[1].Molecular Evolution of Visual Opsin Genes during the Behavioral Shifts between Different Photic Environments in Geckos[J].Asian Herpetological Research,2021,12(3):280-288.[doi:10.16373/j.cnki.ahr.200124]
 Yao CAI,Yuefen FAN,Youxia YUE,et al.Molecular Evolution of Visual Opsin Genes during the Behavioral Shifts between Different Photic Environments in Geckos[J].Asian Herpetological Research(AHR),2021,12(3):280-288.[doi:10.16373/j.cnki.ahr.200124]

Molecular Evolution of Visual Opsin Genes during the Behavioral Shifts between Different Photic Environments in Geckos()

Asian Herpetological Research[ISSN:2095-0357/CN:51-1735/Q]



Molecular Evolution of Visual Opsin Genes during the Behavioral Shifts between Different Photic Environments in Geckos
Yao CAI12 Yuefen FAN1 Youxia YUE1 Peng LI1* Jie YAN1* and Kaiya ZHOU1
1 Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China
2 School of Food Science, Nanjing Xiaozhuang University, Nanjing 211171, Jiangsu, China
Gecko diurnality molecular evolution nocturnality opsin gene
Reptiles are the most morphologically and physiologically diverse tetrapods, with the squamates having the most diverse habitats. Lizard is an important model system for understanding the role of visual ecology, phylogeny and behavior on the structure of visual systems. In this study, we compared three opsin genes (RH2, LWS and SWS1) among 49 reptile species to detect positively selected genes as well as amino acid sites. Our results indicated that visual opsin genes have undergone divergent selection pressures in all lizards and RH2 and LWS suffered stronger positive selection than SWS1. Twelve positively selected sites were picked out for RH2 and LWS. Moreover, many diagnostic sites were found between geckos and non-gecko lizards, most of which were located near the positively selected sites and some of them have already been reported to be responsible for significant shifts of the wavelength of maximum absorption (λmax). The results indicated that the gecko lineage accelerated the evolution of these genes to adapt to the dim-light environment or nocturnality as well as the switch between nocturnality and diurnality.


Anisimova M., Yang Z. 2007. Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Mol Biol Evol, 24: 1219-1228
Bowmaker J. K. 2008. Evolution of vertebrate visual pigments. Vision Res, 48: 2022-2041
Bowmaker J. K., Hunt D. M. 2006. Evolution of vertebrate visual pigments. Curr Biol, 16: R484-489
Fleishman L. J., Loew E. R., Whiting M. J. 2011. High sensitivity to short wavelengths in a lizard and implications for understanding the evolution of visual systems in lizards. Proc Biol Sci, 278: 2891-2899
Fleishman L. J., Persons M. 2001. The influence of stimulus and background colour on signal visibility in the lizard Anolis cristatellus. J Exp Biol, 204: 1559-1575
Gutierrez E. D., Schott R. K., Preston M. W., Loureiro L. O., Lim B. K., Chang B. S. W. 2018. The role of ecological factors in shaping bat cone opsin evolution. P Roy Soc B-Biol Sci, 285: 20172835
Hara Y., Takeuchi M., Kageyama Y., Tatsumi K., Hibi M., Kiyonari H., Kuraku S. 2018. Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes. BMC Biol, 16: 40
Hughes A. L. 2008. The origin of adaptive phenotypes. PNAS, 105: 13193-13194
Kojima D., Okano T., Fukada Y., Shichida Y., Yoshizawa T., Ebrey T. G. 1992. Cone visual pigments are present in gecko rod cells. PNAS, 89: 6841-6845
Kumar S., Stecher G., Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol, 33: 1870-1874
Liu Y., Zhou Q., Wang Y., Luo L., Yang J., Yang L., Liu M., Li Y., Qian T., Zheng Y., Li M., Li J., Gu Y., Han Z., Xu M., Zhu C., Yu B., Yang Y., Ding F., Jiang J., Yang H., Gu X. 2015. Gekko japonicus genome reveals evolution of adhesive toe pads and tail regeneration. Nat Commun, 6: 10033
Loew E. R. 1994. A third, ultraviolet-sensitive, visual pigment in the Tokay gecko (Gekko gecko). Vision Res, 34: 1427-1431
Loew E. R., Fleishman L. J., Foster R. G., Provencio I. 2002. Visual pigments and oil droplets in diurnal lizards: a comparative study of Caribbean anoles. J Exp Biol, 205: 927-938
Macedonia J. M., Lappin A. K., Loew E. R., Mcguire J. A., Hamilton P. S., Plasman M., Brandt Y., Lemos-Espinal J. A., Kemp D. J. 2009. Conspicuousness of Dickerson’s collared lizard (Crotaphytus dickersonae) through the eyes of conspecifics and predators. Biol J Linn Soc 97: 749-765
Meredith R. W., Gatesy J., Emerling C. A., York V. M., Springer M. S. 2013. Rod monochromacy and the coevolution of cetacean retinal opsins. PLoS Genet, 9: e1003432
Pond S. L., Frost S. D. 2005. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics, 21: 2531-2533
Pride D. T. 2000. SWAAP version 1.0.2, sliding windows alignment analysis program: a tool for analyzing patterns of substitutions and similarity in multiple alignments. Distributed by the author
Pyron R. A., Burbrink F. T., Wiens J. J. 2013. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evol Biol, 13: 93
Roll B. 2000. Gecko vision-visual cells, evolution, and ecological constraints. J Neurocytol, 29: 471-484
Roll B. 2001a. Gecko vision-retinal organization, foveae and implications for binocular vision. Vision Res, 41: 2043-2056
Roll B. 2001b. Multiple origin of diurnality in geckos: evidence from eye lens crystallins. Naturwissenschaften, 88: 293-296
Rosler H., Bauer A. M., Heinicke M. P., Greenbaum E., Jackman T., Nguyen T. Q., Ziegler T. 2011. Phylogeny, taxonomy, and zoogeography of the genus Gekko Laurenti, 1768 with the ridation of G. reevesii Gray, 1831 (Sauria: Gekkonidae). Zootaxa: 1-50
Schott R. K., Bhattacharyya N., Chang B. S. W. 2019. Evolutionary signatures of photoreceptor transmutation in geckos reveal potential adaptation and convergence with snakes. Evolution, 73: 1958-1971
Shi Y., Radlwimmer F.B., Yokoyama S. 2001. Molecular genetics and the evolution of ultraviolet vision in vertebrates. PNAS, 98: 11731-11736
Sim?es B. F., Sampaio F. L., Jared C., Antoniazzi M. M., Loew E. R., Bowmaker J. K., Rodriguez A., Hart N. S., Hunt D. M., Partridge J. C., Gower D. J. 2015. Visual system evolution and the nature of the ancestral snake. J Evol Biol, 28: 1309-1320
Stuart-Fox D., Moussalli A., Whiting M. J. 2007. Natural selection on social signals: signal efficacy and the evolution of chameleon display coloration. Am Nat, 170: 916-930
Swanson W. J., Nielsen R., Yang Q. 2003. Pervasive adaptive evolution in mammalian fertilization proteins. Mol Biol Evol, 20: 18-20
Takenaka N., Yokoyama S. 2007. Mechanisms of spectral tuning in the RH2 pigments of Tokay gecko and American chameleon. Gene, 399: 26-32
Terakita A. 2005. The opsins. Genome Biol, 6: 213
Wong W. S., Yang Z., Goldman N., Nielsen, R. 2004. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics, 168: 1041-1051
Woolley S., Johnson J., Smith M. J., Crandall K. A., McClellan D. A. 2003. TreeSAAP: Selection on Amino Acid properties using phylogenetic trees. Bioinformatics, 19: 671-672
Yang Z. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol, 15: 568-573
Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol, 24: 1586-1591
Yang Z., Nielsen R. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol, 46: 409-418
Yang Z., Wong W. S., Nielsen R. 2005. Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol, 22: 1107-1118
Yokoyama S., Blow N. S. 2001. Molecular evolution of the cone visual pigments in the pure rod-retina of the nocturnal gecko, Gekko gecko. Gene, 276: 117-125
Yokoyama S., Radlwimmer F. B. 1998. The “five-sites” rule and the evolution of red and green color vision in mammals. Mol Biol Evol, 15: 560-567
Yokoyama S., Radlwimmer F. B., Blow N. S. 2000. Ultraviolet pigments in birds evolved from violet pigments by a single amino acid change. PNAS, 97: 7366-7371
Yokoyama S., Starmer W. T., Takahashi Y., Tada T. 2006. Tertiary structure and spectral tuning of UV and violet pigments in vertebrates. Gene, 365: 95-103
Yokoyama S., Tada T. 2010. Evolutionary dynamics of rhodopsin type 2 opsins in vertebrates. Mol Biol Evol, 27: 133-141
Yokoyama S., Takenaka N., Blow N. 2007. A novel spectral tuning in the short wavelength-sensitive (SWS1 and SWS2) pigments of bluefin killifish (Lucania goodei). Gene, 396: 196-202
Zhang J. Z., Nielsen R., Yang Z. H. 2005. uation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol, 22: 2472-2479
Zhang X., Wensel T. G., Yuan C. 2006. Tokay gecko photoreceptors achieve rod-like physiology with cone-like proteins. Photochem Photobiol, 82: 1452-1460
Zhang Y. 2008. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40
Zhao H. B., Ru B. H., Teeling E. C., Faulkes C. G., Zhang S. Y., Rossiter S. J. 2009. Rhodopsin molecular evolution in mammals inhabiting low light environments. PLoS One, 4:e8326
Zheng Y. C., Wiens J. J. 2016. Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Mol Phylogenet Evol, 94: 537-547

更新日期/Last Update: 2021-09-25