KIAA1009_otoGar Otolemur garnettii (bushbaby)
not sought    KIAA1009_micMur Microcebus murinus (mouse_lemur)
not sought    KIAA1009_tupBel Tupaia belangeri (tree_shrew)
not sought    KIAA1009_tarSyr Tarsius syrichta (tarsier)
not sought    KIAA1009_dipOrd Dipodomys ordii (kangaroo_rat)
not sought    KIAA1009_dasNov Dasypus novemcinctus (armadillo)

not sought    KIAA1009_proCap Procavia capensis (hyrax)
not sought    KIAA1009_echTel Echinops telfairi (tenrec)
not sought    KIAA1009_macEug Macropus eugenii (wallaby)
not sought    KIAA1009_taeGut Taeniopygia guttata (finch)

chr6 84919393 84919456 -3
human GACTGAAAATCTTCATCATCTTTATCATTTTTCTTGACGTCTAATTCAGCATTCTGATGTTTA
horse GACTGGAAATCTTGATCATCTTTGTCATTT---TTGAGTTCTAACTCAGCATTCCGATGTTTG

human GACTGAAAATCTTCATCATCTTTATCATTTTTCTTGACGTCTAATTCAGCATTCTGATGTTTAA
mibat GACTGGAAATCTTTATCATCTCT---ATTTTTCTTGAGTTCTAACTCAGCATTCTGTTGTTTAA

Insertion in GATA6 in horse and bats not shared by other Laurasiatheres

This is an apparently informative one-residue insertion in the well-conserved terminal exon of GATA6 for horse, microbat, and macrobat but no others. Note though that dog but not cat has an upstream insertion of 3 glycines and vicugna has a serine inserted seemingly at this same upstream site. The horse/bat insertion can be located with confidence given the overall conservation even though it was offset slightly in the original nucleotide alignment. There is no observable polymorphism or ambiguity in the relevent traces for horse or bats. 

TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRPDSWC GATA6_homSap Homo sapiens (human)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_panTro Pan troglodytes (chimp)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_ponPyg Pongo pygmaeus (orang_sumatran)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_macMul Macaca mulatta (rhesus)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_calJac Callithrix jacchus (marmoset)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_tarSyr Tarsius syrichta (tarsier)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_otoGar Otolemur garnettii (bushbaby)
ANPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_micMur Microcebus murinus (mouse_lemur)
TNPENSELKYSGQDGLYIGVSLASPSEVTSS-VRQDSWC GATA6_tupBel Tupaia belangeri (tree_shrew)
.NPENSDLKYSGQDGLYIGVSLSSPAEVTSS-VRQDSWC GATA6_musMus Mus musculus (mouse)
ANPENSDLKYSGQDGLYIGVSLSSPAEVTSS-VRQDSWC GATA6_ratNor Rattus norvegicus (rat)
TNPEGSELKYSGQDGLYIGVSMASPAEVTSS-VRQDSWC GATA6_cavPor Cavia porcellus (guinea_pig)
TNPEYSKLHYSGQNGLHIGFSLALPAEVTSS-VGQDSYC GATA6_speTri Spermophilus tridecemlineatus (squirrel)
PTPENSELKYSVQDGLYIGVSLSSPAEVTSS-VRQDSWC GATA6_dipOrd Dipodomys ordii (kangaroo_rat)
SNPENSELKYSGQDGLYMGVNLASSAEVTSS-VRQDSWC GATA6_oryCun Oryctolagus cuniculus (rabbit)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_ochPri Ochotona princeps (pika)
TNPENGELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_canFam Canis familiaris (dog) NGGGGEL insert
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_felCat Felis catus (cat)
TNPENSELKYSGQDGLYIGVSLASPAEVTSSSVRQDSWC GATA6_equCab Equus caballus (horse)
TNPENSELKYSGQDGLYIGVSLASPAEVTSSSVRQDSWC GATA6_myoLuc Myotis lucifugus (microbat)
TNPENSELKYSGQDGLYIGVSLASPAEVTSSSVRQDSWC GATA6_pteVam Pteropus vampyrus (macrobat)
ANPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_bosTau Bos taurus (cow)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_oviAri Ovis aries (sheep)
ANPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_susScr Sus scrofa (pig)
ANPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_turTru Tursiops truncatus (dolphin)
ANPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_vicVic Vicugna vicugna (vicugna) NSSEL insert
SNLENSELKYSGQDGLFIGVSLASPAEVTSS-VRQDSWC GATA6_eriEur Erinaceus europaeus (hedgehog)
TNPENSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_sorAra Sorex araneus (shrew)
TNPDNSELKYSGQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_dasNov Dasypus novemcinctus (armadillo)
TNPENSELKYSAQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_loxAfr Loxodonta africana (elephant)
TNPENSELKYSAQDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_proCap Procavia capensis (hyrax)
.NPETSELKYSAPDGLYIGVSLASPAEVTSS-VRQDSWC GATA6_echTel Echinops telfairi (tenrec)
TSPESTALKYSGQDGLYSGVSLTSTAEVTAS-VRQDSWC GATA6_monDom Monodelphis domestica (opossum)
TSPESTALKYSGQDGLYSGVSLTSTAEVTAS-VRQDSWC GATA6_triVul Trichosurus vulpecula (possum)
RSPESSALKYSGQQGLFPGVSLTSTAEVTAS-VRQESWC GATA6_ornAna Ornithorhynchus anatinus (platypus)

not available GATA6_oviAri Ovis aries (sheep)
not available GATA6_choHof Choloepus hoffmanni (sloth)
not sought    GATA6_macEug Macropus eugenii (wallaby)
not sought    GATA6_taeGut Taeniopygia guttata (finch)
not sought    GATA6_galGal Gallus gallus (chicken)
not sought    GATA6_taeGut Taeniopygia guttata (finch)
not sought    GATA6_anoCar Anolis carolinensis (lizard)

chr18 18034707 18034767 3
human GCGTCAGTCTCGCCTCGCCGGCCGAAGTCA---CGTCCTCCGTGCGACCGGATTCCTGGTGCG
horse GCGTCAGCCTGGCCTCGCCGGCTGAAGTCACATCGTCTTCGGTGAGACAGGATTCCTGGTGCG

human GCGTCAGTCTCGCCTCGCCGGCCGAAGTCACGTCCTCC---GTGCGACCGGATTCCTGGTGCGC
mibat GCGTCAGCCTGGCCTCACCGGCCGAAGTCACGTCCTCCTCGGTGAGACAGGATTCGTGGTGTGC

Terminal frameshift in RBP3 (IRBP)

The last exon of RBP3, like in many proteins, does not appear to be under a great deal of selective pressure. This surfaces in a certain amount of observed 'terminal wander' as various mutations allow readthru of the original stop codon to the next one that occurs by chance downstream. Here pegasoferae, relative to artiodactyls, all share a one bp indel within coding that causes an altogether novel amino acid sequence to terminate the protein.

The history here is quite complex when tetrapods outside Laurasiatheres are included. Ancestrally, the exon was clearly much shorter, terminating at consistent length just after module M4 ended in the RPB3 internal repeat structure from frog to marsupial divergence. In afrotheres, either the stop codon mutated or a frameshift occured, causing the protein to become longer. The new stop codon in hyrax represents the ancestral placental position. Elephants retain a cryptic stop codon here but evolved an earlier one that is used today. This stop codon and some aspects of sequence was conserved in pegasoferae but not artiodactyls (though by reinstituting the original trinucleotide ggg and former reading frame, residual ancestral sequence as well as the original distal stop codon can still be seen. Shrew and hedgehog diverged by a different scheme and are unhelpful.

In euarchontoglires, the placental stop codon persists only in treeshrew and lemurs. Later diverging primates evolved an earlier stop codon a few residues past the ancestral one; rodents are also short but variable. Despite its complexity, this region of the gene is a strong rare genomic event unlikely to recur. Unfortunately, it is quite clear from outgroup species such as treeshrew and hyrax that the frameshift event took place in stem artiodactyls whose monophylogeny is not in doubt) rather than in stem (bat + horse + carnivores). Note early artiodactyls pig and lama both fixed the frameshift so no phylogenetic resolution is provided within artiodactyls either.

The last exon begins as GERYGSKKSMVILTSSVTAGTAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDTNLYLTIPTARSVGASDGSSWEGVGVTPHVVVPAEEALARAKEM and is followed by the terminal reqions shown below (which are anchored to the QH feature which is reliably locatable in all species: 

QHNQLRVKRSPGLQDHL*                                             human
QHNQLRVKRSPGLQDHL*                                             chimp
QHNQLRVKRSPGLQDHL*                                             gorilla
QHNQLRVKRSPGLQDHP*                                             orang
QHNQLRVKRSPGLQDHP*                                             macaque
QQNQLRVKRSPGLQSHL*                                             marmoset
QYNLPRVRRSPGLQ                                                 tarsier
QHTLLRSRRSASLQGHQ                                              lemur
QHKLLRLRRSTGLQGHSEGGPHGQSPGAGRTSGPSTTSVS----AHGPA*GSWGQRGACQAL mouse_lemur
QHTLRRARRSPGWQSPGLRGLLGGVRGPSPRLSRTSGPQAKGAPARGPA*DPQGQHRGLLSS treeshrew
QHTLLRARRSL----RGQRLRRQRQGRAGPLGHIQRTLGHEVLTEAP KGWKRGLLHSSWA* pig contig
QHTLLRVRRSAGLRGRHKGLLGQHPGRAGPLGHFQGAPRHEVLTEVP KGRKRGVM...    lama
QHTPLRARRSPRLHGRRKGHHRQSQGRAGSLGRNQGVgRPEVLTEAP SGQKRGLLQCG*   cow
QHTLLRARRSPRLQGRRKGHRSQSQKRPGPPGHVQGAPRHEVLTEAP KGQQRGLLPSG*   dolphin
QHTLLRARRSPGLQGCRDDLFQQSPGVGGTSGHTPRAFQHVVLPEAP EGQQRALLSSD*   horse corrected to artiodactyl
QHTLLRARRSP              RMGGTSRPHTKALRHVVLPEAS GFRKGTC*AP     cat corrected to artiodactyl
QHPARRARRSP-------------RAPGTSRRHTRGWRPWPGLPPEA RGSSGACWAP     dog corrected to artiodactyl
QHTLMRVRRSPGQQGPQEGLRGQSPRVSGISGPHIMNAKAPQARGPA*KGQKRALLSSG*   macrobat
QHTLLRARRSPGLQGCRDDLFQQSPGVGGTSGPYPKGI---PACGPA*EGQQRALLSSD*   horse  
QHTLLRARRSP--------------RMGGTSRPHTKGT---PARGPA*               cat
QHPARRARRSP--------------RAPGTSRRHTRRV-AALARAPA*GQGQLRGLLGST   dog
QPTVLRAKRSPSL* 0                                               shrew
QNVQLRVKRNLA-QQGHWESIQGHSSGVGGVTELNIKGA*                       hedgehog
HHSLQMV*RLNAGLQGHRRGLGG*WIEPRAGGASGPRTEGTRARGPA*RSGGQQRGLLSP   elephant
QDSLKAVKLSAGLQGLRAGFGVQSSWVGGTSGPH---TESTSEHGPA*VCWEQEKGMLRS*  hyrax
NHHLQRAK*                                                      opossum
IHHLQRAD*                                                      wallaby
RAHLEHRD*                                                      platypus
NAHLHSSR*                                                      finch
SAHLHSSR*                                                      chicken
KAHLH---*                                                      lizard
ESQLEGRR*                                                      frog

cow terminus before and after frameshift:
 
cagcacactccgctaagggcgaggcgcagcccacgcctgcatggccgccgcaagggccaccacaggcagagccagggaagggcgggatctctgggccgcaaccaaggggtgggcaggcctgaggtcctgactgaggcccccagtgggcagaaaaggggcctgctgcagtgtggt
 Q  H  T  P  L  R  A  R  R  S  P  R  L  H  G  R  R  K  G  H  H  R  Q  S  Q  G  R  A  G  S  L  G  R  N  Q  G  V  G  R  P  E  V  L  T  E  A  P  S  G  Q  K  R  G  L  L  Q  C  G   

cagcacactccgctaagggcgaggcgcagcccacgcctgcatggccgccgcaagggccaccacaggcagagccagggaagggcggatctctgggccgcaaccaaggggtgggcaggcctgaggtcctgactgaggcccccagtgggcagaaaaggggcctgctgcagtgtggt
 Q  H  T  P  L  R  A  R  R  S  P  R  L  H  G  R  R  K  G  H  H  R  Q  S  Q  G  R  A  D  L  W  A  A  T  K  G  W  A  G  L  R  S  -  L  R  P  P  V  G  R  K  G  A  C  C  S  V

SWS1 deletion restricted to Caniformia

This is a one-residue deletion in the second transmembrane helix of this shortwave imaging opsin considered under informative opsin indels. This is too phylogenetically narrow to illuminate Pegasoferae. 

SWS1_homSap  LNAMVLVATLRYKKLRQPLNYILVNVSFG G FLLCIFSV F PVFVASCNGYFVFGRHVC human
SWS1_tarSyr  LNAMVLVATLHYRKLRQPLNYILVNVSLG G FLLCIFSV L PVFIASCRGYFVFGRHVC tarsier
SWS1_oryCun  LNAMVLVATLRYKKLRQPLNYILVNISLA G FLACIFSV F NVFVASCYGYFVFGRFVC rabbit
SWS1_ratNor  LNATVLVATLHYKKLRQPLNYILVNVSLG G FLFCIFSV F TVFIASCHGYFLFGRHVC rat
SWS1_ailMel  LNATVLVATLRYRKLRQPLNYILVNVSLA G FVYCI-SV S TVFIASCHGYFIFGRHVC panda
SWS1_canFam  LNGTVLVATLRYKKLRQPLNYILVNVSLG G FLYCI-SV S TVFIASCQGYFVFGRHVC dog
SWS1_enhLut  LNATVLVATLRYKKLRQPLNYILVNVSLG G FIYCI-SV S SVFIASCHGYFIFGHHIC otter
SWS1_phoVit  LNASVLVATLRYKKLRQPLNYILVNVSLG G FLYCI-SV S SVFIASCQGYFIFGRHVC seal
SWS1_ursMar  LNATVLVATLRYRKLRQPLNYILVNVSLA G FVYCI-SV S TVFIASCHGYFIFGRHVC bear
SWS1_felCat  LNATVLVATLRYRKLRQPLNYILVNVSLG G FLYCVSSV S IVFITSCHAYFIFGRHVC cat
SWS1_hipAmp  LNATVLVATLRYRKLRQPLNYILVNVSLG G FIYCIFSV F VVFITSCHGYFVFGRHVC hippo
SWS1_ptePum  LNATVLVATLRYRKLRQPLNYILVNVSLG G FLFCIFSV F TVFIASCQGYFVFGRHVC bat
SWS1_talEur  LNATVLVATLRYRKLRQPLNYILVNVSLG G FLFCIFSV L TVFIASCKGYFIFGRHVC mole
SWS1_sorAra  LNATVLVPTLRYRKLRQPLNYILVNVSLG G FLFCIFSV F TVIIASCKGYFVIGRHVC shrew
SWS1_susScr  LNATVLVATLRYRKLRQPLNYILVNVSLG G FIYCIFSV F SVFIASCHGYFVFGRRVC pig
SWS1_bosTau  LNATVLVATLRYRKLRQPLNYILVNVSLG G FIYCIFSV F IVFITSCYGYFVFGRHVC cow
SWS1_lamPac  LNATVLIATLRYRKLRQPLNYILVNVSLG G FIYCMFSV F CVFVASCYGYFVFGRRVC lama
SWS1_turTru  LDATVLVATLRYRKLRQPLNYILVNVSLG G FIYCIFSV F VVFITSCHGYFVFGRHVC dolphin
SWS1_echTel  LNAVVLVATLRYRKLRQPLNYILVNVSLA S VLFCVISV F TVFVASCHGYFIFGRHVC hyrax
SWS1_monDom  LNAVVLVATLRYKKLRQPLNYILVNVSLC G FIFCIFAV F TVFISSSQGYFIFGRHVC
SWS1_smiCri  LNGVVLIATLRYKKLRQPLNYILVNISLA G FIFCVFSV F TVFVSSSQGYFVFGRHVC
SWS1_tarRom  LNAVVLIATLRYKKLRQPLNYILVNISLA G FIFCVISV F TVFISSSQGYFIFGRHVC
SWS1_galGal  LNAVVLWVTVRYKRLRQPLNYILVNISAS G FVSCVLSV F VVFVASARGYFVFGKRVC
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