DNA barcoding inferred maternal philopatric affinity of ocean maskray (Neotrygon indica) in the Bay of Bengal

References

• Amos W, Harwood J. 1998. Factors affecting levels of genetic diversity in natural populations. Philos Trans R Soc Lond B Biol Sci. 353:177–186.
   PubMed Web of Science ®Google Scholar
• Arlyza IS, Shen KN, Durand JD, Borsa P. 2013. Mitochondrial haplotypes indicate parapatric-like phylogeographic structure in blue-spotted maskray (Neotrygon kuhlii) from the Coral Triangle region. J Hered. 104:725–733.
   PubMed Web of Science ®Google Scholar
• Arnold BD, Wilkinson GS. 2015. Female natal philopatry and gene flow between divergent clades of pallid bats (Antrozous pallidus). J Mammal. 96:531–540.
   Web of Science ®Google Scholar
• Borsa P, Arlyza IS, Hoareau TB, Shen KN. 2018. Diagnostic description and geographic distribution of four new cryptic species of the blue-spotted maskray species complex (Myliobatoidei: Dasyatidae; Neotrygon spp.) based on DNA sequences. J Oceanol Limnol. 36:827–841.
   Google Scholar
• Borsa P, Shen KN, Arlyza IS, Hoareau TB. 2016. Multiple cryptic species in the blue-spotted maskray (Myliobatoidei: Dasyatidae: Neotrygon spp.): an update. C R Biol. 339:417–426.
   PubMed Web of Science ®Google Scholar
• Bose S, Forrester TD, Brazeal JL, Sacks BN, Casady DS, Wittmer HU. 2017. Implications of fidelity and philopatry for the population structure of female black-tailed deer. Behav Ecol. 28:983–990.
   Web of Science ®Google Scholar
• Burridge CP, Craw D, Jack DC, King TM, Waters JM. 2008. Does fish ecology predict dispersal across a river drainage divide? Evolution. 62:1484–1499.
   PubMed Web of Science ®Google Scholar
• Caparroz R, Miyaki CY, Baker AJ. 2009. Contrasting phylogeographic patterns in mitochondrial DNA and microsatellites: evidence of female philopatry and male-biased gene flow among regional populations of the blue-and-yellow macaw (Psittaciformes: Ara ararauna) in Brazil. Auk. 126:359–370.
   Web of Science ®Google Scholar
• Cerutti-Pereyra F, Meekan MG, Wei NWV, O’Shea O, Bradshaw CJA, Austin CM. 2012. Identification of rays through DNA barcoding: an application for ecologists. PLoS One. 7:e36479.
   PubMed Web of Science ®Google Scholar
• Charlesworth B, Charlesworth D. 1999. The genetic basis of inbreeding depression. Genet Res. 74:329–340.
   PubMed Web of Science ®Google Scholar
• Clement M, Snell Q, Walke P, Posada D, Crandall K. 2002. TCS: estimating gene genealogies. Proceedings 16th International Parallel and Distributed Processing Symposium; Vol. 2; Piscataway (NJ): IEEE; p. 184.
   Google Scholar
• Clutton-Brock T, Sheldon BC. 2010. Individuals and populations: the role of longterm, individual-based studies of animals in ecology and evolutionary biology. Trends Ecol Evol. 25:562–573.
   PubMed Web of Science ®Google Scholar
• Collins RA, Cruickshank RH. 2013. The seven deadly sins of DNA barcoding. Mol Ecol Resour. 13:969–975.
   PubMed Web of Science ®Google Scholar
• Côté SD, Dallas JF, Marshall F, Irvine RJ, Langvatn R, Albon SD. 2002. Microsatellite DNA evidence for genetic drift and philopatry in Svalbard reindeer. Mol Ecol. 11:1923–1930.
   PubMed Web of Science ®Google Scholar
• Dannewitz J, Maes GE, Johansson L, Wickstrom H, Volckaert FAM, Jarvi T. 2005. Panmixia in the European eel: a matter of time. Proc Biol Sci. 272:1129–1137.
   PubMed Web of Science ®Google Scholar
• Ebach MC, Holdrege C. 2005. DNA barcoding is no substitute for taxonomy. Nature. 434:697.
   PubMed Web of Science ®Google Scholar
• FitzSimmons NN, Limpus CJ, Norman JA, Goldizen AR, Miller JD, Moritz C. 1997. Philopatry of male marine turtles inferred from mitochondrial DNA markers. Proc Natl Acad Sci USA. 94:8912–8917.
   PubMed Web of Science ®Google Scholar
• Fricke R. 2019. Eschmeyer’s catalog of fishes: references. [accessed 12.03.2019] http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp. Electronic version accessed 12.03.2019.
   Google Scholar
• Gour DS, Bhagavatula J, Bhavanishankar M, Reddy PA, Gupta JA, Sarkar MS, Hussain SM, Harika S, Gulia R, Shivaji S, et al. 2013. Philopatry and dispersal patterns in tiger (Panthera tigris). PLoS One. 8:e66956.
   PubMed Web of Science ®Google Scholar
• Greenwood P. 1980. Mating systems, philopatry and dispersal in birds and mammals. Anim Behav. 28:1140–1162.
   Web of Science ®Google Scholar
• Hebert PD, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Philos Trans Royal Soc B. 270:313–322.
   PubMed Web of Science ®Google Scholar
• Hubert N, Hanner R, Holm E, Mandrak NE, Taylor E, Burridge M, Watkinson D, Dumont P, Curry A, Bentzen P, et al. 2008. Identifying Canadian freshwater fishes through DNA barcodes. PLoS One. 3:e2490.
   PubMed Web of Science ®Google Scholar
• Hueter RE, Heupel MR, Heist EJ, Keeney DB. 2004. Evidence of philopatry in sharks and implications for the management of shark fisheries. J Northw Atl Fish Sci. 35:239–247.
   Google Scholar
• IUCN. 2018. The IUCN red list of threatened species. Version 2019.1. Gland (Switzerland): IUCN.
   Google Scholar
• Kawecki TJ, Ebert D. 2004. Conceptual issues in local adaptation. Ecol Lett. 7:1225–1241.
   Web of Science ®Google Scholar
• Keller LF, Waller DM. 2002. Inbreeding effects in wild populations. Trends Ecol Evol. 17:230–241.
   Web of Science ®Google Scholar
• Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGAX: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 35:1547–1549.
   PubMed Web of Science ®Google Scholar
• Lakra WS, Singh M, Goswami M, Gopalakrishnan A, Lal KK, Mohindra V, Sarkar UK, Punia PP, Singh KV, Bhatt JP, et al. 2016. DNA barcoding Indian freshwater fishes. Mitochondrial DNA Part A. 27:4510–4517.
   PubMed Web of Science ®Google Scholar
• Laskar BA, Kumar V, Kundu S, Tyagi K, Chandra K. 2018. Taxonomic quest: validating two mahseer fishes (Actinopteri: Cyprinidae) through molecular and morphological data from biodiversity hotspots in India. Hydrobiologia. 815:113–124.
   Web of Science ®Google Scholar
• Last PR, White WT, Seret B. 2016. Taxonomic status of maskrays of the Neotrygon kuhlii species complex (Myliobatoidei: Dasyatidae) with the description of three new species from the Indo-West Pacific. Zootaxa. 4083:533–561.
   PubMed Web of Science ®Google Scholar
• Last PR, White WT. 2008. Resurrection of the genus Neotrygon Castelnau (Myliobatoidei: Dasyatidae) with the description of Neotrygon picta sp. nov., a new species from northern Australia, In: Last PR, White WT, Pogonoski JJ, editors. Descriptions of new Australian chondrichthyans. Hobart Australia: CSIRO; p. 315–325.
   Google Scholar
• Lee PLM, Luschi P, Hays GC. 2006. Detecting female precise natal philopatry in green turtles using assignment methods. Mol Ecol. 16:61–74.
   Web of Science ®Google Scholar
• Leigh JW, Bryant D. 2015. PopART: full-feature software for haplotype network construction. Methods. Ecol Evol. 6:1110–1116.
   Web of Science ®Google Scholar
• Letunic I, Bork P. 2007. Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics. 23:127–128.
   PubMed Web of Science ®Google Scholar
• Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25:1451–1452.
   PubMed Web of Science ®Google Scholar
• Lim KC, Lim PE, Chong VC, Loh KH. 2015. Molecular and morphological analyses reveal phylogenetic relationships of stingrays focusing on the family Dasyatidae (Myliobatiformes). PLoS One. 10:e0120518.
   PubMed Web of Science ®Google Scholar
• Macdonald DW, Johnson DDP. 2001. Dispersal in theory and practice: consequences for conservation biology. In: Clobert J, Danchin E, Dhondt AA, Nichols JD, editors. Dispersal. New York: Oxford University Press; p. 358–372.
   Google Scholar
• Mayr E. 1963. Animal species and evolution. Cambridge (MA): Belknap Press of Harvard University Press.
   Google Scholar
• Moura AE, Natoli A, Rogan E, Hoelzel AR. 2013. Atypical panmixia in a European dolphin species (Delphinus delphis); implications for the evolution of diversity across oceanic boundaries. J Evol Biol. 26:63–75.
   PubMed Web of Science ®Google Scholar
• Nylander JAA. 2004. MrModeltest v2. Program distributed by the author. Uppsala (Sweden): Evolutionary Biology Centre, Uppsala University.
   Google Scholar
• Oliveira LRD, Gehara MCM, Fraga LD, Lopes F, Túnez JI, Cassini MH, Majluf P, Cárdenas-Alayza S, Pavés HJ, Crespo EA, et al. 2017. Ancient female philopatry, asymmetric male gene flow, and synchronous population expansion support the influence of climatic oscillations on the evolution of South American sea lion (Otaria flavescens). PLoS One. 12:e0179442.
   PubMed Web of Science ®Google Scholar
• Pavan-Kumar A, Kumar R, Pitale P, Shen K, Borsa P. 2018. Neotrygon indica sp. nov., the Indian Ocean blue-spotted maskray (Myliobatoidei, Dasyatidae). C R Biol. 341:120–130.
   PubMed Web of Science ®Google Scholar
• Puckridge M, Last PR, White WT, Andreakis N. 2013. Phylogeography of the Indo-West Pacific maskrays (Dasyatidae, Neotrygon): a complex example of Chondrichthyan radiation in the Cenozoic. Ecol Evol. 3:217–232.
   PubMed Web of Science ®Google Scholar
• Purdue JR, Smith MH, Patton JC. 2000. Female philopatry and extreme spatial genetic heterogeneity in white-tailed deer. J Mammal. 81:179–185.
   Web of Science ®Google Scholar
• Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572–1574.
   PubMed Web of Science ®Google Scholar
• Salles OC, Pujol B, Maynard JA, Almany GR, Berumen ML, Jones GP, Saenz-Agudelo P, Srinivasan M, Thorrold SR, Planes S. 2016. First genealogy for a wild marine fish population reveals multigenerational philopatry. Proc Natl Acad Sci USA. 113:13245–13250.
   PubMed Web of Science ®Google Scholar
• Sheldon BC. 1994. Male phenotype, fertility, and the pursuit of extra-pair copulations by female birds. Proc R Soc Lond B. 257:25–30.
   Web of Science ®Google Scholar
• Shields WM. 1982. Philopatry, inbreeding, and the evolution of sex. Albany (NY): State University of New York Press.
   Google Scholar
• Stepien CA, Murphy DJ, Lohner RN, Sepulveda-Villet OJ, Haponski AE. 2009. Signatures of vicariance, postglacial dispersal and spawning philopatry: population genetics of the walleye Sander vitreus. Mol Ecol. 18:3411–3428.
   PubMed Web of Science ®Google Scholar
• Stiebens VA, Merino SE, Roder C, Chain FJJ, Lee PLM, Eizaguirre C. 2013. Living on the edge: how philopatry maintains adaptive potential. Proc R Soc Lond B Biol Sci. 280:20130305.
   Web of Science ®Google Scholar
• Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876–4882.
   PubMed Web of Science ®Google Scholar
• van Noordwijk MA, Arora N, Willems EP, Dunkel LP, Amda RN, Mardianah N, Ackermann C, Krützen M, van Schaik CP. 2012. Female philopatry and its social benefits among Bornean orangutans. Behav Ecol Sociobiol. 66:823–834.
   Web of Science ®Google Scholar
• Ward RD, Hanner R, Hebert PD. 2009. The campaign to DNA barcode all fishes, FISH-BOL. J Fish Biol. 74:329–356.
   PubMed Web of Science ®Google Scholar
• Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD. 2005. DNA barcoding Australia’s fish species. Philos Trans R Soc Lond B Biol Sci. 360:1847–1857.
   PubMed Web of Science ®Google Scholar