Li C, Corrigan S, Yang L, Straube N, Harris M, Hofreiter M, et al. DNA capture reveals transoceanic gene flow in endangered river sharks. Proc Natl Acad Sci USA. 2015;112(43):13302–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pall-Gergely B. Should we describe genera without molecular phylogenies? Zootaxa. 2017;4232(4):593–6.
Article
Google Scholar
Fišer C, Robinson CT, Malard F. Cryptic species as a window into the paradigm shift of the species concept. Mol Ecol. 2018;27(3):613–35.
Article
PubMed
Google Scholar
Beheregaray LB, Caccone A. Cryptic biodiversity in a changing world. J Biol. 2007;6(4):9-.
de Queiroz K. Species concepts and species delimitation. Syst Biol. 2007;56(6):879–86.
Article
PubMed
Google Scholar
Bickford D, Lohman DJ, Sodhi NS, Ng PKL, Meier R, Winker K, et al. Cryptic species as a window on diversity and conservation. Trends Ecol Evol. 2006;22(3):148–55.
Article
PubMed
Google Scholar
Feckler A, Schulz R, Bundschuh M. Cryptic lineages—same but different? Integr Environ Assess Manage. 2013;9(1):172–3.
Article
Google Scholar
Freudenstein JV, Broe MB, Folk RA, Sinn BT. Biodiversity and the species concept — Lineages are not enough. Syst Biol. 2017;66(4):644–56.
PubMed
Google Scholar
Struck TH, Feder JL, Bendiksby M, Birkeland S, Cerca J, Gusarov VI, et al. Finding evolutionary processes hidden in cryptic species. Trends Ecol Evol. 2018;33(3):153–63.
Article
PubMed
Google Scholar
Sukumaran J, Knowles LL. Multispecies coalescent delimits structure, not species. Proc Natl Acad Sci. 2017;114(7):1607.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carstens BC, Pelletier TA, Reid NM, Satler JD. How to fail at species delimitation. Mol Ecol. 2013;22(17):4369–83.
Article
PubMed
Google Scholar
Coates DJ, Byrne M, Moritz C. Genetic diversity and conservation units: Dealing with the species-population continuum in the age of genomics. Front Ecol Evol. 2018;6:165.
Article
Google Scholar
Cook LG, Edwards RD, Crisp MD, Hardy NB. Need morphology always be required for new species descriptions? Invertebr Syst. 2010;24(3):322–6.
Article
Google Scholar
Frankham R, Ballou JD, Dudash MR, Eldridge MDB, Fenster CB, Lacy RC, et al. Implications of different species concepts for conserving biodiversity. Biol Conserv. 2012;153:25–31.
Article
Google Scholar
Stanton DWG, Frandsen P, Waples RK, Heller R, Russo I-RM, Orozco-terWengel PA, et al. More grist for the mill? Species delimitation in the genomic era and its implications for conservation. Conserv Genet. 2019;20(1):101–13.
Article
Google Scholar
Zachos FE, Apollonio M, Bärmann EV, Festa-Bianchet M, Göhlich U, Habel JC, et al. Species inflation and taxonomic artefacts—A critical comment on recent trends in mammalian classification. Mamm Biol. 2013;78(1):1–6.
Article
Google Scholar
Knowlton N. Sibling species in the sea. Annu Rev Ecol Evol Syst. 1993;24:189–216.
Article
Google Scholar
Naylor GJP, Caira JN, Jensen K, Rosana KAM, White WT, Last PR. A DNA sequence-based approach to the identification of shark and ray species and its implications for global elasmobranch diversity and parasitology. Bull Am Mus Nat Hist. 2012;367:1–262.
Article
Google Scholar
Naylor GJP, Caira JN, Jensen K, Rosana KAM, Straube N, Lakner C. Elasmobranch phylogeny: A mitochondrial estimate based on 595 species. In: Carrier JC, Musick JA, Heithaus MR, editors. Biology of Sharks and Their Relatives. 2nd ed. Boca Raton: CRC Press; 2012. p. 31–56.
Chapter
Google Scholar
Hosegood J, Humble E, Ogden R, de Bruyn M, Creer S, Stevens G, et al. Genome-wide data for effective conservation of manta and devil ray species. BioRxiv. 2019;1:458141.
Google Scholar
Compagno LJV. Sharks. In: Fischer W, Bianchi G, editors. FAO species identification sheets for fishery purposes Western Indian Ocean; (Fishing Area 51) Prepared and printed with the support of the Danish International Development Agency (DANIDA). Rome: Food and Agricultural Organization of the United Nations; 1984. p. 1–6.
Google Scholar
Compagno LJV. Species catalogue for fishery purpose. Sharks of the world an annotated and illustrated catalogue of sharks species known to date. Bullhead, mackerel and carpet sharks (Heterodontiformes, Lamniformes and Orectolobiformes). Rome: FAO; 2001. 269 p.
Compagno LJV, Dando M, Fowler SL. Sharks of the world. New Jersey: Princeton University Press; 2005. p. 368.
Google Scholar
Last PR, Stevens JD. Sharks and Rays of Australia. 2nd edition. Victoria: CSIRO Publishing; 2009.
Compagno LJV. FAO species catalogue. Sharks of the world. An annotated and illustrated catalogue of sharks species known to date. Part 1: Hexancathiformes to Lamniformes. Rome: FAO; 1984. 1–249 p.
Arai T, Azri A. Diversity, occurrence and conservation of sharks in the southern South China Sea. PLoS ONE. 2019;14(3):e0213864.
Dharmadi, Fahmi, White WT. Species composition and aspects of the biology of Orectolobiformes from Indonesian waters. J Fish Biol. 2015;86(2):484–92.
Kass RE, Raftery AE. Bayes factors. J Am Stat Assoc. 1995;90(430):773–95.
Article
Google Scholar
White WT, Last PR, Stevens JD, Yearsley GK, Fahmi, Dharmadi. Economically important sharks and rays of Indonesia. Canberra: Australian Centre for International Agricultural Research; 2006. 329 p.
Yano K, Ahmad A, Gambang AC, Idris AH, Solahuddin AR, Aznan Z. Sharks and Rays of Malaysia and Brunei Darussalam. Kuala Trengganu: Southeast Asian Fisheries Development Center; 2005. 557 p.
White WT, Baje I, Sabub B, Appleyard SA, Pogonosky JJ, Mana RR. Sharks and rays of Papua New Guinea. Canberra: Australian Centre for International Agricultural Research; 2017. 327 p.
Heupel MR, Simpfendorfer A. Science or slaughter: Need for lethal sampling of sharks. Conserv Biol. 2010;24(5):1212–8.
Article
CAS
PubMed
Google Scholar
Last PR, Pogonoski JJ, White WT. A new wobbegong shark, Orectolobus leptolineatus sp. nov. (Orectolobiformes: Orectolobidae), from the Western Central Pacific. In: Last Peter R, White WT, Pogonoski JJ, editors. Descriptions of new sharks and rays from Borneo. Hobart: CSIRO Marine and Atmospheric Research Paper No. 32; 2010. p. 1–16.
Last PR, White WT. Two new stingrays (Chondrichthyes: Dasyatidae) from the eastern Indonesian Archipelago. Zootaxa. 2013;3722(1):1–21.
Article
PubMed
Google Scholar
Last PR, White WT, Naylor G. Three new stingrays (Myliobatiformes: Dasyatidae) from the Indo-West Pacific. Zootaxa. 2016;4147(4):377–402.
Article
PubMed
Google Scholar
Dingerkus G, DeFino TC. A revision of the orectolobiform shark family Hemiscyllidae. Bull Am Mus Nat Hist. 1983;176(1):1–94.
Google Scholar
Last PR, White WT, deCarvalho MR, Seret B, Stehmann MFW, Naylor GJP, et al. Rays of the World. Clayton, Vic.: CSIRO Publishing; 2016. 800 p.
Last PR, White WT, Seret B. 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. 2016;4083(4):533–61.
Article
PubMed
Google Scholar
White WT, Last PR, Stevens JD. Halaelurus maculosus n. sp. and H. sellus n. sp., two new species of catshark (Carcharhiniformes: Scyliorhinidae) from the Indo-West Pacific. Zootaxa. 2007;1639:1–21.
Article
Google Scholar
White WT. A redescription of Carcharhinus dussumieri and C. sealei, with resurrection of C. coatesi and C. tjutjot as valid species (Chondrichthyes: Carcharhinidae). Zootaxa. 2012;3241:1–34.
Article
Google Scholar
White WT, Last PR, Baje L. Aetomylaeus caeruleofasciatus, a new species of eagle ray (Myliobatiformes: Myliobatidae) from northern Australia and New Guinea. Ichthyol Res. 2016;63(1):94–109.
Article
Google Scholar
Hindley JA, Graham BA, Pulgarin-R PC, Burg TM. The influence of latitude, geographic distance, and habitat discontinuities on genetic variation in a high latitude montane species. Sci Rep. 2018;8(1):11846.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dudgeon CL, Blower DC, Broderick D, Giles JL, Holmes BJ, Kashiwagi T, et al. A review of the application of molecular genetics for fisheries management and conservation of sharks and rays. J Fish Biol. 2012;80(5):1789–843.
Article
CAS
PubMed
Google Scholar
Pavan-Kumar A, Gireesh-Babu P, Babu PPS, Jaiswar AK, Hari Krishna V, Prasasd KP, et al. Molecular phylogeny of elasmobranchs inferred from mitochondrial and nuclear markers. Mol Biol Rep. 2014;41(1):447–57.
Article
CAS
PubMed
Google Scholar
Moore ABM, White WT, Ward RD, Naylor GJP, Peirce R. Rediscovery and redescription of the smoothtooth blacktip shark, Carcharhinus leiodon (Carcharhinidae), from Kuwait, with notes on its possible conservation status. Mar Freshw Res. 2011;62(6):528–39.
Article
CAS
Google Scholar
Dudgeon CL, Corrigan S, Yang L, Allen GR, Erdmann MV, Fahmi, et al. Walking, swimming or hitching a ride? Phylogenetics and biogeography of the walking shark genus Hemiscyllium. Mar Freshw Res. 2020;71(9):1107–17.
Fields AT, Feldheim KA, Gelsleichter J, Pfoertner C, Chapman DD. Population structure and cryptic speciation in bonnethead sharks Sphyrna tiburo in the south-eastern U.S.A. and Caribbean. J Fish Biol. 2016;89(5):2219–33.
Article
CAS
PubMed
Google Scholar
Espíndola A, Ruffley M, Smith ML, Carstens B, Tank D, Sullivan J. Identifying cryptic diversity with predictive phylogeography. Proc R Soc B. 2016;283:20161529.
Article
PubMed
PubMed Central
Google Scholar
Knowlton N. Molecular genetic analyses of species boundaries in the sea. Hydrobiologia. 2000;420:73–90.
Article
CAS
Google Scholar
Pavan-Kumar A, Kumar R, Pitale P, Shen K-N, Borsa P. Neotrygon indica sp. Nov., the Indian Ocean blue-spotted maskray (Myliobatoidei, Dasyatidae). C R Biol. 2018;341(2):120–30.
Article
PubMed
Google Scholar
White WT, Furumitsu K, Yamaguchi A. A new species of eagle ray Aetobatus narutobiei from the Northwest Pacific: An example of the critical role taxonomy plays in fisheries and ecological sciences. PLoS ONE. 2014;8(12):e83785.
Article
CAS
Google Scholar
White WT, Corrigan S, Yang L, Henderson AC, Bazinet AL, Swofford DL, et al. Phylogeny of the manta and devilrays (Chondrichthyes: mobulidae), with an updated taxonomic arrangement for the family. Zool J Linn Soc. 2017;182(1):50–75.
Article
Google Scholar
Isaac NJB, Mallet J, Mace GM. Taxonomic inflation: its influence on macroecology and conservation. Trends Ecol Evol. 2004;19(9):464–9.
Article
PubMed
Google Scholar
Nelson JS. Editorial and introduction: the species concept in fish biology. Rev Fish Biol Fish. 1999;9(4):277–80.
Article
Google Scholar
Fennessy J, Bidon T, Reuss F, Kumar V, Elkan P, Nilsson Maria A, et al. Multi-locus analyses reveal four giraffe species instead of one. Curr Biol. 2016;26(18):2543–9.
Article
CAS
PubMed
Google Scholar
Richardson BJ. Subspecies definitions and legislation: from eastern wallaroo (Osphranter robustus robustus) to euro (Osphranter robustus erubescens). Aust Mammal. 2019;41(1):65–75.
Article
Google Scholar
Froese R. The good, the bad, and the ugly: A critical look at species and their institutions from a user’s perspective. Rev Fish Biol Fish. 1999;9(4):375–8.
Article
Google Scholar
Kullander SO. Fish species - how and why. Rev Fish Biol Fish. 1999;9(4):325–52.
Article
Google Scholar
Eschmeyer WN, Fricke R, Fong JD, Polack DA. Marine fish diversity: history of knowledge and discovery (Pisces). Zootaxa. 2010;2525:19–50.
Article
Google Scholar
Konstantinou H, McEachran JD, Woolley JB. The systematics and reproductive biology of the Galeus arae subspecific complex (Chondrichthyes: Scyliorhinidae). Environ Biol Fishes. 2000;57(2):117–29.
Article
Google Scholar
Springer S. A revision of the catsharks, Family Scyliorhinidae. USA: U.S. Department of Commerce; 1979.
Book
Google Scholar
Soares KDA, De Carvalho MR. The catshark genus Scyliorhinus (Chondrichthyes: Carcharhiniformes:Scyliorhinidae): taxonomy, morphology and distribution. Zootaxa. 2019;4601(1):1–147.
Article
Google Scholar
Springer S, Sadowsky V. Subspecies of the western Atlantic catshark, Scyliorhinus retifer. Proc Biol Soc Washington. 1970;83(7):83–98.
Google Scholar
Myagkov NA, Kondyurin VV. Dogfishes, Squalus (Squalidae) of the Atlantic Ocean and comparative notes on the species of this genus from other regions. J Ichthyol. 1986;26(6):1–18.
Google Scholar
Heemstra PC. A review of the smooth-hound sharks (genus Mustelus, family Triakidae) of the western Atlantic Ocean, with descriptions of two new species and a new subspecies. Bull Mar Sci. 1970;60:894–928.
Google Scholar
Lim DD, Motta P, Mara K, Martin AP. Phylogeny of hammerhead sharks (Family Sphyrnidae) inferred from mitochondrial and nuclear genes. Mol Phylogen Evol. 2010;55(2):572–9.
Article
Google Scholar
Richards VP, Henning M, Witzell W, Shivji MS. Species delineation and evolutionary history of the globally distributed spotted eagle ray (Aetobatus narinari). J Hered. 2009;100(3):273–83.
Article
CAS
PubMed
Google Scholar
Last PR, Weigmann S, Yang L. Changes to the nomenclature of the skates (Chondrichthyes: Rajiformes). In: Last PR, White WT, de Carvalho MR, Séret B, Stehmann MFW, Naylor GJP, editors. Rays of the world. Melbourne: CSIRO Publishing; 2016. p. 11–34.
Chapter
Google Scholar
Weigmann S. Annotated checklist of the living sharks, batoids and chimaeras (Chondrichthyes) of the world, with a focus on biogeographical diversity. J Fish Biol. 2016;88(3):837–1037.
Article
CAS
PubMed
Google Scholar
Lee MSY, Palci A. Morphological phylogenetics in the genomic age. Curr Biol. 2015;25:922–9.
Article
CAS
Google Scholar
Arunrugstichai S, True JD, White WT. Catch composition and aspects of the biology of sharks caught by Thai commercial fisheries in the Andaman Sea. J Fish Biol. 2018;92(5):1487–504.
Article
CAS
PubMed
Google Scholar
Borsa P, Arlyza IS, Hoareau TB, Shen KN. 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. 2018;36(3):827–41.
Article
Google Scholar
Khan S, Nabi G, Ullah MW, Yousaf M, Manan S, Siddique R, et al. Overview on the role of advance genomics in conservation biology of endangered species. Int J Genomics. 2016;2016:3460416.
PubMed
PubMed Central
Google Scholar
Ndebele P, Musesengwa R. Will developing countries benefit from their participation in genetics research? Malawi Med J. 2008;20(2):67–9.
PubMed
PubMed Central
Google Scholar
Padial JM, De la Riva I. Taxonomic inflation and the stability of species lists: the perils of ostrich’s behavior. Syst Biol. 2006;55(5):859–67.
Article
PubMed
Google Scholar
Niemiller ML, Near TJ, Fitzpatrick BM. Delimiting species using multilocus data: Diagnosing cryptic diversity in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae). Evolution. 2012;66(3):846–66.
Article
PubMed
Google Scholar
Pinheiro HT, Bernardi G, Simon T, Joyeux J, Macieira RM, Gasparini JL, et al. Island biogeography of marine organisms. Nature. 2017;549(7670):82–5.
Article
CAS
PubMed
Google Scholar
Dharmadi, Mahiswara, Kasim K. Catch composition and some biological aspects of sharks in western Sumatera waters of Indonesia. Indon Fish Res J. 2016;22(2):99–108.
Sunnucks P, Hales DF. Numerous transposed sequences of mitochondrial cytochrome oxidase I–II in aphids of the genus Sitobion (Hemiptera: Aphididae). Mol Biol Evol. 1996;13:510–24.
Article
CAS
PubMed
Google Scholar
Posada D, Crandall KA. Modeltest: testing the model of DNA substitution. Bioinformatics. 1998;14:817–8.
Article
CAS
PubMed
Google Scholar
Swofford DL. PAUP*. Phylogenetic Analysis Using Parsimony (* and other methods). Version 4.0a163. Sunderland, Massachusetts: Sinauer Associates; 2017. 500 p.
Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39:783–91.
Article
PubMed
Google Scholar
Huson DH, Scornavacca C. Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. Syst Biol. 2012;61(6):1061–7.
Article
PubMed
Google Scholar
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol. 2018;35:1547–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bandelt HJ, Forster P, Röhl A. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 1999;16(1):37–48.
Article
CAS
PubMed
Google Scholar
Leigh JW, Bryant D. Popart: full-feature software for haplotype network construction. Methods Ecol Evol. 2015;6(9):1110–6.
Article
Google Scholar
Kilian A, Wenzl P, Huttner E, Carling J, Xia L, Blois H, et al. Diversity Arrays Technology: A generic genome profiling technology on open platforms. In: Pompanon F, Bonin A, editors., et al., Data production and analysis in population genomics: Methods and protocols. Totowa, NJ: Humana Press; 2012. p. 67–89.
Chapter
Google Scholar
Georges A, Gruber B, Pauly GB, White D, Adams M, Young MJ, et al. Genomewide SNP markers breathe new life into phylogeography and species delimitation for the problematic short-necked turtles (Chelidae: Emydura) of eastern Australia. Mol Ecol. 2018;27(24):5195–213.
Article
PubMed
Google Scholar
Gruber B, Unmack PJ, Berry OF, Georges A. DARTr: An R package to facilitate analysis of SNP data generated from reduced representation genome sequencing. Mol Ecol Resour. 2017;18:691–9.
Article
Google Scholar
Gower JC. Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika. 1966;53(3–4):325–38.
Article
Google Scholar
Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution. 1984;38(6):1358–70.
CAS
PubMed
Google Scholar
Unmack PJ, Young MJ, Gruber B, White D, Kilian A, Zhang X, et al. Phylogeography and species delimitation of Cherax destructor (Decapoda: Parastacidae) using genome-wide SNPs. Mar Freshw Res. 2019;70(6):857–69.
Article
Google Scholar
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bryant D, Bouckaert R, Felsenstein J, Rosenberg NA, RoyChoudhury A. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol Biol Evol. 2012;29(8):1917–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H, Xie D, et al. BEAST 2: a software platform for bayesian evolutionary analysis. PLoS Comp Biol. 2014;10(4):e1003537.
Article
CAS
Google Scholar
Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, et al. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comp Biol. 2019;15(4):e1006650.
Article
CAS
Google Scholar
Leaché AD, Fujita MK, Minin VN, Bouckaert RR. Species delimitation using genome-wide SNP data. Syst Biol. 2014;63(4):534–42.
Article
PubMed
PubMed Central
Google Scholar