The Andaman day gecko paradox: an ancient endemic without pronounced phylogeographic structure

Heaney, L. R. Is a new paradigm emerging for oceanic island biogeography?. J. Biogeogr. 34, 753–757 (2007).

Google Scholar 

Avise, J. C. Molecular Markers, Natural History and Evolution (Springer, New York, 2012).

Google Scholar 

Ali, J. R. Islands as biological substrates: Classification of the biological assemblage components and the physical island types. J. Biogeogr. 44, 984–994 (2017).

Google Scholar 

de Wit, M. J. Madagascar: Heads it’s a continent, tails it’s an island. Annu. Rev. Earth Planet. Sci. 31, 213–248 (2003).

ADS  Google Scholar 

Das, I. Biogeography of the amphibians and reptiles of the Andaman and Nicobar Islands, India. In Tropical Island Herpetofauna. Origin, Current Diversity and Current Status 43–77 (Elsevier, 1999).

Bandopadhyay, P. C. & Carter, A. Chapter 6 geological framework of the Andaman–Nicobar Islands. Geol. Soc. Lond. Mem. 47, 75–93 (2017).

Google Scholar 

Ali, J. R. Islands as biological substrates: Continental. J. Biogeogr. 45, 1003–1018 (2018).

Google Scholar 

Smith, M. A. The herpetology of the Andaman and Nicobar Islands. Proc. Linn. Soc. London 153, 150–158 (1941).

Biswas, S. & Sanyal, D. A report on the Reptilia fauna of Andaman and Nicobar Islands in the collection of Zoological Survey of India. Rec. Zool. Surv. India 77, 255–292 (1980).

Google Scholar 

Smith, W. H. F. & Sandwell, D. T. Global sea floor topography from satellite altimetry and ship depth soundings. Science 277, 1956–1962 (1997).

CAS  Google Scholar 

Harikrishnan, S., Vasudevan, K. & Choudhury, B. C. A review of herpetofaunal descriptions and studies from Andaman and Nicobar Islands, with an updated checklist in Recent trends in biodiversity of Andaman and Nicobar Islands (Zoological Survey of India, Kolkata, 2010).

Google Scholar 

Chakravarty, R., Chattopadhyay, B., Ramakrishnan, U. & Sivasundar, A. Comparative population structure in species of bats differing in ecology and morphology in the Andaman Islands India. Acta Chiropt. 20, 85–98 (2018).

Google Scholar 

Mohan, A. V., Swamy, P. & Shanker, K. Population structure in the Andaman keelback, Xenochrophis tytleri: Geographical distance and oceanic barriers to dispersal influence genetic divergence on the Andaman archipelago. PeerJ 6, 5752. https://doi.org/10.7717/peerj.5752 (2018).

Article  Google Scholar 

Rocha, S. et al. Phylogenetic systematics of day geckos, genus Phelsuma, based on molecular and morphological data (Squamata: Gekkonidae). Zootaxa 2429, 1 (2010).

Google Scholar 

Austin, J. J., Arnold, E. N. & Jones, C. G. Reconstructing an island radiation using ancient and recent DNA: The extinct and living day geckos (Phelsuma) of the Mascarene islands. Mol. Phylogenet. Evol. 31, 109–122 (2004).

CAS  PubMed  Google Scholar 

Rocha, S., Posada, D., Carretero, M. A. & Harris, D. J. Phylogenetic affinities of Comoroan and East African day geckos (genus Phelsuma): Multiple natural colonisations, introductions and island radiations. Mol. Phylogenet. Evol. 43, 685–692 (2007).

CAS  PubMed  Google Scholar 

Rocha, S., Vences, M., Glaw, F., Posada, D. & Harris, D. J. Multigene phylogeny of Malagasy day geckos of the genus Phelsuma. Mol. Phylogenet. Evol. 52, 530–537 (2009).

CAS  PubMed  Google Scholar 

Rocha, S. Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands. BMC Evol. Biol. 13, 3. https://doi.org/10.1186/1471-2148-13-3 (2013).

Article  PubMed  PubMed Central  Google Scholar 

Cheke, A. & Hume, J. P. Lost Land of the Dodo: The Ecological History of Mauritius, Réunion and Rodrigues (Bloomsbury Publishing, London, 2010).

Google Scholar 

Harmon, L. J., Harmon, L. L. & Jones, C. G. Competition and community structure in diurnal arboreal geckos (genus Phelsuma) in the Indian Ocean. Oikos 116, 1863–1878 (2007).

Google Scholar 

Ratnam, J. Distribution and Behavioural Ecology of the Andaman Day Gecko (Phelsuma andamanensis). MSc dissertation, Pondicherry University (1992).

Humphrey, J. E. & Ward, C. F. M. Madagascan Day Geckos (Phelsuma spp.) exhibit differing responses along a gradient of land-use change. Trop. Conserv. Sci. https://doi.org/10.1177/1940082918760282 (2018).

Article  Google Scholar 

Boumans, L., Vieites, D. R., Glaw, F. & Vences, M. Geographical patterns of deep mitochondrial differentiation in widespread Malagasy reptiles. Mol. Phylogenet. Evol. 45, 822–839 (2007).

CAS  PubMed  Google Scholar 

Gehring, P.-S., Glaw, F., Gehara, M., Ratsoavina, F. M. & Vences, M. Northern origin and diversification in the central lowlands? Complex phylogeography and taxonomy of widespread day geckos (Phelsuma) from Madagascar. Org. Divers. Evol. 13, 605–620 (2013).

Google Scholar 

Mohan, A. V. Comparative phylogeography and patterns of deep genetic differentiation of two gecko species, Paroedura gracilis and Phelsuma guttata, across north-eastern Madagascar. Salamandra 55, 211–220 (2019).

Google Scholar 

Beaumont, M. A. Approximate Bayesian computation in evolution and ecology. Annu. Rev. Ecol. Evol. Syst. 41, 379–406 (2010).

Google Scholar 

Csilléry, K., Blum, M. G., Gaggiotti, O. E. & François, O. Approximate Bayesian computation (ABC) in practice. Trends Ecol. & Evol. 25, 410–418 (2010).

Google Scholar 

Arbogast, B. S. & Kenagy, G. J. Comparative phylogeography as an integrative approach to historical biogeography: guest editorial. J. Biogeogr. 28, 819–825 (2008).

Google Scholar 

Crottini, A. et al. Vertebrate time-tree elucidates the biogeographic pattern of a major biotic change around the K-T boundary in Madagascar. Proc. Natl. Acad. Sci. 109, 5358–5363 (2012).

ADS  CAS  PubMed  Google Scholar 

Kumar, S., Stecher, G., Suleski, M. & Hedges, S. B. TimeTree: a resource for timelines, timetrees, and divergence times. Mol. Biol. Evol. 34, 1812–1819 (2017).

CAS  PubMed  Google Scholar 

Meirmans, P. G. & Hedrick, P. W. Assessing population structure: FST and related measures: invited technical review. Mol. Ecol. Resour. 11, 5–18 (2011).

PubMed  Google Scholar 

Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).

CAS  PubMed  PubMed Central  Google Scholar 

Verity, R. & Nichols, R. A. Estimating the number of subpopulations (K) in structured populations. Genetics 203, 1827–1839 (2016).

PubMed  PubMed Central  Google Scholar 

Hubisz, M. J., Falush, D., Stephens, M. & Pritchard, J. K. Inferring weak population structure with the assistance of sample group information. Mol. Ecol. Resour. 9, 1322–1332 (2009).

PubMed  PubMed Central  Google Scholar 

Thangaraj, K. et al. Genetic affinities of the Andaman Islanders, a vanishing human population. Curr. Biol. 13, 86–93 (2003).

CAS  PubMed  Google Scholar 

Chaubey, G. & Endicott, P. The Andaman Islanders in a regional genetic context: Reexamining the evidence for an early peopling of the archipelago from South Asia. Human Bio. 85, 153–172 (2013).

Google Scholar 

Rico, C. et al. Null alleles are ubiquitous at microsatellite loci in the Wedge Clam (Donax trunculus). 10.7717/peerj.3188 (2017).

Lambeck, K., Rouby, H., Purcell, A., Sun, Y. & Sambridge, M. Sea level and global ice volumes from the Last Glacial Maximum to the Holocene. Proc. Natl. Acad. Sci. 111, 15296–15303 (2014).

ADS  CAS  PubMed  Google Scholar 

Sharief, M. U. Ethnobotanical studies of the dwindling aboriginal Jarawa tribe in Andaman Islands India. Gen. Res. Crop Evol. 64, 1861–1872 (2017).

Google Scholar 

Chandramouli, S. R. First record of a Phelsuma Gray, 1825 (Sauria: Gekkonidae) from the Nicobar Archipelago, Bay of Bengal. Sauria 39, 49–51 (2017).

Google Scholar 

Oro, D., Genovart, M., Tavecchia, G., Fowler, M. S. & Martínez-Abraín, A. Ecological and evolutionary implications of food subsidies from humans. Ecol. Lett. 16, 1501–1514 (2013).

PubMed  Google Scholar 

Andrews, H. V., Vasumati, S. & others. Sustainable management of protected areas in the Andaman and Nicobar Islands. In Sustainable Management of Protected Areas in the Andaman Nicobar Island (2002).

Sekhsaria, P. & Pandya, V. Jarawa Tribal Reserve dossier: cultural & biological diversities in the Andaman Islands (UNESCO, 2010).

Shen, X.-X., Liang, D. & Zhang, P. The development of three long universal nuclear protein-coding locus markers and their application to osteichthyan phylogenetics with nested PCR. PLoS ONE 7, 39256. https://doi.org/10.1371/journal.pone.0039256 (2012).

ADS  CAS  Article  Google Scholar 

Bauer, A. M., de Silva, A., Greenbaum, E. & Jackman, T. A new species of day gecko from high elevation in Sri Lanka, with a preliminary phylogeny of Sri Lankan Cnemaspis (Reptilia, Squamata, Gekkonidae). Mitteilungen aus dem Museum für Naturkunde Berlin Zool. Reihe 83, 22–32 (2007).

Google Scholar 

Leaché, A. D. & McGuire, J. A. Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: Evidence for a misleading mitochondrial gene tree. Mol. Phylogenet. Evol. 39, 628–644 (2006).

PubMed  Google Scholar 

Gamble, T., Bauer, A. M., Greenbaum, E. & Jackman, T. R. Evidence for Gondwanan vicariance in an ancient clade of gecko lizards. J. Biogeogr. 35, 88–104 (2008).

Google Scholar 

Silvestro, D. & Michalak, I. raxmlGUI: a graphical front-end for RAxML. Org. Divers. Evol. 12, 335–337 (2012).

Google Scholar 

Perl, R. G. B. et al. Population genetic analysis of the recently rediscovered Hula painted frog (Latonia nigriventer) reveals high genetic diversity and low inbreeding. Sci. Rep. 8, 5588. https://doi.org/10.1038/s41598-018-23587-w (2018).

ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

Schuelke, M. An economic method for the fluorescent labeling of PCR fragments. Nat. Biotechnol. 18, 233–234 (2000).

CAS  PubMed  Google Scholar 

Bruford, M. Single-locus and multilocus DNA fingerprint. In: Hoelzel, A.R. (Ed.), Molecular Genetic Analysis of Populations: A Practical Approach. IRL Press, Oxford, pp. 225–270 (1992).

Ryan, W. B. F. et al. Global multi-resolution topography synthesis: Global multi-resolution topography synthesis. Geochem. Geophys. Geosyst. 10, 03014. https://doi.org/10.1029/2008GC002332 (2009).

ADS  Article  Google Scholar 

Kalinowski, S. T., Taper, M. L. & Marshall, T. C. Revising how the computer program cervus accommodates genotyping error increases success in paternity assignment: Cervus likelihood model. Mol. Ecol. 16, 1099–1106 (2007).

PubMed  Google Scholar 

Kamvar, Z., Tabima, J. & Grünwald, N. Poppr: An R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ. 2, 281. https://doi.org/10.7717/peerj.281 (2014).

Article  Google Scholar 

Rousset, F. genepop’007: A complete re-implementation of the genepop software for Windows and Linux. Mol. Ecol. Resour. 8, 103–106 (2008).

PubMed  Google Scholar 

Fisher, R. The logic of scientific inference. J. R. Stat. Soc. 98, 39–54 (1935).

MATH  Google Scholar 

Adamack, A. T. & Gruber, B. Pop gen report: Simplifying basic population genetic analyses in R. Methods Ecol. Evol. 5, 384–387 (2014).

Google Scholar 

Jombart, T. & Ahmed, I. adegenet 1.3–1: New tools for the analysis of genome-wide SNP data. Bioinformatics 27, 3070–3071 (2011).

CAS  PubMed  PubMed Central  Google Scholar 

Paradis, E. pegas: An R package for population genetics with an integrated-modular approach. Bioinformatics 26, 419–420 (2010).

CAS  PubMed  Google Scholar 

Dieringer, D. & Schlötterer, C. Microsatellite analyser (MSA): A platform independent analysis tool for large microsatellite data sets: Program note. Mol. Ecol. Notes 3, 167–169 (2003).

CAS  Google Scholar 

Keenan, K., McGinnity, P., Cross, T. F., Crozier, W. W. & Prodöhl, P. A. diveRsity : An R package for the estimation and exploration of population genetics parameters and their associated errors. Methods Ecol. Evol. 4, 782–788 (2013).

Google Scholar 

Francis, R. M. Pophelper: An R package and web app to analyse and visualize population structure. Mol. Ecol. Resour. 17, 27–32 (2017).

CAS  PubMed  Google Scholar 

Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software structure: A simulation study. Mol. Ecol. 14, 2611–2620 (2005).

CAS  PubMed  Google Scholar 

Janes, J. K. et al. The K = 2 conundrum. Mol. Ecol. 26, 3594–3602 (2017).

PubMed  Google Scholar 

Kopelman, N. M., Mayzel, J., Jakobsson, M., Rosenberg, N. A. & Mayrose, I. Clumpak: A program for identifying clustering modes and packaging population structure inferences across K. Mol. Ecol. Resour. 15, 1179–1191 (2015).

CAS  PubMed  PubMed Central  Google Scholar 

Jakobsson, M. & Rosenberg, N. A. CLUMPP: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 1801–1806 (2007).

CAS  PubMed  Google Scholar 

Piry, S. et al. Mapping averaged pairwise information (MAPI): A new exploratory tool to uncover spatial structure. Methods Ecol. Evol. 7, 1463–1475 (2016).

Google Scholar 

Cornuet, J.-M. et al. DIYABC v2.0: A software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data. Bioinformatics 30, 1187–1189 (2014).

CAS  PubMed  Google Scholar 

Estoup, A., Jarne, P. & Cornuet, J.-M. Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Mol. Ecol. 11, 1591–1604 (2002).

CAS  PubMed  Google Scholar 

Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3, 294–299 (1994).

CAS  PubMed  Google Scholar 

Palumbi, S. Simple fool’s guide to PCR. (1991).

Kumar, S., Stecher, G. & Tamura, K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874 (2016).

CAS  PubMed  Google Scholar 

Librado, P. & Rozas, J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451–1452 (2009).

CAS  PubMed  Google Scholar 

Bandelt, H. J., Forster, P. & Rohl, A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16, 37–48 (1999).

CAS  PubMed  Google Scholar 

Winter, D. J. mmod: An R library for the calculation of population differentiation statistics. Mol. Ecol. Resour. 12, 1158–1160 (2012).

CAS  PubMed  Google Scholar