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Part III - Genomic Perspectives

Published online by Cambridge University Press:  30 July 2022

Edited by
David J. Gower  and
Hussam Zaher
David J. Gower
Affiliation:
Natural History Museum, London
Hussam Zaher
Affiliation:
Universidade de São Paulo
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The Origin and Early Evolutionary History of Snakes , pp. 207 - 268
Publisher: Cambridge University Press
Print publication year: 2022

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References

References

Kerkkamp, H. M. I., Manjunatha Kini, R., Pospelov, A. S., et al., Snake genome sequencing: Results and future prospects. Toxins (Basel), 8 (2016), 360.Google Scholar
Degnan, J. H. and Rosenberg, N. A., Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology and Evolution, 24 (2009), 332–40.CrossRefGoogle ScholarPubMed
Zhang, C., Rabiee, M., Sayyari, E., and Mirarab, S., ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics 19 (2018), 153.Google Scholar
Streicher, J. W. and Wiens, J. J., Phylogenomic analyses reveal novel relationships among snake families. Molecular Phylogenetics and Evolution, 100 (2016), 160–169.Google Scholar
Burbrink, F. T., Grazziotin, F. G., Pyron, R. A., et al., Interrogating genomic-scale data for Squamata (lizards, snakes, and amphisbaenians) shows no support for key traditional morphological relationships. Systematic Biology, 69 (2020), 502–520.CrossRefGoogle ScholarPubMed
Huson, D. H., Rupp, R., and Scornavacca, C., Phylogenetic Networks: Concepts, Algorithms and Applications (Cambridge: Cambridge University Press, 2010).Google Scholar
Brandley, M. C., Warren, D. L., Leaché, A. D., and McGuire, J. A., Homoplasy and clade support. Systematic Biology, 58 (2009), 184–198.Google Scholar
Boore, J. L. and Fuerstenberg, S. I., Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction. Philosophical Transactions of the Royal Society London B, 363 (2008), 1445–1451.Google Scholar
Boore, J. L.,The use of genome-level characteristics for phylogenetic reconstruction. Trends in Ecology and Evolution, 21 (2006), 439–446.CrossRefGoogle Scholar
Kellaway, C. H. and Williams, F. E., The serological and blood relationships of some common Australian snakes. Australian Journal of Experimental Biology and Medical Science, 8 (1931), 123–132.CrossRefGoogle Scholar
Bond, G. C., Serological Studies of the Reptilia: I. Hemagglutinins and hemagglutinogens of snake blood. The Journal of Immunology, 36 (1939), 1–9.Google Scholar
Bond, G. C. and Sherwood, N. P., Serological studies of the Reptilia: II. The hemolytic property of snake serum. The Journal of Immunology, 36 (1939), 11–16.Google Scholar
George, D. W. and Dessauer, H. C., Immunological correspondence of transferrins and the relationships of colubrid snakes. Comparative Biochemistry and Physiology, 33 (1970), 617–627.Google Scholar
Cohen, E., Immunological studies of the serum proteins of some reptiles. The Biological Bulletin, 109(1955), 394–403.CrossRefGoogle Scholar
Crawford, N. G., Faircloth, B. C., McCormack, J. E., et al., More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biology Letters, 8 (2012), 783–6.Google Scholar
Field, D. J., Gauthier, J. A., King, B. L., et al., Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles. Evolution & Development, 16 (2014), 189–196.Google Scholar
Pearson, D. D., Serological and immuno-electrophoretic comparisons among species of snakes. Bulletin of the Serological Museum 36 (1966), 8.Google Scholar
Dessauer, H. C., Fox, W., and Ramírez, J. R., Preliminary attempt to correlate paper-electrophoretic migration of hemoglobins with phylogeny in Amphibia and Reptilia. Archives of Biochemistry and Biophysics, 71 (1957), 11–16.Google Scholar
Dessauer, H. C., Molecular approach to the taxonomy of colubrid snakes. Herpetologica, 23 (1967), 148–155.Google Scholar
Dowling, H. G., Hemipenes and other characters in colubrid classification. Herpetologica, 2(1967), 138–142.Google Scholar
Underwood, G. L., A Contribution to the Classification of Snakes (London: British Museum (Natural History), 1967).Google Scholar
Mao, S. -H. and Dessauer, H. C., Selectively neutral mutations, transferrins and the evolution of natricine snakes. Comparative Biochemistry and Physiology Part A: Physiology, 40 (1971), 669–680.Google Scholar
Mao, S. -H., Chen, B. -Y., and Chang, H. -M., The evolutionary relationships of sea snakes suggested by immunological cross-reactivity of transferrins. Comparative Biochemistry and Physiology Part A: Physiology, 57 (1977), 403–406.Google Scholar
Lawson, R. and Dessauer, H. C., Electrophoretic evaluation of the colubrid genus Elaphe (Fitzinger). Isozyme Bulletin, 14 (1981), 83.Google Scholar
Dowlings, H. G., Highton, R., Maha, G. C., and Maxson, L. R., Biochemical evaluation of colubrid snake phylogeny. Journal of Zoology, 201 (1983), 309–329.Google Scholar
Cadle, J. E., Dessauer, H. C., Gans, C., and Gartside, D. F., Phylogenetic relationships and molecular evolution in uropeltid snakes (Serpentes: Uropeltidae): allozymes and albumin immunology. Biological Journal of the Linnean Society, 40 (1990), 293–320.Google Scholar
Slowinski, J. B., A phylogenetic analysis of the New World coral snakes (Elapidae: Leptomicrurus, Micruroides, and Micrurus) based on allozymic and morphological characters. Journal of Herpetology, 29 (1995), 325–338.CrossRefGoogle Scholar
Cadle, J. E. (1988). Phylogenetic relationships among advanced snakes: a molecular perspective. University of California Publications in Zoology, 119 (1988), 1–77.Google Scholar
Feldman, C. R. and Spicer, G. S. (2002). Mitochondrial variation in sharp-tailed snakes (Contia tenuis): Evidence of a cryptic species. Journal of Herpetology, 36 (2002), 648.Google Scholar
Kraus, F. and Brown, W. M., Phylogenetic relationships of colubroid snakes based on mitochondrial DNA sequences. Zoological Journal of the Linnean Society, 122 (1998), 455–487.CrossRefGoogle Scholar
Slowinski, J. B. and Keogh, J. S., Phylogenetic relationships of elapid snakes based on cytochrome b mtDNA sequences. Molecular Phylogenetics and Evolution, 15 (2000), 157–164.CrossRefGoogle ScholarPubMed
Burbrink, F. T., Lawson, R., and Slowinski, J. B., Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): a critique of the subspecies concept. Evolution, 54 (2000), 2107–2118.Google Scholar
Funk, D. J. and Omland, K. E., Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution, and Systematics, 34 (2003), 397–423.Google Scholar
Rubinoff, D. and Holland, B. S., Between two extremes: mitochondrial DNA is neither the panacea nor the nemesis of phylogenetic and taxonomic inference. Systematic Biology, 54 (2005), 952–961.Google Scholar
Lawson, R., Slowinski, J. B., Crother, B. I., and Burbrink, F. T., Phylogeny of the Colubroidea (Serpentes): new evidence from mitochondrial and nuclear genes. Molecular Phylogenetics and Evolution, 37 (2005), 581–601.CrossRefGoogle ScholarPubMed
Wiens, J. J., Kuczynski, C. A., Smith, S. A., et al., Branch lengths, support, and congruence: Testing the phylogenomic approach with 20 nuclear loci in snakes. Systematic Biology, 57 (2008), 420–431.CrossRefGoogle ScholarPubMed
Kubatko, L. S., Gibbs, H. L., and Bloomquist, E. W., Inferring species-level phylogenies and taxonomic distinctiveness using multilocus data in Sistrurus rattlesnakes. Systematic Biology, 60 (2011), 393–409.Google Scholar
Sanders, K. L., Lee, M. S. Y., Mumpuni, T. Bertozzi, and Rasmussen, A. R., Multilocus phylogeny and recent rapid radiation of the viviparous sea snakes (Elapidae: Hydrophiinae). Molecular Phylogenetics and Evolution, 66 (2013), 575–591.Google Scholar
Streicher, J. W. and Ruane, S., Phylogenomics of snakes. In eLS . Chichester: John Wiley & Sons Ltd, 2018, DOI: 10.1002/9780470015902.a0027476).Google Scholar
Faircloth, B. C., McCormack, J. E., Crawford, N. G., et al., Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Systematic Biology, 61 (2012), 717–726.Google Scholar
Lemmon, A. R., Emme, S. A., and Lemmon, E. M., Anchored hybrid enrichment for massively high-throughput phylogenomics. Systematic Biology, 61 (2012), 727–44.Google Scholar
Singhal, S., Grundler, M., Colli, G., and Rabosky, D. L., Squamate conserved loci (SqCL): A unified set of conserved loci for phylogenomics and population genetics of squamate reptiles. Molecular Ecology Resources, 17 (2017), e12–e24.Google Scholar
Karin, B. R., Gamble, T., and Jackman, T. R., Optimizing phylogenomics with rapidly evolving long exons: Comparison with anchored hybrid enrichment and ultraconserved element. Molecular Biology and Evolution, 37 (2020), 904–922.CrossRefGoogle Scholar
Chen, X., Lemmon, A. R., Lemmon, E. M., Pyron, R. A., and Burbrink, F. T., Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes. Molecular Phylogenetics and Evolution, 111 (2017), 206–218.Google Scholar
Castoe, T. A., Spencer, C. L., and Parkinson, C. L., Phylogeographic structure and historical demography of the western diamondback rattlesnake (Crotalus atrox): A perspective on North American desert biogeography. Molecular Phylogenetics and Evolution, 42 (2007), 193–212.Google Scholar
Schield, D. R., Card, D. C., Hales, N. R., et al., The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes. Genome Research, 29 (2019), 590–601.Google Scholar
Singhal, S., Colston, T. J., Grundler, M. R., et al., Congruence and conflict in the higher-level phylogenetics of squamate reptiles: An expanded phylogenomic perspective. Systematic Biology, 70 (2021), 542–557.Google Scholar
Sims, G. E., Jun, S. -E., Wu, G. A., and Kim, S. -H., Whole-genome phylogeny of mammals: Evolutionary information in genic and nongenic regions. Proceedings of the National Academy of Sciences USA, 106 (2009), 1777–17082.Google Scholar
Castoe, T. A., de Koning, A. P. J., K. T. Hall, et al., The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences USA, 110 (2013), 20645–20650.Google Scholar
Giorgianni, M. W., Dowell, N. L., Griffin, S., et al., The origin and diversification of a novel protein family in venomous snakes. Proceedings of the National Academy of Sciences USA, 117 (2020), 10911–10920.Google Scholar
Pasquesi, G. I. M., Adams, R. H., Card, D. C., et al., Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals. Nature Communications, 9 (2018), 2774.CrossRefGoogle ScholarPubMed
Gilbert, C., Meik, J. M., Dashevsky, D., et al., Endogenous hepadaviruses, bornaviruses and circoviruses in snakes. Proceedings of the Royal Society B, 281 (2014), 1122.Google Scholar
Augstenová, B., Johnson Pokorná, M., Altmanová, M., et al., ZW, XY, and yet ZW: Sex chromosome evolution in snakes even more complicated. Evolution, 72 (2018), 1701–1707.Google Scholar
Palvildis, P., Jensen, J. D., Stephan, W., and Stamatakis, A., A critical assessment of storytelling: gene ontology categories and the importance of validating genome scans. Molecular Biology and Evolution, 29 (2012), 3237–3248.Google Scholar
Archie, J. W., Methods for coding variable morphological features for numerical taxonomic analysis. Systematic Zoology, 34 (1985), 326–345.Google Scholar
Thorpe, R. S., Coding morphometric characters for constructing distance Wagner networks. Evolution, 38 (1984), 244–255.Google Scholar
Freudenstein, J. V., Characters, states and homology. Systematic Biology, 54 (2005), 965–973.Google Scholar
Yin, W., Wang, Z-J., Li, Q-Y., et al., Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper. Nature Communications, 7 (2016), 13107.Google Scholar
Li, J. -T., Gao, Y. -D., Xie, L. , et al., Comparative genomics investigation of high elevation adaptation in ectothermic snakes. Proceedings of the National Academy of Sciences USA, 115 (2018), 8406–8411.Google Scholar
Card, D. C., Adams, R. H., Schield, D. R., et al., Genomic basis of convergent island phenotypes in boa constrictors. Genome Biology and Evolution, 11 (2019), 3123–3143.Google Scholar
Organ, C. L., Godínez Moreno, R., and Edwards, S. V., Three tiers of genome evolution in reptiles. Integrative and Comparative Biology, 48 (2008), 494–504.Google Scholar
Kriegs, J. O., Churalov, G., Kiefmann, M., et al., Retrotransposed elements as archives for the evolutionary history of placental mammals. PLoS Biology, 4 (2006), e91.Google Scholar
Vitales, D., Garcia, S., and Dodsworth, S., Reconstructing phylogenetic relationships based on repeat sequence similarities. Molecular Phylogenetics and Evolution, 147 (2020), 106766.Google Scholar
Smith, E. N. and Gutberlet, R. L. Jr., Generalized frequency coding: A method of preparing polymorphic multistate characters for phylogenetic analysis. Systematic Biology, 50 (2001), 156–169.Google Scholar
Wiens, J. J., Character analysis in morphological phylogenetics: problems and solutions. Systematic Biology, 50 (2001), 689–699.CrossRefGoogle ScholarPubMed
Lawing, A. M., Meik, J. M., and Schargel, W. E., Coding meristic characters for phylogenetic analysis: A comparison of step-matrix gap weighting and generalized frequency coding. Systematic Biology, 57 (2008), 167–173.Google Scholar
Wiens, J. J., Polymorphic characters in phylogenetic systematics. Systematic Biology, 44 (1995), 482–500.Google Scholar
Schliep, K. P., Phangorn: phylogenetic analysis in R. Bioinformatics, 27 (2011), 592–593.Google Scholar
R Development Core Team, R: A Language and Environment for Statistical Computing (Vienna: R Foundation for Statistical Computing, 2019).Google Scholar
Jukes, T. H. and Cantor, C. R., Evolution of protein molecules. In Munro, H. N., ed. Mammalian protein metabolism. Volume 3 (New York: Academic Press, 1969), pp. 21–132.CrossRefGoogle Scholar
Murphy, J. C. and Sanders, K. L., First molecular evidence for the phylogenetic placement of the enigmatic snake genus Brachyorrhos (Serpentes: Caenophidia). Molecular Phylogenetics and Evolution, 61 (2011), 953–957.Google Scholar
Lawson, R., Slowinski, J. B., and Burbrink, F. T., A molecular approach to discerning the phylogenetic placement of the enigmatic snake Xenophidion schaeferi among the Alethinophidia. Journal of Zoology, 263 (2004), 285–294.Google Scholar
Deepak, V., Ruane, S., and Gower, D. J., A new subfamily of fossorial colubroid snakes from the Western Ghats of peninsular India. Journal of Natural History, 52 (2018), 2919–2934.Google Scholar
Heise, P. J., Maxson, L. R., Dowling, H. G., and Hedges, S. B., Higher-level snake phylogeny inferred from mitochondrial DNA sequences of 12S rRNA and 16S rRNA genes. Molecular Biology and Evolution, 12 (1995), 259–265.Google Scholar
Dowling, H. G., Hass, C. A., Hedges, S. B., and Highton, R., Snake relationships revealed by slow evolving proteins: a preliminary survey. Journal of Zoology, 240 (1996), 1–28.Google Scholar
Slowinski, J. B. and Lawson, R., Snake phylogeny: evidence from nuclear and mitochondrial genes. Molecular Phylogenetics and Evolution, 24 (2002), 194–202.Google Scholar
Pyron, R. A., Burbrink, F. T., Colli, G. R., et al., The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees. Molecular Phylogenetics and Evolution, 58 (2011), 329–342.Google Scholar
Pyron, R. A., Kandambi, H. K. D., Hendry, C. R., et al., Genus-level phylogeny of snakes reveals the origins of species richness in Sri Lanka. Molecular Phylogenetics and Evolution, 66 (2013), 969–978.Google Scholar
Wiens, J. J., Hutter, C. R., Mulcahy, D. G., et al., Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species. Biology Letters, 8 (2012), 1043–1046.Google Scholar
Figueroa, A., McKelvy, A. D., Grismer, L. L., Bell, C. D., and Lailvaux, S. P., A species-level phylogeny of extant snakes with description of a new colubrid subfamily and genus. PloS ONE, 11 (2016), e0161070.CrossRefGoogle ScholarPubMed
Zaher, H., Murphy, R. W., Arredondo, J. C., et al., Large-scale molecular phylogeny, morphology, divergence-time estimation, and the fossil record of advanced caenophidian snakes (Squamata: Serpentes). PloS ONE, 14 (2019), e0216148.Google Scholar
Zheng, Y. and Wiens, J. J., Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Molecular Phylogenetics and Evolution, 94 (2016), 537–547.Google Scholar
Miralles, A., Marin, L., Markus, D., et al., Molecular evidence for the paraphyly of Scolecophidia and its evolutionary implications. Journal of Evolutionary Biology, 31 (2018), 1782–1793.Google Scholar
Pyron, R. A., R. A., Burbrink, F. T., and Wiens, J. J., A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evolutionary Biology, 13 (2013), 93.Google Scholar
Rokas, A. and Carroll, S. B., Bushes in the tree of life. PLoS Biology, 4 (2006), e352.Google Scholar
Estes, R. K., de Queiroz, K., and Gauthier, J., Phylogenetic relationships within Squamata. In Estes, R. and Pregill, G., eds., Phylogenetic Relationships of the Lizard Families (Stanford: Stanford University Press 1988), pp.119–281.Google Scholar
Saint, K. M., Austin, C. C., Donnellan, S. C., and Hutchinson, M. N., C-mos, a nuclear marker useful for squamate phylogenetic analysis. Molecular Phylogenetics and Evolution, 10 (1998), 259–263.Google Scholar
Townsend, T. M., Larson, A., Louis, E., and Macey, J. R., Molecular phylogenetics of Squamata: the position of snakes, amphisbaenians, and dibamids, and the root of the squamate tree. Systematic Biology, 53 (2004), 735–757.Google Scholar
Vidal, N. and Hedges, S. B., The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes. Comptes Rendus Biologies, 328 (2005), 1000–1008.Google Scholar
Streicher, J. W. and Wiens, J. J., Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families. Biology Letters, 13 (2017), 20170393.Google Scholar
Siegel, D. S., Miralles, A., and Aldridge, R. D., R. D., Controversial snake relationships supported by reproductive anatomy. Journal of Anatomy, 218 (2011), 342–348.Google Scholar
Schield, D. R., Card, D. C., Adams, R. H., et al., Incipient speciation with biased gene flow between two lineages of the Western Diamondback Rattlesnake (Crotalus atrox). Molecular Phylogenetics and Evolution, 83 (2015), 213–223.Google Scholar
Williams, T. A., Szöllosi, G. J., Spang, A., et al., Integrative modeling of gene and genome evolution roots the archaeal tree of life. Proceedings of the National Academy of Sciences USA, 114 (2017), E4602–4611.CrossRefGoogle ScholarPubMed
Ruane, S. and Austin, C. C., Phylogenomics using formalin-fixed and 100+ year-old intractable natural history specimens. Molecular Ecology Resources, 17 (2017), 1003–1008.Google Scholar
Ruane, S., New data from old specimens. Copeia (in press).Google Scholar
Feigin, C. Y., Newton, A. H., Doronina, L., et al., Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore. Nature Ecology and Evolution, 2 (2018), 182–192.Google Scholar
Shibata, H., Chijiwa, T., Oda-Ueda, N., et al., The habu genome reveals accelerated evolution of venom protein genes. Scientific Reports, 8 (2018), 11300.Google Scholar
Adler, K., Contributions to the History of Herpetology, Volume 3 (Vancouver: Society for the Study of Amphibians and Reptiles, 1012), 564 pp.Google Scholar
Thorpe, R. S., Garth Underwood (1919–2002): A vision of reptile systematics. Herpetological Review, 34 (2003), 6–7.Google Scholar
Liner, E. A. and Cole, C. J., Herbert C. Dessauer. Copeia, 2003 (2003), 195–199.Google Scholar
Bradnam, K. R., Fass, J. N., Alexandrov, A., et al., Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience, 2 (2013), 2047-217x-2-10.Google Scholar
McGlothlin, J. W., Chuckalovcak, J. P., Janes, D. E., et al., Parallel evolution of tetrodotoxin resistance in three voltage-gated sodium channel genes in the garter snake Thamnophis sirtalis . Molecular Biology and Evolution, 31 (2014), 2836–2846.Google Scholar
Ullate-Agote, A., Milinkovitch, M. C., and Tzikia, A. C., The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates. International Journal of Developmental Biology, 58 (2014), 881–888.Google Scholar
Earl, S. T. H., Birrell, G. W., Wallis, T. P., et al., Post-translational modification accounts for the presence of varied forms of nerve growth factor in Australian elapid snake venoms. Proteomics, 6 (2006), 6554–6665.Google Scholar
Kishida, T., Go, Y., Tatsumoto, S., et al., Loss of olfaction in sea snakes provides new perspectives on the aquatic adaptation of amniotes. Proceedings of the Royal Society B, 286 (2019), 2019.1828.Google Scholar
Peng, C., Ren, J-L., Deng, C., et al., The genome of Shaw’s seasnake (Hydrophis curtus) reveals secondary adaptation to its marine environment. Molecular Biology and Evolution, 37 (2020), 1744–1760.Google Scholar
Suryamohan, K., Krishnankutty, S. P., Guillory, J., et al., The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins. Nature Genetics, 52 (2020), 106–117.Google Scholar
Vonk, F. J., Casewell, N. R., Henkel, C. V., et al., The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proceedings of the National Academy of Sciences USA, 110 (2013), 20651–20656.Google Scholar
Aird, S. D., Arora, J., Barua, A., et al., Population genomic analysis of a pitviper reveals microevolutionary forces underlying venom chemistry. Genome Biology and Evolution, 9 (2018), 2640–2649.Google Scholar
van Hoek, M. L., Prickett, M. D., Settlage, R. E., et al., The Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clusters. BMC Genomics, 20 (2019), 684.Google Scholar
Georges, A., Li, Q., Lian, J., et al., High-coverage sequencing and annotate assembly of the genome of the Australian dragon lizard Pogona vitticeps . GigaScience, 4 (2015), 45.Google Scholar
Alföldi, J., Di Palma, F., Grabherr, M., et al., The genome of the green anole lizards and a comparative analysis with birds and mammals. Nature, 477 (2011), 587–591.Google Scholar
Liu, Y., Zhou, Q., Wang, Y., et al., Gekko japonicus genome reveals evolution of adhesive toe pads and tail regeneration. Nature Communications, 6 (2015), 10033.Google Scholar

References

Castoe, T. A., De Koning, A. P. J., Hall, K. T, et al., The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences USA, 110 (2013), 20645–20650.Google Scholar
Vonk, F. J., Casewell, N. R., Henkel, C. V., et al., The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proceedings of the National Academy of Sciences USA, 110 (2013), 20651–20656.Google Scholar
Ullate-Agote, A., Milinkovitch, M. C., and Tzikia, A. C., The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates. International Journal of Developmental Biology, 58 (2014), 881–888.Google Scholar
Emerling, C. A., Genomic regression of claw keratin, taste receptor and light-associated genes provides insights into biology and evolutionary origins of snakes. Molecular Phylogenetics and Evolution, 115 (2017), 40–49.Google Scholar
Infante, C. R., Mihala, A. G., Park, S., et al., Shared enhancer activity in the limbs and phallus and functional divergence of a limb-genital cis-regulatory element in snakes. Developmental Cell, 35 (2015), 107–119.Google Scholar
Kvon, E. Z., Kamneva, O. K., Melo, U. S., et al., Progressive Loss of function in a limb enhancer during snake evolution. Cell, 167 (2016), 633-642.e11.Google Scholar
Kishida, T., Go, Y., Tatsumoto, S., et al., Loss of olfaction in sea snakes provides new perspectives on the aquatic adaptation of amniotes. Proceedings of the Royal Society B, 286 (2019), 2019.1828.Google Scholar
Zhong, H., Shang, S., Wu, X., et al., Genomic evidence of bitter taste in snakes and phylogenetic analysis of bitter taste receptor genes in reptiles. PeerJ, 5 (2017), e3708.Google Scholar
Perry, B. W., Card, D. C., McGlothlin, J. W., et al., Molecular adaptations for sensing and securing prey and insight into amniote genome diversity from the garter snake genome. Genome Biology and Evolution, 10 (2018), 2110–2129.Google Scholar
Meiri, S., Traits of lizards of the world: Variation around a successful evolutionary design. Global Ecology and Biogeography, 27 (2018), 1168–1172.Google Scholar
Grundler, M. C., SquamataBase: A natural history database and R package for comparative biology of snake feeding habits. Biodiversity Data Journal, 8 (2020), e49943.Google Scholar
Rowe, T., DigiMorph. www.DigiMorph.org (2020)Google Scholar
Chenand, Y. H., and Zhao, H., Evolution of digestive enzymes and dietary diversification in birds. PeerJ, 7 (2019), e6840.Google Scholar
German, D. P., Nagle, B. C., Villeda, J. M., et al., Evolution of herbivory in a carnivorous clade of minnows (Teleostei: Cyprinidae): Effects on gut size and digestive physiology. Physiological and Biochemical Zoology, 83 (2010), 1–18.Google Scholar
Jeuniaux, C., Chitinase: an addition to the list of hydrolases in the digestive tract of vertebrates. Nature, 192 (1961), 135–136.Google Scholar
Emerling, C. A., Delsuc, F., and Nachman, M. W., Chitinase genes (CHIAs) provide genomic footprints of a post-Cretaceous dietary radiation in placental mammals. Science Advances, 4 (2018), eaar6478.Google Scholar
Janiak, M. C., Chaney, M. E., and Tosi, A. J., Evolution of acidic mammalian chitinase genes (CHIA) is related to body mass and insectivory in primates. Molecular Biology and Evolution, 35 (2018), 607–622.Google Scholar
Wang, K., Tian, S., Galindo-González, J., et al., Molecular adaptation and convergent evolution of frugivory in Old World and neotropical fruit bats. Molecular Ecology, 29 (2020), 4366–4381.Google Scholar
Boot, R. G., Blommaart, E. F. C., Swart, E., et al., Identification of a novel acidic mammalian chitinase distinct from chitotriosidase. Journal of Biological Chemistry, 276 (2001), 6770–6778.Google Scholar
Strobel, S., Roswag, A., Becker, N. I., Trenczek, T. E., and Encarnação, J. A., Insectivorous bats digest chitin in the stomach using acidic mammalian chitinase. PLoS One, 8 (2013), e72770.Google Scholar
Ohno, M., Kimura, M., Miyakazi, H., et al. Acidic mammalian chitinase is a proteases-resistant glycosidase in mouse digestive system. Scientific Reports, 6 (2016), 37756.Google Scholar
Fong, D., Kane, T., and Culver, D., Vestigialization and loss of nonfunctional characters. Annual Review of Ecology and Systematics, 26 (1995), 249–268.Google Scholar
Emerling, C. A. and Springer, M. S., Eyes underground: Regression of visual protein networks in subterranean mammals. Molecular Phylogenetics and Evolution, 78 (2014), 260–270.Google Scholar
Meredith, R. W., Zhang, G., Gilbert, M. T. P., Jarvis, E. D., and Springer, M. S., Evidence for a single loss of mineralized teeth in the common avian ancestor. Science, 346 (2014), 1254390.CrossRefGoogle ScholarPubMed
Albalat, R. and Cañestro, C., Evolution by gene loss. Nature Reviews Genetics, 17 (2016), 379–391.Google Scholar
Feng, P., Zheng, J., Rossiter, S. J., Wang, D., and Zhao, H., Massive losses of taste receptor genes in toothed and baleen whales. Genome Biology and Evolution, 6 (2014), 1254–1265.Google Scholar
Marsh, R. S., Moe, C., Lomneth, R. B., Fawcett, J. D., and Place, A., Characterization of gastrointestinal chitinase in the lizard Sceloporus undulatus garmani (Reptilia: Phrynosomatidae). Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 128 (2001), 675–682.Google Scholar
Koludarov, I., Jackson, T. N. W., op den Brouw, B., et al., Enter the dragon: The dynamic and multifunctional evolution of Anguimorpha lizard venoms. Toxins, 9 (2017), 242.Google Scholar
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D., Basic local alignment search tool. Journal of Molecular Biology, 215 (1990), 403–410.Google Scholar
Kearse, M., Moir, R., Wilson, A., et al., Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28 (2012), 1647–1649.Google Scholar
Burbrink, F. T., Grazziotin, F. G., Pyron, R. A., et al., Interrogating genomic-scale data for Squamata (lizards, snakes, and amphisbaenians) shows no support for key traditional morphological relationships. Systematic Biology, 69 (2020), 502–520.Google Scholar
Edgar, R. C., MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32 (2004), 1792–1797.Google Scholar
Stamatakis, A., RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30 (2014), 1312–1313.Google Scholar
Olland, A. M., Strand, J., Presman, E., et al., Triad of polar residues implicated in pH specificity of acidic mammalian chitinase. Protein Science, 18 (2009), 569–578.Google Scholar
Tjoelker, L. W., Gosting, L., Frey, S., et al., Structural and functional definition of the human chitinase chitin-binding domain. Journal of Biological Chemistry, 275 (2000), 514–520.Google Scholar
Hussain, M. and Wilson, J. B., New paralogues and revised time line in the expansion of the vertebrate GH18 family. Journal of Molecular Evolution, 76 (2013), 240–260.Google Scholar
Miller, M. A., Pfeiffer, W., and Schwartz, T., Creating the CIPRES Science Gateway for inference of large phylogenetic trees. 2010 Gateway Computing Environments Workshop (GCE) (2010), 1–8.Google Scholar
Chen, J. M., Cooper, D. N., Chuzhanova, N., Férec, C., and Patrinos, G. P., Gene conversion: Mechanisms, evolution and human disease. Nature Reviews Genetics, 8 (2007), 762–775.Google Scholar
Renkema, G. H., Boot, R. G., Au, F. L., et al., Chitotriosidase a chitinase, and the 39-kDa human cartilage glycoprotein, a chitin-binding lectin, are homologues of family 18 glycosyl hydrolases secreted by human macrophages. European Journal of Biochemistry, 251 (1998), 504–509.Google Scholar
Irisarri, I., Baurain, D., Brinkmann, H., et al., Phylotranscriptomic consolidation of the jawed vertebrate timetree. Nature Ecology and Evolution, 1 (2017), 1370–1378.Google Scholar
Zheng, Y. and Wiens, J. J., Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Molecular Phylogenetics and Evolution, 94 (2016), 537–547.Google Scholar
Lozano-Fernandez, J., Tanner, A. R., Puttick, M. N., et al., A Cambrian–Ordovician terrestrialization of arachnids. Frontiers in Genetics, 11 (2020), 182.Google Scholar
Lins, L. S. F., Ho, S. Y. W., and Lo, N., An evolutionary timescale for terrestrial isopods and a lack of molecular support for the monophyly of Oniscidea (Crustacea: Isopoda). Organisms, Diversity and Evolution, 17 (2017), 813–820.Google Scholar
Misof, B., Liu, S., Meusemann, K., et al., Phylogenomics resolves the timing and pattern of insect evolution. Science, 346 (2014), 763–767.Google Scholar
Fernández, R., Edgecombe, G. D., and Giribet, G., Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies. Scientific Reports, 8 (2018), 83 Google Scholar
Modesto, S. P., Scott, D. M., and Reisz, R. R., Arthropod remains in the oral cavities of fossil reptiles support inference of early insectivory. Biology Letters, 5 (2009), 838–840.Google Scholar
Melstrom, K. M., The relationship between diet and tooth complexity in living dentigerous saurians. Journal of Morphology, 278 (2017), 500–522.Google Scholar
Martill, D. M., Tischlinger, H., and Longrich, N. R., A four-legged snake from the Early Cretaceous of Gondwana. Science, 349 (2015), 416–419.Google Scholar
Caldwell, M. W., Nydam, R. L., Palci, A., and Apesteguía, S., The oldest known snakes from the Middle Jurassic-Lower Cretaceous provide insights on snake evolution. Nature Communications, 6 (2015), 5996.Google Scholar
Longrich, N. R., Bhullar, B. A. S., and Gauthier, J. A., A transitional snake from the Late Cretaceous period of North America. Nature, 488 (2012), 205–208.CrossRefGoogle ScholarPubMed
Caldwell, M. W. and Lee, M. S. Y., A snake with legs from the marine Cretaceous of the Middle East. Nature, 386 (1997), 705–708.Google Scholar
Haas, G., On a new snakelike reptile from the Lower Cenomanian of Ein Jabrud, near Jerusalem. Bulletin du Muséum National d’Histoire Naturelle Paris, 1 (1979), 51–64.Google Scholar
Wilson, J. A., Mohabey, D. M., Peters, S. E., and Head, J. J., Predation upon hatchling dinosaurs by a new snake from the Late Cretaceous of India. PLoS Biology, 8 (2010), e1000322.Google Scholar
Sanders, J. G., Beichman, A. C., Roman, J., et al., Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores. Nature Communications, 6 (2015), 8285.Google Scholar

References

Schendel, V., Rash, L. D., Jenner, R. A., and Undheim, E. A. B., The diversity of venom: the importance of behavior and venom system morphology in understanding its ecology and evolution. Toxins (Basel), 11 (2019), 666.Google Scholar
Fry, B. G., Roelants, K., Champagne, D. E., et al., The toxicogenomic multiverse: convergent recruitment of proteins into animal venoms. Annual Review of Genomics and Human Genetics, 10 (2009), 483–511.Google Scholar
Fry, B. G., From genome to ‘venome’: molecular origin and evolution of the snake venom proteome inferred from phylogenetic analysis of toxin sequences and related body proteins. Genome Research, 15 (2005), 403–420.Google Scholar
Fry, B. G., Scheib, H., van der Weerd, L., et al., Evolution of an arsenal: structural and functional diversification of the venom system in the advanced snakes (Caenophidia). Molecular and Cellular Proteomics, 7 (2008), 215–46.Google Scholar
Fry, B. G., Vidal, N., van der Weerd, L., Kochva, E., and Renjifo, C., Evolution and diversification of the Toxicofera reptile venom system. Journal of Proteomics, 72 (2009), 127–136.Google Scholar
Vidal, N. and Hedges, S. B.. The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes. Comptes Rendus Biologies, 328 (2005), 1000–1008.Google Scholar
Kochva, E., Oral glands of the Reptilia. Biology of the Reptilia. 8 (1978), 43–162.Google Scholar
Pough, F. H., Andrews, R. M., Cadle, J. E., et al., Herpetology 3rd edn. (New Jersey: Prentice Hall, 2004).Google Scholar
Kardong, K. V., Weinstein, S. A., and Smith, T. L., Reptile venom glands: form, function, and future. In Mackessy, S. P., ed., Handbook of Venoms and Toxins of Reptiles (Boca Raton, FL: CRC Press, 2009), pp. 65–91.Google Scholar
Burbrink, F. T., Grazziotin, F. G., Pyron, R. A., et al. Interrogating genomic-scale data for Squamata (lizards, snakes, and amphisbaenians) shows no support for key traditional morphological relationships. Systematic Biology, 69 (2020), 502–520.Google Scholar
Daltry, J. C., Wüster, W., and Thorpe, R. S., Diet and snake venom evolution. Nature, 379 (1996), 537–40.Google Scholar
Gibbs, H. L., Sanz, L., Chiucchi, J. E., Farrell, T. M., and Calvete, J. J., Proteomic analysis of ontogenetic and diet-related changes in venom composition of juvenile and adult Dusky Pigmy rattlesnakes (Sistrurus miliarius barbouri). Journal of Proteomics, 74 (2011), 2169–2179.Google Scholar
Zancolli, G., Calvete, J. J., Cardwell, M. D., et al., When one phenotype is not enough: divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species. Proceedings of the Royal Society B, 286 (2019), 20182735.Google Scholar
Casewell, N. R., Jackson, T. N. W., Laustsen, A. H., and Sunagar, K., Causes and Consequences of Snake Venom Variation. Trends in Pharmacological Sciences, 41 (2020), 570–581.Google Scholar
Jackson, T. N. W., Jouanne, H., and Vidal, N., Snake venom in context: Neglected clades and concepts. Frontiers in Ecology and Evolution, 7 (2019), 332.Google Scholar
Modica, M. V., Sunagar, K., Holford, M., and Dutertre, S.,. Diversity and evolution of animal venoms: Neglected targets, ecological iInteractions, future perspectives. Frontiers in Ecology and Evolution, 8 (2020), 65.Google Scholar
Cardoso, F. C., Ferraz, C. R., Arrahman, A., et al., Multifunctional toxins in snake venoms and therapeutic implications: from pain to hemorrhage and necrosis. Frontiers in Ecology and Evolution, 7 (2019), 218.Google Scholar
Casewell, N. R., Harrison, R. A., Wüster, W., and Wagstaff, S. C., Comparative venom gland transcriptome surveys of the saw-scaled vipers (Viperidae: Echis) reveal substantial intra-family gene diversity and novel venom transcripts. BMC Genomics, 10 (2009), 564.Google Scholar
Currier, R. B., Harrison, R. A., Rowley, P. D., Laing, G. D., and Wagstaff, S. C., Intra-specific variation in venom of the African Puff Adder (Bitis arietans): Differential expression and activity of snake venom metalloproteinases (SVMPs). Toxicon, 55 (2010), 864–873.Google Scholar
Senji Laxme, R. R., Khochare, S., de Souza, H. F., et al., Beyond the ‘big four’: Venom profiling of the medically important yet neglected Indian snakes reveals disturbing antivenom deficiencies. PLoS Neglected Tropical Diseases, 13 (2019), e0007899.Google Scholar
Sunagar, K., Undheim, E. A., Scheib, H., et al., Intraspecific venom variation in the medically significant Southern Pacific Rattlesnake (Crotalus oreganus helleri): biodiscovery, clinical and evolutionary implications. Journal of Proteomics, 99 (2014), 68–83.Google Scholar
Jackson, T. N., Koludarov, I., Ali, S. A., et al., Rapid radiations and the race to redundancy: An investigation of the evolution of Australian elapid snake venoms. Toxins (Basel), 8 (2016), 309.Google Scholar
Mackessy, S. P., Williams, K., and Ashton, K. G., Ontogenetic variation in venom composition and diet of Crotalus oreganus concolor: a case of venom paedomorphosis? Copeia, 2003 (2003), 769–782.Google Scholar
Rokyta, D. R., Margres, M. J., Ward, M. J., and Sanchez, E. E., The genetics of venom ontogeny in the eastern diamondback rattlesnake (Crotalus adamanteus). PeerJ, 5 (2017), e3249.Google Scholar
Sanz, L., Gibbs, H. L., Mackessy, S. P., and Calvete, J. J., Venom proteomes of closely related Sistrurus rattlesnakes with divergent diets. Journal of Proteome Research. 5 (2006), 2098–2112.Google Scholar
Barlow, A., Pook, C. E., Harrison, R. A., and Wüster, W., Coevolution of diet and prey-specific venom activity supports the role of selection in snake venom evolution. Proceedings of the Royal Society B, 276 (2009), 2443–2449.Google Scholar
Mackessy, S. P., Sixberry, N. M., Heyborne, W. H., and Fritts, T., Venom of the Brown Treesnake, Boiga irregularis: ontogenetic shifts and taxa-specific toxicity. Toxicon, 47 (2006), 537–548.CrossRefGoogle ScholarPubMed
Li, M., Fry, B. G., and Kini, R. M., Eggs-only diet: its implications for the toxin profile changes and ecology of the marbled sea snake (Aipysurus eydouxii). Journal of Molecular Evolution, 60 (2005), 81–89.Google Scholar
Durban, J., Perez, A., Sanz, L., et al., Integrated ‘omics’ profiling indicates that miRNAs are modulators of the ontogenetic venom composition shift in the Central American rattlesnake, Crotalus simus simus. BMC Genomics, 14 (2013), 234.Google Scholar
Ujvari, B., Casewell, N. R., Sunagar, K., et al., Widespread convergence in toxin resistance by predictable molecular evolution. Proceedings of the National Academy of Sciences of the USA, 112 (2015), 11911–11916.Google Scholar
Rowe, A. H., Xiao, Y., Rowe, M. P., Cummins, T. R., and Zakon, H. H., Voltage-gated sodium channel in grasshopper mice defends against bark scorpion toxin. Science, 342 (2013), 441–446.Google Scholar
Holding, M. L., Drabeck, D. H., Jansa, S. A., and Gibbs, H. L., Venom resistance as a model for understanding the molecular basis of complex coevolutionary adaptations. Integrative and Comparative Biology, 56 (2016), 1032–1043.Google Scholar
Biardi, J. E., Chien, D. C., and Coss, R. G.. California ground squirrel (Spermophilus beecheyi) defenses against rattlesnake venom digestive and hemostatic toxins. Journal of Chemical Ecology, 32 (2006), 137–154.Google Scholar
Jansa, S. A. and Voss, R. S., Adaptive evolution of the venom-targeted vWF protein in opossums that eat pitvipers. PLoS One, 6 (2011), e20997.Google Scholar
Holding, M. L., Biardi, J. E., and Gibbs, H. L., Coevolution of venom function and venom resistance in a rattlesnake predator and its squirrel prey. Proceedings of the Royal Society B, 283 (2016), 20152841.Google Scholar
Barchan, D., Kachalsky, S., Neumann, D., et al., How the mongoose can fight the snake: the binding site of the mongoose acetylcholine receptor. Proceedings of the National Academy of Sciences of the USA, 89 (1992), 7717–7721.Google Scholar
Drabeck, D. H., Dean, A. M., and Jansa, S. A.. Why the honey badger don’t care: Convergent evolution of venom-targeted nicotinic acetylcholine receptors in mammals that survive venomous snake bites. Toxicon, 99 (2015), 68–72.Google Scholar
Sunagar, K., Casewell, N., Varma, S., et al., Deadly innovations: unraveling the molecular evolution of animal venoms. In Gopalakrishnakone, P. and Calvete, J. J., eds., Venom Genomics and Proteomics (Dordrecht: Springer, 2014), pp. 1–23.Google Scholar
Sunagar, K. and Moran, Y.. The rise and fall of an evolutionary innovation: Contrasting strategies of venom evolution in ancient and young animals. PLoS Genetics, 11 (2015), e1005596.Google Scholar
Girish, K. S., Jagadeesha, D. K., Rajeev, K. B., and Kemparaju, K.. Snake venom hyaluronidase: an evidence for isoforms and extracellular matrix degradation. Molecular and Cellular Biochemistry, 240 (2002), 105–110.Google Scholar
Tu, A. T. and Hendon, R. R., Characterization of lizard venom hyaluronidase and evidence for its action as a spreading factor. Comparative Biochemistry and Physiology B, 76 (1983), 377–383.Google Scholar
Katkar, G. D., Sundaram, M. S., NaveenKumar, S. K., et al., NETosis and lack of DNase activity are key factors in Echis carinatus venom-induced tissue destruction. Nature Communications, 7 (2016), 11361.Google Scholar
Lu, Q., Clemetson, J. M., and Clemetson, K. J.. Snake venoms and hemostasis. Journal of Thrombosis and Haemostasis, 3 (2005), 1791–1799.Google Scholar
Xiong, S. and Huang, C.. Synergistic strategies of predominant toxins in snake venoms. Toxicology Letters, 287 (2018), 142–154.Google Scholar
Modahl, C. M. and Mackessy, S. P., Venoms of rear-fanged snakes: New proteins and novel activities. Frontiers in Ecology and Evolution, 7 (2019), 279.Google Scholar
Tasoulis, T. and Isbister, G. K., A review and database of snake venom proteomes. Toxins (Basel), 9 (2017), 9.Google Scholar
Fry, B. G., Undheim, E. A., Ali, S. A, et al., Squeezers and leaf-cutters: differential diversification and degeneration of the venom system in toxicoferan reptiles. Molecular and Cellular Proteomics, 12 (2013), 1881–1899.Google Scholar
Sunagar, K., Jackson, T. N., Undheim, E. A., et al., Three-fingered RAVERs: Rapid Accumulation of Variations in Exposed Residues of snake venom toxins. Toxins (Basel), 5 (2013), 2172–2208.Google Scholar
Jackson, T. N., Young, B., Underwood, G., et al., Endless forms most beautiful: The evolution of ophidian oral glands, including the venom system, and the use of appropriate terminology for homologous structures. Zoomorphology, 136 (2017), 107–130.Google Scholar
Sanggaard, K. W., Dyrlund, T. F., Thomsen, L. R., et al., Characterization of the gila monster (Heloderma suspectum suspectum) venom proteome. Journal of Proteomics, 117 (2015), 1–11.Google Scholar
Yap, M. K. K. and Misuan, N., Exendin-4 from Heloderma suspectum venom: From discovery to its latest application as type II diabetes combatant. Basic & Clinical Pharmacology & Toxicology, 124 (2019), 513–527.Google Scholar
Kochva, E.. The origin of snakes and evolution of the venom apparatus. Toxicon, 25 (1987), 65–106.Google Scholar
Auffenberg, W.. The Behavioral Ecology of the Komodo Monitor (Gainsville, FL: University Presses of Florida, 1981).Google Scholar
Fry, B. G., Wroe, S., Teeuwisse, W., et al., A central role for venom in predation by Varanus komodoensis (Komodo Dragon) and the extinct giant Varanus (Megalania) priscus . Proceedings of the National Academy of Sciences of the USA, 106 (2009), 8969–8974.Google Scholar
Koludarov, I., Jackson, T. N., op den Brouw, B., et al., Enter the dragon: The dynamic and multifunctional evolution of Anguimorpha lizard venoms. Toxins (Basel), 9 (2017), 242.Google Scholar
Fry, B. G., Vidal, N., Norman, J. A., et al., Early evolution of the venom system in lizards and snakes. Nature, 439 (2006), 584–588.Google Scholar
Nei, M., Gu, X., and Sitnikova, T., Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proceedings of the National Academy of Sciences of the USA, 94 (1997), 7799–7806.Google Scholar
Fry, B. G., Wüster, W., Kini, R. M., et al., Molecular evolution and phylogeny of elapid snake venom three-finger toxins. Journal of Molecular Evolution, 57 (2003), 110–129.Google Scholar
Casewell, N. R., Wagstaff, S. C., Harrison, R. A., Renjifo, C., and Wüster, W., Domain loss facilitates accelerated evolution and neofunctionalization of duplicate snake venom metalloproteinase toxin genes. Molecular Biology and Evolution, 28 (2011), 2637–2649.Google Scholar
Suryamohan, K., Krishnankutty, S. P., Guillory, J., et al., The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins. Nature Genetics, 52 (2020), 106–117.Google Scholar
Brown, D. D., Wensink, P. C., and Jordan, E., A comparison of the ribosomal DNA’s of Xenopus laevis and Xenopus mulleri: the evolution of tandem genes. Journal of Molecular Biology, 63 (1972), 57–73.Google Scholar
Moran, Y., Weinberger, H., Sullivan, J. C., et al., Concerted evolution of sea anemone neurotoxin genes is revealed through analysis of the Nematostella vectensis genome. Molecular Biology and Evolution, 25 (2008), 737–747.Google Scholar
Brust, A., Sunagar, K., Undheim, E. A. B., et al., Differential evolution and neofunctionalization of snake venom metalloprotease domains. Molecular and Cellular Proteomics, 12 (2013), 651–663.Google Scholar
Kordis, D. and Gubensek, F., Adaptive evolution of animal toxin multigene families. Gene, 261 (2000), 43–52.Google Scholar
Casewell, N. R., Wüster, W., Vonk, F. J., Harrison, R. A., and Fry, B. G.. Complex cocktails: the evolutionary novelty of venoms. Trends in Ecology and Evolution, 28 (2013), 219–229.Google Scholar
Hargreaves, A. D., Swain, M. T., Hegarty, M. J., Logan, D. W., and Mulley, J. F., Restriction and recruitment-gene duplication and the origin and evolution of snake venom toxins. Genome Biology and Evolution, 6 (2014), 2088–2095.Google Scholar
Reyes-Velasco, J., Card, D. C., Andrew, A. L., et al., Expression of venom gene homologs in diverse python tissues suggests a new model for the evolution of snake venom. Molecular Biology and Evolution, 32 (2015), 173–183.Google Scholar
Lei, Q., Li, C., Zuo, Z., et al., Evolutionary Insights into RNA trans-Splicing in Vertebrates. Genome Biology and Evolution, 8 (2016), 562–577.Google Scholar
Ogawa, T., Oda-Ueda, N., Hisata, K., et al., Alternative mRNA splicing in three venom families underlying a possible production of divergent venom proteins of the Habu Snake, Protobothrops flavoviridis. Toxins (Basel), 11 (2019), 581.Google Scholar
Cousin, X., Bon, S., Massoulie, J., and Bon, C., Identification of a novel type of alternatively spliced exon from the acetylcholinesterase gene of Bungarus fasciatus. Molecular forms of acetylcholinesterase in the snake liver and muscle. Journal of Biological Chemistry, 273 (1998), 9812–9820.Google Scholar
Fry, B. G., Winter, K., Norman, J. A., et al., Functional and structural diversification of the Anguimorpha lizard venom system. Molecular and Cellular Proteomics, 9 (2010), 2369–2390.Google Scholar
Lynch, V. J., Inventing an arsenal: adaptive evolution and neofunctionalization of snake venom phospholipase A2 genes. BMC Evolutionary Biology, 7 (2007), 2.Google Scholar
Sunagar, K., Johnson, W. E., O’Brien, S. J., Vasconcelos, V., and Antunes, A., Evolution of CRISPs associated with toxicoferan-reptilian venom and mammalian reproduction. Molecular Biology and Evolution, 29 (2012), 1807–1822.Google Scholar
Jackson, K., The evolution of venom-delivery systems in snakes. Zoological Journal of the Linnean Society, 137 (2003), 337–354.Google Scholar
Koludarov, I., Jackson, T. N., Pozzi, A., and Mikheyev, A. S., Family saga: reconstructing the evolutionary history of a functionally diverse gene family reveals complexity at the genetic origins of novelty. bioRxiv, (2019), 583344.Google Scholar
Taub, A. M.. Ophidian cephalic glands. Journal of Morphology, 118 (1966), 529–542.Google Scholar
Vonk, F. J., Admiraal, J. F., Jackson, K., et al., Evolutionary origin and development of snake fangs. Nature, 454 (2008), 630–633.Google Scholar
Phisalix, M. and Caius, R.. L’extension de la fonction venimeuse dans l’ordre entière des ophidiens et son existence chez des familles ou elle n’avait pas été soupçonnée jusqu’içi. Journal de Physiologie et de Pathologie Générale, 17 (1918), 923–964.Google Scholar
Fry, B. G., Casewell, N. R., Wüster, W., et al., The structural and functional diversification of the Toxicofera reptile venom system. Toxicon, 60 (2012), 434–448.Google Scholar
Jackson, T. N. and Fry, B. G., A tricky trait: Applying the fruits of the ‘function debate’ in the philosophy of biology to the ‘venom debate’ in the science of toxinology. Toxins, 8 (2016), 263.Google Scholar
Hargreaves, A. D., Swain, M. T., Logan, D. W., and Mulley, J. F., Testing the Toxicofera: comparative transcriptomics casts doubt on the single, early evolution of the reptile venom system. Toxicon, 92 (2014), 140–156.Google Scholar
Townsend, T., Larson, A., Louis, E., and Macey, J. R.. Molecular phylogenetics of squamata: the position of snakes, amphisbaenians, and dibamids, and the root of the squamate tree. Systematic Biology 53 (2004), 735–757.Google Scholar
Conesa, A., Madrigal, P., Tarazona, S., et al., A survey of best practices for RNA-seq data analysis. Genome Biology, 17 (2016), 13.Google Scholar

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  • Genomic Perspectives
  • Edited by David J. Gower, Natural History Museum, London, Hussam Zaher, Universidade de São Paulo
  • Book: The Origin and Early Evolutionary History of Snakes
  • Online publication: 30 July 2022
  • Chapter DOI: https://doi.org/10.1017/9781108938891.013
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  • Genomic Perspectives
  • Edited by David J. Gower, Natural History Museum, London, Hussam Zaher, Universidade de São Paulo
  • Book: The Origin and Early Evolutionary History of Snakes
  • Online publication: 30 July 2022
  • Chapter DOI: https://doi.org/10.1017/9781108938891.013
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  • Genomic Perspectives
  • Edited by David J. Gower, Natural History Museum, London, Hussam Zaher, Universidade de São Paulo
  • Book: The Origin and Early Evolutionary History of Snakes
  • Online publication: 30 July 2022
  • Chapter DOI: https://doi.org/10.1017/9781108938891.013
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