A molecular-genetics perspective on the systematics of the parthenogenetic flowerpot blindsnake Indotyphlops braminus (Daudin, 1803) (Squamata: Serpentes: Typhlopidae)

References

• Adalsteinsson, S. A., Branch, W. R., Trape, S., Vitt, L. J., & Blair Hedges, S. (2009). Molecular phylogeny, classification, and biogeography of snakes of the family Leptotyphlopidae (Reptilia, Squamata). Zootaxa, 2244, 1–50. https://doi.org/10.11646/zootaxa.2244.1.1
   Google Scholar
• Bandelt, H. J., Forster, P., & Rohl, A. (1999). Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37–48. https://doi.org/10.1093/oxfordjournals.molbev.a026036
   PubMed Web of Science ®Google Scholar
• Broadley, D. G., & Wallach, V. (2009). A review of the eastern and southern African blind-snakes (Serpentes: Typhlopidae), excluding Letheobia Cope, with the description of two new genera and a new species [Monograph]. Zootaxa, 2255, 1–100. pp. https://doi.org/10.11646/zootaxa.2255.1.1
   Google Scholar
• Bossuyt, F., Beenaerts, N., Meegaskumbura, M., Gower, D. J., Pethiyagoda, R., Roelants, K., Mannaert, A., Wilkinson, M., Bahir, M. M., Manamendra-Arachchi, K., Oommen, O. V., Ng, P. K. L., Schneider, C. J., & Milinkovitch, M. C. (2004). Local endemism within the Western Ghats-Sri Lanka biodiversity hotspot. Science (New York, N.Y.), 306, 479–481. https://doi.org/10.1126/science.1100167
   PubMed Web of Science ®Google Scholar
• Campbell, B. N. (1997). Hic sunt serpentes: Molecular phylogenetics and the Boidae (Serpentes: Booidea) [Unpublished doctoral dissertation]. Queen's University, Kingston, Canada.
   Google Scholar
• Daudin, F. M. (1803). Histoire naturelle générale et particulière des reptiles. Tome septième. F. Dufart, Paris.
   Google Scholar
• de Silva, A. (1990). Colour guide to the snakes of Sri Lanka. R & A Publishing Ltd.
   Google Scholar
• Deraniyagala, P. E. P. (1955). A colored atlas of some vertebrates from Ceylon: Vol 3. Serpentoid Reptilia. Colombo National Museum.
   Google Scholar
• Edgar, R. C. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792–1797. https://doi.org/10.1093/nar/gkh340
   PubMed Web of Science ®Google Scholar
• Gans, C. (1998). Some whys (and hows) of herpetological study, with Sri Lankan examples. In A. de Silva (Ed.), Biology and conservation of amphibians, reptiles and their habitats in South Asia (pp. 97–107). ARROS.
   Google Scholar
• Gower, D. J., Bahir, M., Mapatuna, Y., Pethiyagoda, R., Raheem, D., & Wilkinson, M. (2005). Molecular phylogenetics of Sri Lankan Ichthyophis (Amphibia: Gymnophiona: Ichthyophiidae), with discovery of a cryptic species. The Raffles Bulletin of Zoology, 12, 153–161.
   Google Scholar
• Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Systematic Biology, 59, 307–321. https://doi.org/10.1093/sysbio/syq010
   PubMed Web of Science ®Google Scholar
• Günther, A. (1864). The reptiles of British India. Taylor & Francis.
   Google Scholar
• Hedges, S. B., Marion, A. B., Lipp, K. M., Marin, J., Vidal, N. (2014). A taxonomic framework for typhlopid snakes from the Caribbean and other regions (Reptilia, Squamata). Caribbean Herpetology, 49, 1–61. www.caribbeanherpetology.orgArticleregistration:http://zoobank.org/urn:lsid:zoobank.org:pub:47191405-862B-4FB6-8A28-29AB7E25FBDD
   Google Scholar
• Jukes, T. H., & Cantor, C. R. (1969). Evolution of protein molecules. In H. N. Munro (Ed.), Mammalian protein metabolism (pp. 21–132). Elsevier.
   Google Scholar
• Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P., & Drummond, A. (2012). Geneious basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics (Oxford, England), 28, 1647–1649. https://doi.org/10.1093/bioinformatics/bts199
   PubMed Web of Science ®Google Scholar
• Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870–1874. https://doi.org/10.1093/molbev/msw054
   PubMed Web of Science ®Google Scholar
• Lanfear, R., Calcott, B., Ho, S. Y. W., & Guindon, S. (2012). PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution, 29, 1695–1701. https://doi.org/10.1093/molbev/mss020
   PubMed Web of Science ®Google Scholar
• Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T., & Calcott, B. (2017). PartitionFinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution, 34, 772–773. https://doi.org/10.1093/molbev/msw260
   PubMed Web of Science ®Google Scholar
• Leigh, J. W., & Bryant, D. (2015). Popart: Full-feature software for haplotype network construction. Methods in Ecology and Evolution, 6, 1110–1116. https://doi.org/10.1111/2041-210X.12410
   Web of Science ®Google Scholar
• Nagy, Z. T., Marion, A. B., Glaw, F., Miralles, A., Nopper, J., Vences, M., & Hedges, S. B. (2015). Molecular systematics and undescribed diversity of Madagascan scolecophidian snakes (Squamata: Serpentes). Zootaxa, 4040, 31–47. https://doi.org/10.11646/zootaxa.4040.1.3
   PubMed Web of Science ®Google Scholar
• Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015). IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32, 268–274. https://doi.org/10.1093/molbev/msu300
   PubMed Web of Science ®Google Scholar
• Noonan, B. P., & Chippindale, P. T. (2006). Dispersal and vicariance: The complex evolutionary history of boid snakes. Molecular Phylogenetics and Evolution, 40, 347–358. https://doi.org/10.1016/j.ympev.2006.03.010
   PubMed Web of Science ®Google Scholar
• Pethiyagoda, R., & Sudasinghe, H. (2021). The ecology and biogeography of Sri Lanka: A context for freshwater fishes. WHT Publications Limited.
   Google Scholar
• Presswell, B., Gower, D. J., Oommen, O. V., Measey, G. J., & Wilkinson, M. (2002). Scolecophidian snakes in the diets of south Asian caecilians (Amphibia: Gymnophiona). Herpetological Journal, 12, 123–126.
   Google Scholar
• Pyron, R. A., Ganesh, S. R., Sayyed, A., Sharma, V., Wallach, V., & Somaweera, R. (2016). A catalogue and systematic overview of the shield-tailed snakes (Serpentes: Uropeltidae). Zoosystema, 38, 453–506. https://doi.org/10.5252/z2016n4a2
   Web of Science ®Google Scholar
• Pyron, R. A., Kandambi, H. K. D., Hendry, C. R., Pushpamal, V., Burbrink, F. T., & Somaweera R. (2013). Genus-level phylogeny of snakes reveals the origins of species richness in Sri Lanka. Molecular Phylogenetics and Evolution. 66, 969–978. https://doi.org/10.1016/j.ympev.2012.12.004
   Google Scholar
• Pyron, R. A., & Wallach, V. (2014). Systematics of the blindsnakes (Serpentes: Scolecophidia: Typhlopoidea) based on molecular and morphological evidence. Zootaxa, 3829, 1–81. https://doi.org/10.11646/zootaxa.3829.1.1
   PubMed Web of Science ®Google Scholar
• Rambaut, A. (2014). FigTree [WWW Document]. http://tree.bio.ed.ac.uk/software/figtree/
   Google Scholar
• Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018). Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology, 67, 901–904. https://doi.org/10.1093/sysbio/syy032
   PubMed Web of Science ®Google Scholar
• Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A., & Huelsenbeck, J. P. (2012). MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61, 539–542. https://doi.org/10.1093/sysbio/sys029
   PubMed Web of Science ®Google Scholar
• Sidharthan, C., & Karanth, K. P. (2021). India's biogeographic history through the eyes of blindsnakes – filling the gaps in the global typhlopoid phylogeny. Molecular Phylogenetics and Evolution, 157, 107064. https://doi.org/10.1016/j.ympev.2020.107064
   PubMed Web of Science ®Google Scholar
• Slowinski, J. B., & Lawson, R. (2002). Snake phylogeny: Evidence from nuclear and mitochondrial genes. Molecular Phylogenetics and Evolution, 24, 194–202. https://doi.org/10.1016/S1055-7903(02)00239-7
   PubMed Web of Science ®Google Scholar
• Somasekaram, T., Perera, L. A. G., Perera, M. P., de Silva, M. B. G., Karunanayake, M. M., & Epitawatte, D. S. (1988). The national atlas of Sri Lanka. Survey Department.
   Google Scholar
• Somaweera, R. (2006). ශ්‍රී ලංකාවේ සර්පයින් [The snakes of Sri Lanka]. Wildlife Heritage Trust of Sri Lanka.
   Google Scholar
• Stamatakis, A. (2006). RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (Oxford, England), 22, 2688–2690. https://doi.org/10.1093/bioinformatics/btl446
   PubMed Web of Science ®Google Scholar
• Swofford, D. L. (2003). PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4. Sinauer Associates.
   Google Scholar
• Taylor, E. H. (1947). Comments on Ceylonese snakes of the genus Typhlops with descriptions of new species. The University of Kansas Science Bulletin, 31, 283–298. http://biostor.org/reference/49271http://creativecommons.org/licenses/by-nc/2.5/ https://doi.org/10.5962/bhl.part.1248
   Google Scholar
• Uetz, P., Freed, P., Aguilar, R., Hošek, J. (2021). Indotyphlops braminus: The Reptile Database. https://reptile-database.reptarium.cz/species?genus=Indotyphlops&species=braminus
   Google Scholar
• Vidal, N., Marin, J., Morini, M., Donnellan, S., Branch, W. R., Thomas, R., Vences, M., Wynn, A., Cruaud, C., & Hedges, S. B. (2010). Blindsnake evolutionary tree reveals long history on Gondwana. Biology Letters, 6, 558–561. https://doi.org/10.1098/rsbl.2010.0220
   PubMed Web of Science ®Google Scholar
• Wall, F. (1921). Ophidia taprobanica [The snakes of Ceylon] (p. 582). H. R. Cottle.
   Google Scholar
• Wadia, D. N. (1945). The three superposed peneplains of Ceylon. Ceylon Department of Mineralogy, Prof. Paper, 1, 25–32.
   Google Scholar
• Wallach, V. (2009). Ramphotyphlops braminus. Hamadryad, 34, 34–61.
   Google Scholar
• Wallach, V. (2020). How to easily identify the flowerpot blindsnake, Indotyphlops braminus (Daudin, 1803), with proposal of a new genus (Serpentes: Typhlopidae). Pod@rcis, 11, 4–12.
   Google Scholar
• Wallach, V. (2021). Addendum to the proposal for a new generic name, Virgotyphlops, for the species Eryx braminus Daudin, 1803 (Serpentes Typhlopidae). Pod@rcis, 12, 16–18.
   Google Scholar
• Wallach, V., & Pauwels, O. S. G. (2004). Typhlops lazelli, a new species of Chinese blindsnake from Hong Kong (Serpentes: Typhlopidae). Breviora, 512, 1–21.
   Google Scholar
• Wallach, V., Williams, K. L., & Boundy, J. (2014). Snakes of the world: A catalogue of living and extinct species. Routledge.
   Google Scholar
• Wiens, J. J., Kuczynski, C. A., Smith, S. A., Mulcahy, D. G., Sites, J. W., Townsend, T. M., & Reeder, T. W. (2008). Branch lengths, support, and congruence: Testing the phylogenomic approach with 20 nuclear loci in snakes. Systematic Biology, 57(3), 420–431. https://doi.org/10.1080/10635150802166053
   PubMed Web of Science ®Google Scholar
• Williams, R., Gower, D. J., Labisko, J., Morel, C., Bristol, R. M., Wilkinson, M., & Maddock, S. T. (2020). Are the Mascarene frog (Ptychadena mascareniensis) and Brahminy blind snake (Indotyphlops braminus) really alien species in the Seychelles? Herpetological Bulletin, 153, 17–21.
   Google Scholar
• Wynn, A. H., Diesmos, A. C., & Brown, R. M. (2016). Two new species of Malayotyphlops from the northern Philippines, with redescriptions of Malayotyphlops luzonensis (Taylor) and Malayotyphlops ruber (Boettger). Journal of Herpetology, 50, 157–168. https://doi.org/10.1670/14-104
   Web of Science ®Google Scholar
• Yan, J., Li, H., & Zhou, K. (2008). Evolution of the mitochondrial genome in snakes: Gene rearrangements and phylogenetic relationships. BMC Genomics, 9, 569. 569. https://doi.org/10.1186/1471-2164-9-569[19038056
   PubMed Web of Science ®Google Scholar