{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,3]],"date-time":"2026-05-03T07:45:33Z","timestamp":1777794333178,"version":"3.51.4"},"reference-count":87,"publisher":"The Royal Society","issue":"2027","license":[{"start":{"date-parts":[[2024,7,24]],"date-time":"2024-07-24T00:00:00Z","timestamp":1721779200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/royalsociety.org\/-\/media\/journals\/author\/Licence-to-Publish-20062019-final.pdf"},{"start":{"date-parts":[[2024,7,24]],"date-time":"2024-07-24T00:00:00Z","timestamp":1721779200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/royalsociety.org\/journals\/ethics-policies\/data-sharing-mining\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["royalsocietypublishing.org"],"crossmark-restriction":true},"short-container-title":["Proc. R. Soc. B."],"published-print":{"date-parts":[[2024,8]]},"abstract":"<jats:p>\n            Infrared vision is a highly specialized sensory system that evolved independently in three clades of snakes. Apparently, convergent evolution occurred in the transient receptor potential ankyrin 1 (\n            <jats:italic>TRPA1<\/jats:italic>\n            ) proteins of infrared-sensing snakes. However, this gene can only explain how infrared signals are received, and not the transduction and processing of those signals. We sequenced the genome of\n            <jats:italic>Xenopeltis unicolor<\/jats:italic>\n            , a key outgroup species of pythons, and performed a genome-wide analysis of convergence between two clades of infrared-sensing snakes. Our results revealed pervasive molecular adaptation in pathways associated with neural development and other functions, with parallel selection on loci associated with trigeminal nerve structural organization. In addition, we found evidence of convergent amino acid substitutions in a set of genes, including\n            <jats:italic>TRPA1<\/jats:italic>\n            and\n            <jats:italic>TRPM2<\/jats:italic>\n            . The analysis also identified convergent accelerated evolution in non-coding elements near 12 genes involved in facial nerve structural organization and optic nerve development. Thus, convergent evolution occurred across multiple dimensions of infrared vision in vipers and pythons, as well as amino acid substitutions, non-coding elements, genes and functions. These changes enabled independent groups of snakes to develop and use infrared vision.\n          <\/jats:p>","DOI":"10.1098\/rspb.2024.0818","type":"journal-article","created":{"date-parts":[[2024,7,23]],"date-time":"2024-07-23T23:06:33Z","timestamp":1721775993000},"update-policy":"https:\/\/doi.org\/10.1098\/crossmark-policy","source":"Crossref","is-referenced-by-count":5,"title":["Comparative genomics sheds new light on the convergent evolution of infrared vision in snakes"],"prefix":"10.1098","volume":"291","author":[{"given":"Dahu","family":"Zou","sequence":"first","affiliation":[{"name":"Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, Hubei 443002, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Song","family":"Huang","sequence":"additional","affiliation":[{"name":"The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shilin","family":"Tian","sequence":"additional","affiliation":[{"name":"Novogene Bioinformatics Institute, Beijing 100000, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Felista Kasyoka","family":"Kilunda","sequence":"additional","affiliation":[{"name":"Key Laboratory of Genetic Evolution and Animal Models and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert W.","family":"Murphy","sequence":"additional","affiliation":[{"name":"Reptilia Zoo and Education Centre, 2501 Rutherford Road, Vaughan, ON L4K 2N6, Canada"},{"name":"Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 2C6, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hollis A.","family":"Dahn","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 2C6, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2844-2463","authenticated-orcid":true,"given":"Youbing","family":"Zhou","sequence":"additional","affiliation":[{"name":"Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, Hubei 443002, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ping-Shin","family":"Lee","sequence":"additional","affiliation":[{"name":"The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6432-7721","authenticated-orcid":true,"given":"Jin-Min","family":"Chen","sequence":"additional","affiliation":[{"name":"The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"175","published-online":{"date-parts":[[2024,7,24]]},"reference":[{"key":"e_1_3_8_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature12511"},{"key":"e_1_3_8_3_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msab130"},{"key":"e_1_3_8_4_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aat7244"},{"key":"e_1_3_8_5_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.244251.118"},{"key":"e_1_3_8_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3198"},{"key":"e_1_3_8_7_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.25884"},{"key":"e_1_3_8_8_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msy161"},{"key":"e_1_3_8_9_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msv091"},{"key":"e_1_3_8_10_2","first-page":"1008","article-title":"Genome-wide convergence during evolution of mangroves from woody plants","volume":"34","author":"Xu S","year":"2017","unstructured":"Xu S, He Z, Guo Z, Zhang Z, Wyckoff GJ, Greenberg A, Wu CI, Shi S. 2017 Genome-wide convergence during evolution of mangroves from woody plants. Mol. Biol. Evol. 34, 1008\u20131015. (doi:10.1093\/molbev\/msw277)","journal-title":"Mol. Biol. Evol."},{"key":"e_1_3_8_11_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz468"},{"key":"e_1_3_8_12_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1813593115"},{"key":"e_1_3_8_13_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature08943"},{"key":"e_1_3_8_14_2","doi-asserted-by":"publisher","DOI":"10.1670\/10-238.1"},{"key":"e_1_3_8_15_2","doi-asserted-by":"publisher","DOI":"10.5115\/acb.2011.44.1.8"},{"key":"e_1_3_8_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/0006-8993(74)90560-5"},{"key":"e_1_3_8_17_2","doi-asserted-by":"publisher","DOI":"10.1002\/cne.901880104"},{"key":"e_1_3_8_18_2","doi-asserted-by":"publisher","DOI":"10.1002\/cne.23644"},{"key":"e_1_3_8_19_2","doi-asserted-by":"publisher","DOI":"10.1002\/cne.901910309"},{"key":"e_1_3_8_20_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.628839"},{"key":"e_1_3_8_21_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msq267"},{"key":"e_1_3_8_22_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-69843-w"},{"key":"e_1_3_8_23_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0831-x"},{"key":"e_1_3_8_24_2","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.add0141"},{"key":"e_1_3_8_25_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz891"},{"key":"e_1_3_8_26_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_3_8_27_2","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.7334.1"},{"key":"e_1_3_8_28_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41477-019-0487-8"},{"key":"e_1_3_8_29_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"e_1_3_8_30_2","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbm048"},{"key":"e_1_3_8_31_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm286"},{"key":"e_1_3_8_32_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti1003"},{"key":"e_1_3_8_33_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti1018"},{"key":"e_1_3_8_34_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/27.2.573"},{"key":"e_1_3_8_35_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr342"},{"key":"e_1_3_8_36_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.1865504"},{"key":"e_1_3_8_37_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_3_8_38_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1883"},{"key":"e_1_3_8_39_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg770"},{"key":"e_1_3_8_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp120"},{"key":"e_1_3_8_41_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl200"},{"key":"e_1_3_8_42_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-5-59"},{"key":"e_1_3_8_43_2","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-1-r7"},{"key":"e_1_3_8_44_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg213"},{"key":"e_1_3_8_45_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv318"},{"key":"e_1_3_8_46_2","first-page":"555","article-title":"PAML: a program package for phylogenetic analysis by maximum likelihood","volume":"13","author":"Yang Z","year":"1997","unstructured":"Yang Z. 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555\u2013556. (doi:10.1093\/bioinformatics\/13.5.555)","journal-title":"Comput. Appl. Biosci."},{"key":"e_1_3_8_47_2","doi-asserted-by":"publisher","DOI":"10.1111\/1749-4877.12723"},{"key":"e_1_3_8_48_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.1933104"},{"key":"e_1_3_8_49_2","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbq072"},{"key":"e_1_3_8_50_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv416"},{"key":"e_1_3_8_51_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv351"},{"key":"e_1_3_8_52_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02134-9"},{"key":"e_1_3_8_53_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4318"},{"key":"e_1_3_8_54_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2020.106807"},{"key":"e_1_3_8_55_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2510-7"},{"key":"e_1_3_8_56_2","doi-asserted-by":"publisher","DOI":"10.1172\/JCI65853"},{"key":"e_1_3_8_57_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2009.03.003"},{"key":"e_1_3_8_58_2","first-page":"5063","article-title":"Inherited optic atrophy gene discovery using whole exome sequencing","volume":"57","author":"Borchert JS","year":"2016","unstructured":"Borchert JS, Nakata I, Navarro-Gomez D, Janessian M, Delbono E, Wiggs JL. 2016 Inherited optic atrophy gene discovery using whole exome sequencing. Invest. Ophthalmol. Vis. Sci. 57, 5063. (https:\/\/iovs.arvojournals.org\/article.aspx?articleid=2563225)","journal-title":"Invest. Ophthalmol. Vis. Sci."},{"key":"e_1_3_8_59_2","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddq473"},{"key":"e_1_3_8_60_2","first-page":"22","volume-title":"Georgia Undergraduate Research Conference (2014\u20132015)","author":"Doolittle S","year":"2015","unstructured":"Doolittle S. 2015 The role of topoisomerase 3B (top3b) in autism spectrum disorder through neural development of zebrafish embryos. In Georgia Undergraduate Research Conference (2014\u20132015), Georgia Southern University, p. 22. https:\/\/digitalcommons.georgiasouthern.edu\/gurc\/2015\/2015\/22."},{"key":"e_1_3_8_61_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2021.110280"},{"key":"e_1_3_8_62_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.conb.2009.12.003"},{"key":"e_1_3_8_63_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrn1397"},{"key":"e_1_3_8_64_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuchi.2009.01.001"},{"key":"e_1_3_8_65_2","doi-asserted-by":"publisher","DOI":"10.1038\/scientificamerican0508-60"},{"key":"e_1_3_8_66_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1182213"},{"key":"e_1_3_8_67_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.pbiomolbio.2015.04.001"},{"key":"e_1_3_8_68_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.51275"},{"key":"e_1_3_8_69_2","doi-asserted-by":"publisher","DOI":"10.1007\/s12264-020-00541-3"},{"key":"e_1_3_8_70_2","doi-asserted-by":"publisher","DOI":"10.1242\/dev.015412"},{"key":"e_1_3_8_71_2","doi-asserted-by":"publisher","DOI":"10.3390\/jdb8040033"},{"key":"e_1_3_8_72_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2023.05.030"},{"key":"e_1_3_8_73_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0028644"},{"key":"e_1_3_8_74_2","article-title":"Temperature acclimation in hot-spring snakes and the convergence of cold response","volume":"3","author":"Yan C","year":"2022","unstructured":"Yan C, Wu W, Dong W, Zhu B, Chang J, Lv Y, Yang S, Li JT. 2022 Temperature acclimation in hot-spring snakes and the convergence of cold response. Innovation 3, 100295. (doi:10.1016\/j.xinn.2022.100295)","journal-title":"Innovation"},{"key":"e_1_3_8_75_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1613870114"},{"key":"e_1_3_8_76_2","doi-asserted-by":"publisher","DOI":"10.1080\/19336950.2017.1344801"},{"key":"e_1_3_8_77_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-201X.2007.01690.x"},{"key":"e_1_3_8_78_2","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.25.2.685-698.2005"},{"key":"e_1_3_8_79_2","doi-asserted-by":"publisher","DOI":"10.1523\/JNEUROSCI.1099-23.2023"},{"key":"e_1_3_8_80_2","doi-asserted-by":"publisher","DOI":"10.1186\/1749-8104-5-6"},{"key":"e_1_3_8_81_2","doi-asserted-by":"publisher","DOI":"10.1523\/JNEUROSCI.0947-09.2009"},{"key":"e_1_3_8_82_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0896-6273(00)80373-6"},{"key":"e_1_3_8_83_2","doi-asserted-by":"publisher","DOI":"10.1186\/1749-8104-7-24"},{"key":"e_1_3_8_84_2","doi-asserted-by":"publisher","DOI":"10.1242\/dev.110205"},{"key":"e_1_3_8_85_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12929-019-0584-z"},{"key":"e_1_3_8_86_2","unstructured":"Genome Warehouse. A Public Repository Housing Genome-scale Data. See https:\/\/ngdc.cncb.ac.cn\/gwh\/ (accessed 20 May 2024)."},{"key":"e_1_3_8_87_2","unstructured":"Zou D. 2024 Data for: Comparative genomics sheds new light on the convergent evolution of infrared vision in snakes. Dryad Digital Repository (doi:10.5061\/dryad.z8w9ghxnc)"},{"key":"e_1_3_8_88_2","unstructured":"Zou D Huang S Tian S Kilunda FK Murphy RW Dahn HA et al. 2024 Supplementary material from: Comparative genomics sheds new light on the convergent evolution of infrared vision in snakes. Figshare (doi:10.6084\/m9.figshare.c.7355005)"}],"container-title":["Proceedings of the Royal Society B: Biological Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/royalsocietypublishing.org\/doi\/pdf\/10.1098\/rspb.2024.0818","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/royalsocietypublishing.org\/doi\/full-xml\/10.1098\/rspb.2024.0818","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/royalsocietypublishing.org\/doi\/pdf\/10.1098\/rspb.2024.0818","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,23]],"date-time":"2024-07-23T23:09:08Z","timestamp":1721776148000},"score":1,"resource":{"primary":{"URL":"https:\/\/royalsocietypublishing.org\/doi\/10.1098\/rspb.2024.0818"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,24]]},"references-count":87,"journal-issue":{"issue":"2027","published-print":{"date-parts":[[2024,8]]}},"alternative-id":["10.1098\/rspb.2024.0818"],"URL":"https:\/\/doi.org\/10.1098\/rspb.2024.0818","relation":{},"ISSN":["0962-8452","1471-2954"],"issn-type":[{"value":"0962-8452","type":"print"},{"value":"1471-2954","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,24]]},"assertion":[{"value":"2024-04-08","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-05-30","order":1,"name":"revised","label":"Revised","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-06-19","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-07-24","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"20240818"}}