McGowen MR, Grossman LI, Wildman DE. Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown. Proc R Soc B. 2012;279(1743):3643–51.

Article  PubMed  PubMed Central  Google Scholar 

Sun YB, Zhou WP, Liu HQ, Irwin DM, Shen YY, Zhang YP. Genome-Wide scans for candidate genes involved in the aquatic adaptation of dolphins. Genome Biol Evol. 2013;5(1):130–9.

Article  PubMed  Google Scholar 

Foote AD, Liu Y, Thomas GWC, Vinař T, Alföldi J, Deng J, et al. Convergent evolution of the genomes of marine mammals. Nat Genet. 2015;47(3):272–5.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chikina M, Robinson JD, Clark NL. Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals. Mol Biol Evol. 2016;33(9):2182–92.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gayk ZG, Le Duc D, Horn J, Lindsay AR. Genomic insights into natural selection in the common loon (Gavia immer): evidence for aquatic adaptation. BMC Evol Biol. 2018;18:64.

Article  PubMed  PubMed Central  Google Scholar 

Li A, Wang J, Sun K, Wang S, Zhao X, Wang T, et al. Two reference-quality sea snake genomes reveal their divergent evolution of adaptive traits and venom systems. Nowick K, editor. Mol Biol Evol. 2021;38(11):4867–83.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Peng C, Ren JL, Deng C, Jiang D, Wang J, Qu J, et al. The genome of Shaw’s sea snake (Hydrophis curtus) reveals secondary adaptation to its marine environment. Liu L, editor. Mol Biol Evol. 2020;37(6):1744–60.

CAS  PubMed  Google Scholar 

Whiteley SL, Holleley CE, Wagner S, Blackburn J, Deveson IW, Marshall Graves JA, et al. Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination. Aboobaker AA, editor. PLoS Genet. 2021;17(4):e1009465.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Seymour RogerS. Physiological adaptations to aquatic life. In: Biology of the reptilia, physiological ecology. New York: Academic Press; 1982. p. 1–51.

Rasmussen AR, Murphy JC, Ompi M, Gibbons JW, Uetz P. Marine Reptiles. Clifton J, editor. PLoS One. 2011;6(11):e27373.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee MSY, Sanders KL, King B, Palci A. Diversification rates and phenotypic evolution in venomous snakes (Elapidae). R Soc open sci. 2016;3(1):150277.

Article  PubMed  PubMed Central  Google Scholar 

Sanders KL, Lee MSY, Leys R, Foster R, Keogh JS. Molecular phylogeny and divergence dates for Australasian elapids and sea snakes (hydrophiinae): evidence from seven genes for rapid evolutionary radiations. J Evol Biol. 2008;21(3):682–95.

Article  CAS  PubMed  Google Scholar 

Brischoux F, Shine R. Morphological adaptations to marine life in snakes. J Morphol. 2011;272(5):566–72.

Article  PubMed  Google Scholar 

Sanders KL, Rasmussen AR, Elmberg J. Independent Innovation in the Evolution of Paddle-Shaped Tails in Viviparous Sea Snakes (Elapidae: Hydrophiinae). Integr Comp Biol. 2012;52(2):311–20.

Article  PubMed  Google Scholar 

Heatwole H, Seymour R. Pulmonary and cutaneous oxygen uptake in sea snakes and a file snake. Comp Biochem Physiol A Physiol. 1975;51(2):399–405.

Article  CAS  Google Scholar 

Heatwole H, Seymour R. The biology of sea snakes. Baltimore: University Park Press; 1975.

Graham JB. Aquatic respiration in the sea snake Pelamis Platurus. Respir Physiol. 1974;21(1):1–7.

Article  CAS  PubMed  Google Scholar 

Palci A, Seymour RS, Van Nguyen C, Hutchinson MN, Lee MSY, Sanders KL. Novel vascular plexus in the head of a sea snake (Elapidae, Hydrophiinae) revealed by high-resolution computed tomography and histology. R Soc open sci. 2019;6(9):191099.

Article  PubMed  PubMed Central  Google Scholar 

Seymour RS, Webster MED. Gas transport and blood acid-base balance in diving sea snakes. J Exp Zool. 1975;191(2):169–81.

Article  CAS  PubMed  Google Scholar 

Simões BF, Gower DJ, Rasmussen AR, Sarker MAR, Fry GC, Casewell NR, et al. Spectral diversification and trans-species allelic polymorphism during the land-to-sea transition in snakes. Curr Biol. 2020;30(13):2608-2615.e4.

Article  PubMed  Google Scholar 

Crowe-Riddell JM, Williams R, Chapuis L, Sanders KL. Ultrastructural evidence of a mechanosensory function of scale organs (sensilla) in sea snakes (Hydrophiinae). R Soc open sci. 2019;6(4):182022.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Crowe-Riddell JM, Snelling EP, Watson AP, Suh AK, Partridge JC, Sanders KL. The evolution of scale sensilla in the transition from land to sea in elapid snakes. Open Biol. 2016;6(6):160054.

Article  PubMed  PubMed Central  Google Scholar 

Crowe-Riddell JM, Simões BF, Partridge JC, Hunt DM, Delean S, Schwerdt JG, et al. Phototactic tails: Evolution and molecular basis of a novel sensory trait in sea snakes. Mol Ecol. 2019;28(8):2013–28.

Article  PubMed  Google Scholar 

Ukuwela KDB, de Silva A, Mumpuni, Fry BG, Sanders KL. Multilocus phylogeography of the sea snake Hydrophis curtus reveals historical vicariance and cryptic lineage diversity. Zoolog Script. 2014;43(5):472–84.

Article  Google Scholar 

Ou S, Chen J, Jiang N. Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res. 2018;46(21): e126.

PubMed  PubMed Central  Google Scholar 

Sanders KL, Mumpuni, Lee MSY. Uncoupling ecological innovation and speciation in sea snakes (Elapidae, Hydrophiinae, Hydrophiini). J Evol Biol. 2010;23(12):2685–93.

Article  CAS  PubMed  Google Scholar 

Zaher H, Murphy RW, Arredondo JC, Graboski R, Machado-Filho PR, Mahlow K, et al. Large-scale molecular phylogeny, morphology, divergence-time estimation, and the fossil record of advanced caenophidian snakes (Squamata: Serpentes). Joger U, editor. PLoS One. 2019;14(5):e0216148.

Article  PubMed  PubMed Central  Google Scholar 

Kowalczyk A, Chikina M, Clark NL. A cautionary tale on proper use of branch-site models to detect convergent positive selection. bioRxiv. 2021. https://doi.org/10.1101/2021.10.26.465984.

iGEM/UCSD evolutionary biology and bioinformatics group. hyphy-analyses. https://github.com/veg/hyphy-analyses. Accessed 22 Mar 2023.

Álvarez-Carretero S, Kapli P, Yang Z. Beginner’s guide on the use of PAML to detect positive selection. Crandall K, editor. Mol Biol Evol. 2023;40(4):041.

Article  Google Scholar 

Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, et al. Gene-wide identification of episodic selection. Mol Biol Evol. 2015;32(5):1365–71.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wertheim JO, Murrell B, Smith MD, Kosakovsky Pond SL, Scheffler K. RELAX: detecting relaxed selection in a phylogenetic framework. Mol Biol Evol. 2015;32(3):820–32.

Article  CAS  PubMed  Google Scholar 

Mi H, Muruganujan A, Huang X, Ebert D, Mills C, Guo X, et al. Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0). Nat Protoc. 2019;14(3):703–21.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Thomas PD, Ebert D, Muruganujan A, Mushayahama T, Albou L, Mi H. PANTHER: making genome-scale phylogenetics accessible to all. Protein Sci. 2022;31(1):8–22.

Article  CAS  PubMed  Google Scholar 

Supek F, Bošnjak M, Škunca N, Šmuc T. REVIGO summarizes and visualizes long lists of gene ontology terms. Gibas C, editor. PLoS One. 2011;6(7):e21800.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Card DC, Jennings WB, Edwards SV. Genome evolution and the future of phylogenomics of non-avian reptiles. Animals. 2023;13(3):471.

Article  PubMed  PubMed Central  Google Scholar 

Sanders KL, Lee MSY, Mumpuni, Bertozzi T, Rasmussen AR. Multilocus phylogeny and recent rapid radiation of the viviparous sea snakes (Elapidae: Hydrophiinae). Mol Phylogenet Evol. 2013;66(3):575–91.

Article  PubMed  Google Scholar 

Waters PD, Patel HR, Ruiz-Herrera A, Álvarez-González L, Lister NC, Simakov O, et al. Microchromosomes are building blocks of bird, reptile, and mammal chromosomes. Proc Natl Acad Sci USA. 2021;118(45):e2112494118.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Oguiura N, Ferrarezzi H, Batistic RF. Cytogenetics and molecular data in snakes: a phylogenetic approach. Cytogenet Genome Res. 2009;127(2–4):128–42.

Article  CAS  PubMed  Google Scholar 

Singh L. Evolution of karyotypes in snakes. Chromosoma. 1972;38(2):185–236.

Article  CAS