Opsin evolution: update blog

This cluster of web articles on opsin evolution is updated almost daily. Because those changes are hard to track in longish articles, this simple directory and blog of significant changes may be helpful.

• Introduction to the opsin classifier and curated sequence collection
• A massive anchored alignment of 119 opsins
• Tutorial on genes from traces, intron patterns, resolving indels
• Key critters: species with genome projects and their photoreceptors
• Color vision in the platypus and ancestral mammal
• Tracking significant updates
• Informative coding indels (under development)
• Intron gain and lost (under development)
• Ancestral opsins: lowering the noise level (in progress)
• The photoreceptor fossil record (planned)
• Subscholarly opsin literature and defective evolutionary inference (planned)
• Opsin evolution: the bottom line (in progress)
• Comparative genomics of other eye developmental and structural genes (volunteers needed)

Reverse Chronological Update Blog

17 Dec 07: added new ciliary opsins from Daphnia, Tribolium, Aedes, and Culex genomes

16 Dec 07; developed new page on ancestral ciliary opsin intron pattern 
14 Dec 07: upgraded sponge photoreceptor account, found final exon of new Platynereis ciliary exon
13 Dec 07: extended JGI staff models of 3 intronless ciliary encephalopsins from Nematostella to full length
12 Dec 07: added Nematostella and Hydra sections awaiting clarification
11 Dec 07: finished larval and adult photoreception in Ciona

10 Dec 07: expanded section on Ciona to include possible otolith paralogous photoreceptor
09 Dec 07: added a treatment of two tunicate pinopsin-like opsins and their ancient introns
08 Dec 07: added a section on intron cross-comparison to the annotation tutorial
08 Dec 07: added treatment of two platyhelminthes to Lophotrochozoa area
07 Dec 07: added 2 trematode and 1 planaria opsins, exon pattern matches melanopsin

06 Dec 07: added cnidarian larval rhabdomeric single-cell eye and adult rhopalium imagery
05 Dec 07: added Capitella literature survey and a new melanopsin from genome assembly
04 Dec 07: added Helobedella literature survey and new opsins from genome assembly
03 Dec 07: added Lottia, reviewed genome assembly, found an opsin but could not locate anything on ocelli
02 Dec 07: added Aplysia eye anatomy and apparent melanopsin ortholog to key critters

29 Nov 07: added platynereis story to critters, described second new ciliary opsin
29 Nov 07: added graphics comparing eye systems in deuts and lophs, illustrated everse and inverse eyes
29 Nov 07: added sea urchin opsins to critter discussion, graphic of expression in larva and adult
29 Nov 07: added 6 sea urchin reference opsins by repairing gene models, adding introns, and reclassifying.
28 Nov 07: added Xenoturbella and Convoluta section to basal key critters, no opsins available

28 Nov 07: upgraded key critters with treatment of Saccoglossus
28 Nov 07: found first hemichordate opsin, put methods into detailed tutorial
28 Nov 07: received copywrite permissions for use of handdrawn invertebrate eyes illustrations
28 Nov 07: added jump navigation to key critters as article is getting fairly long
27 Nov 07: added scallop Go opsins from an important historic study
27 Nov 07: reorganized curated sequences into deuterostome, ecdysozoa, lophotrochozoa blocks sorted by receptor type.