Opsin evolution: update blog

This cluster of web articles on opsin evolution is updated almost daily. Because those changes are hard to track systematically, this simple article 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 gene extraction from trace reads
• 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)

Reverse Chronological Update Blog

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.