The comb jelly opsins and the origins of animal phototransduction

Genome Biology and Evolution

Volumn 6, Issue 8, 2014, Pages 1964-1971

  Feuda, Roberto ^a   Rota Stabelli, Omar ^b   Oakley, Todd H ^c   Pisani, Davide ^d  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b RESEARCH AND INNOVATION CENTRE   (Italy)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

Comb jelly; Ctenophora; Evolution; Metazoa; Opsin; Vision

Indexed keywords

OPSIN;

ANIMAL; CNIDARIA; CTENOPHORA; GENETICS; METABOLISM; MOLECULAR EVOLUTION; PHOTOTRANSDUCTION; PHYLOGENY; PHYSIOLOGY;

ANIMALS; CNIDARIA; CTENOPHORA; EVOLUTION, MOLECULAR; LIGHT SIGNAL TRANSDUCTION; OPSINS; PHYLOGENY;

EID: 84924325807     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evu154     Document Type: Article

References (33)

1. AnisimovaM, Gil M, Dufayard JF, Dessimoz C, Gascuel O. 2011. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol. 60: 685-699.
2. Dohrmann M, Wörheide G. 2013. Novel scenarios of early animal evolution-is it time to rewrite textbooks? Integr Comp Biol. 53:503-511.
3. Dunn CW, et al. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749.
4. Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113.
5. Feuda R, Hamilton SC, McInerney JO, Pisani D. 2012. Metazoan opsin evolution reveals a simple route to animal vision. Proc Natl Acad Sci U S A. 109:18868-18872.
6. Fredriksson R, Lagerstrom MC, Lundin LG, Schioth HB. 2003. The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol Pharmacol. 63:1256-1272.
7. Goldman N. 1993. Statistical tests of models of DNA substitution. J Mol Evol. 36:182-198.
8. Guindon S, et al. 2010. New algorithms and methods to estimate maximum- likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59:307-321.
9. Hejnol A, et al. 2009. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc Biol Sci. 276:4261-4270.
10. Koyanagi M, et al. 2008. Jellyfish vision starts with cAMP signaling mediated by opsin-G(s) cascade. Proc Natl Acad Sci U S A. 105: 15576-15580.
11. Lartillot N, Brinkmann H, Philippe H. 2007. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol. 7:S4.
12. Lartillot N, Lepage T, Blanquart S. 2009. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25:2286-2288.
13. Lartillot N, Philippe H. 2004. A Bayesian mixture model for across-site heterogeneities in the amino-Acid replacement process. Mol Biol Evol. 21:1095-1109.
14. Mason B, et al. 2012. Evidence formultiple phototransduction pathways in a reef-building coral. PLoS One 7:e50371.
15. Moroz LL, et al. 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature 510:109-114.
16. Nielsen C. 2012. Animal evolution: interelationship of the living phyla. Oxford: Oxford University Press.
17. Nosenko T, et al. 2013. Deep metazoan phylogeny: when different genes tell different stories. Mol Phylogenet Evol. 67:223-233.
18. Philippe H, et al. 2009. Phylogenomics revives traditional views on deep animal relationships. Curr Biol. 19:706-712.
19. Philippe H, et al. 2011. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 9:e1000602.
20. Pick KS, et al. 2010. Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol. 27: 1983-1987.
21. Plachetzki DC, Degnan BM, Oakley TH. 2007. The origins of novel protein interactions during animal opsin evolution. PLoS One 2:e1054.
22. Porter ML, et al. 2011. Shedding new light on opsin evolution. Proc Biol Sci. 279:3-14.
23. Quang LS, Gascuel O, Lartillot N. 2008. Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics 24: 2317-2323.
24. Rivera AS, et al. 2012. Blue-light-receptive cryptochrome is expressed in a sponge eye lacking neurons and opsin. J Exp Biol. 215:1278-1286.
25. Rota-Stabelli O, Lartillot N, Philippe H, Pisani D. 2013. Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study. Syst Biol. 62:121-133.
26. Rota-Stabelli O, Telford MJ. 2008. A multi criterion approach for the selection of optimal outgroups in phylogeny: recovering some support for Mandibulata over Myriochelata using mitogenomics. Mol Phylogenet Evol. 48:103-111.
27. Ryan JF, et al. 2013. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342:1242592.
28. Schnitzler CE, et al. 2012. Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a newview of ctenophore photocytes. BMC Biol. 10:107.
29. Shimodaira H, Hasegawa M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247.
30. Srivastava M, et al. 2010. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 466:720-726.
31. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
32. Suga H, Schmid V, GehringWJ. 2008. Evolution and functional diversity of jellyfish opsins. Curr Biol. 18:51-55.
33. Terakita A. 2005. The opsins. Genome Biol. 6:213.