Coding indels: PRNP

The prion gene PRNP exhibits a 6bp indel in its amino-terminal signal peptide that contributed historically to establishing the clade Euarchontoglires. The indel, from consideration of outgroups, is a deletion present in all sequenced species of rodents, rabbits, treeshrews, flying lemurs and primates but not in any other species of mammal.

Remarkably, this indel distribution has held up (remained homoplasy-free) even as the number of species sequenced has come to exceed 100. (A typical mammalian gene as of June 07 can only be recovered from about 40 species.)

Consequently this data set strongly conflicts with recent proposals placing mouse basal relative to dog and human, ie (mouse,(dog,human)), because it would require a global revision of the super-ordinal mammalian tree based or assuming non-parsimonious multiple events bizarrely timed to very near divergence stems.

However signal region indels are very rare among the 4500-odd genes with signal peptides no doubt due to steric requirements of the binding pocket of the signal processing complex SRP, making multiple independent events within a particular signal peptide highly implausible.

Below is data from 96 species:

MA--NLGCWMLFLFVATWSDLGLCKKRPKPG	Callithrix jacchus
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG	Cebus apella
MA--NLGCWMLVVFVATWSDLGLCKKRPKPG	Cercopithecus aethiops
MA--NLGCWMLVVFVATWSDLGLCKKRPKPG	Cercopithecus dianae
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG	Colobus guereza
ME--NLGCWMLILFVATWSDIGLCKKRPKPG	Cynocephalus variegatus
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG	Gorilla gorilla
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG	Homo sapiens
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG	Hylobates lar
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG	Macaca arctoides
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG	Macaca fascicularis
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG	Macaca fuscata
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG	Macaca mulatta
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG	Macaca nemestrina
MA--NLGCWMLVVFVATWSDVGLCKKRPKPG	Microcebus murinus
MA--RLGCWMLVLFVATWSDIGLCKKRPKPG	Otolemur garnettii
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG	Pan troglodytes
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG	Papio hamadryas
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG	Pongo pygmaeus
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG	Presbytis francoisi
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG	Saimiri sciureus
MA--NLGCWMLVLFVATWSDLGLCKKRPKPG	Symphalangus syndactylus
MA--QLGCWLMVLFVATWSDVGLCKKRPKPG	Tupaia belangeri
MA--NLGYWLLALFVTTWTDVGLCKKRPKPG	Apodemus sylvaticus
MA--NAGCWLLVLFVATWSDTGLCKKRPKPG	Cavia porcellus
MA--HLSYWLLVLFVAAWSDVGLCKKRPKPG	Ochotona princeps
MA--NLGCWLLVLFVATWSDLGLCKKRTKPG	Dipodomys ordii
MA--NLSYWLLAFFVTTWTDVGLCKKRPKPG	Clethrionomys glareolus
MA--NLSYWLLALFVATWTDVGLCKKRPKPG	Cricetulus griseus
MA--NLSYWLLALFVATWTDVGLCKKRPKPG	Cricetulus migratorius
MA--NLGYWLLALFVTMWTDVGLCKKRPKPG	Meriones unguiculatus
MA--NLSYWLLALFVAMWTDVGLCKKRPKPG	Mesocricetus auratus
MA--NLGYWLLALFVTMWTDVGLCKKRPKPG	Mus musculus
MA--HLGYWMLLLFVATWSDVGLCKKRPKPG	Oryctolagus cuniculus
MA--NLGYWLLALFVTTCTDVGLCKKRPKPG	Rattus norvegicus
MA--NLGYWLLALFVTTCTDVGLCKKRPKPG	Rattus rattus
MA--NLGYWLLALFVATWTDVGLCKKRPKPG	Sigmodon fulviventer
MA--NLGYWLLALFVATWTDVGLCKKRPKPG	Sigmodon hispiedis
MV--NPGCWLLVLFVATLSDVGLCKKRPKPG	Spermophilus tridecemlineatus
MV--NPGYWLLVLFVATLSDVGLCKKRPKPG	Sciurus vulgaris

MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Bos taurus
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Bison bison
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Rangifer tarandus
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Alces alces
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Capreolus capreolus
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Kobus megaceros
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Connochaetes taurinus
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Ammotragus lervia
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Hippotragus niger
MVKSHMGSWILVLFVVTWSDVGLCKKRPKPG	Camelus dromedarius
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Capris hircus
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Cervus elaphus
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Cervus elaphus nelsoni
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Dama dama
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Odocoileus hemionus
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Odocoileus virginianus
MVKSHIGSWILVLFVAMWSDVALCKKRPKPG	Oryx leucoryx
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Ovibos moschatus
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Ovis aries
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Ovis canadensis
MVKSHIGGWILVLFVAAWSDIGLCKKRPKPG	Sus scrofa
MVKSHIGSWILVLFVAMWSDVALCKKRPKPG	Tragelaphus strepsiceros
MVKSHIGGWILLLFVATWSDVGLCKKRPKPG	Canis lupus familiaris
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Felis catus
MVKSHIGSWLLVLFVATWSDIGFCKKRPKPG	Mustela putorius
MVKSHIGSWLLVLFVATWSDIGFCKKRPKPG	Mustela vison
MVKSHIGSWILVLFVAMWSDVGLCKKRPKPG	Ailuropoda melanoleuca
MVKSHVGGWILVLFVATWSDVGLCKKRPKPG	Equus caballus
MVRSHVGGWILVLFVATWSDVGLCKKRPKPG	Diceros bicornis
MVKNHVGCWLLVLFVATWSEVGLCKKRPKPG	Erinaceus europaeus
MVTGHLGCWLLVLFMATWSDVGLCKKRPKPG	Sorex araneus
MVKSLVGGWILLLFVATWSDVGLCKKRPKPG	Myotis lucifugus
MVKNYIGGWILVLFVATWSDVGLCKKRPKPG	Pteropus vampyrus
MVKSHIANWILVLFVATWSDMGFCKKRPKPG	Tursiops truncatus
MVKSHLGCWIMVLFVATWSEVGLCKKRPKPG	Cyclopes didactylus
MVKGTVSCWLLVLVVAACSDMGLCKKRPKPG	Echinops telfairi
MVKSSLGCWILVLFVATWSDMGLCKKRPKPG	Elephas maximus
MVKSSLGCWILVLFVATWSDMGLCKKRPKPG	Loxodonta africana
MVKSSLGCWMLVLFVATWSDVGLCKKRPKPG	Procavia capensis
MMKSGLGCWILVLFVATWSDVGLCKKRPKPG	Orycteropus afer
MVKSGLGCWILVLFVATWSDVGVCKKRPKPG	Trichechus manatus
MVRSRVGCWLLLLFVATWSELGLCKKRPKPG	Dasypus novemcinctus
MAKIQLGYWILALFIVTWSELGLCKKPKTRPG	Macropus eugenii
MGKIHLGYWFLALFIMTWSDLTLCKKPKPRPG	Monodelphis domestica
MGKIQLGYWILVLFIVTWSDLGLCKKPKPRPG	Trichosurus vulpecular
MARLLTTCCLLALLLAACTDVALSKKGKGKPS	Gallus gallus
MAKLPGTSCLLLLLLLLGADLASCKKGKGKPG	Taeniopygia guttata
MGKHQMTCWLAIFLLLIQANVSLAKK-KPKPS	Anolis carolinensis
MRRFLVTCWIAVFLILLQTDVSLSKKGKNKPG	Gekko gekkko
MGRYRLTCWIVVLLVVMWSDVSFSKKGKGKGG	Trachemys scripta
MGRHLISCWIIVLFVAMWSDVSLAKKGKGKTG	Pelodiscus sinensis
MPQSLWTCLVLISLICTLTVSSKKSGGGKSKTG	Xenopus laevis
MLRSLWTSLVLISLVCALTVSSKKSGSGKSKTG	Xenopus topicalis