Phylogeographic investigation on the spiny frog Quasipaa shini (Amphibia: Anura: Dicroglossidae) using mitochondrial DNA: cryptic species and species complex

References

• Ahl E. 1930. Beiträge zur Lurch- und Kriechtierfauna Kwangsi’s. 3. Frösche. Sitzungsberichte Der Gesellschaft Naturforschender Freunde zu Berlin. 1930:315–319.
   Google Scholar
• Baric S, Sturmbauer C. 1999. Ecological parallelism and cryptic species in the genus Ophiothrix derived from mitochondrial DNA sequences. Mol Phylogenet Evol. 11:157–162.
   PubMed Web of Science ®Google Scholar
• Borisenko AV, Lim BK, Ivanova NV, Hanner RH, Hebert PDN. 2008. DNA barcoding in surveys of small mammal communities: a field study in Suriname. Mol Ecol Resour. 8:471–479.
   PubMed Web of Science ®Google Scholar
• Braukmann TW, Kuzmina ML, Sills J, Zakharov EV, Hebert PD. 2017. Testing the efficacy of DNA barcodes for identifying the vascular plants of Canada. PLoS One. 12:e0169515.
   PubMed Web of Science ®Google Scholar
• Che J, Chen HM, Yang JX, Jin JQ, Jiang KE, Yuan ZY, Murphy RW, Zhang YP. 2012. Universal COI primers for DNA barcoding amphibians. Mol Ecol Resour. 12:247–258.
   PubMed Web of Science ®Google Scholar
• Che J, Zhou WW, Hu JS, Yan F, Papenfuss TJ, Wake DB, Zhang YP. 2010. Spiny frogs (Paini) illuminate the history of the Himalayan region and Southeast Asia. Proc Natl Acad Sci USA. 107:13765–13770.
   PubMed Web of Science ®Google Scholar
• Clement M, Posada D, Crandall K. 2000. TCS: a computer program to estimate gene genealogies. Mol Ecol. 9:1657–1660.
   PubMed Web of Science ®Google Scholar
• Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat Meth. 9:772.
   PubMed Web of Science ®Google Scholar
• De Queiroz K. 2007. Species concepts and species delimitation. Syst Biol. 56:879–886.
   PubMed Web of Science ®Google Scholar
• Excoffier L, Laval G, Schneider S. 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform. 1:47–50.
   PubMed Web of Science ®Google Scholar
• Fei L, Hu SQ, Ye CY, Huang YZ. 2009. Fauna sinica, amphibia Vol. 3, Anura ranidae. Beijing: Science Press.
   Google Scholar
• Fei L, Ye CY, Jiang JP. 2012. Colored atlas of Chinese Amphibians and their distributions. Chengdu: Sichuan Publishing House of Science and Technology.
   Google Scholar
• Ferguson JWH. 2002. On the use of genetic divergence for identifying species. Biol J Linn Soc. 75:509–516.
   Web of Science ®Google Scholar
• Frost DR. 2018. Amphibian Species of the World Version 6.0. New York, USA: American Museum of Natural History. Available from: http://research.amnh.org/vz/herpetology/amphibia/ (accessed 20 October 2018).
   Google Scholar
• Fu YX. 1997. Statistical test of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 147:915–925.
   PubMed Web of Science ®Google Scholar
• Guindon S, Dufayard JF, 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. Syst Biol. 59:307–321.
   PubMed Web of Science ®Google Scholar
• Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696–704.
   PubMed Web of Science ®Google Scholar
• Jiang ZG, Jiang JP, Wang YZ, Zhang E, Zhang YY, Li LL, Xie F, Cai B, Cao L, Zheng GM, et al. 2016. Red list of China’s vertebrates. Biodiv Sci. 24: 500–551.
   Google Scholar
• Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30:3059–3066.
   PubMed Web of Science ®Google Scholar
• Li YM, Wu XY, Zhang HB, Yan P, Xue H, Wu XB. 2015. Vicariance and its impact on the molecular ecology of a Chinese Ranid frog species-complex (Odorrana schmackeri, Ranidae). Plos One. 10:e0138757.
   PubMed Web of Science ®Google Scholar
• Li SZ, Xu N, Lv JC, Jiang JP, Wei G, Wang B. 2018. A new species of the odorous frog genus Odorrana (Amphibia, Anura, Ranidae) from southwestern China. PeerJ. 6:e5695.
   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
• Liu HX, Li Y, Liu XL, Xiong DM, Wang LX, Zou GW, Wei QW. 2015. Phylogeographic structure of Brachymystax lenok tsinlingensis (Salmonidae) populations in the Qinling Mountains, Shaanxi, based on mtDNA control region. Mitochondrial DNA. 26:532–537.
   PubMed Web of Science ®Google Scholar
• Lu B, Bi K, Fu J. 2014. A phylogeographic evaluation of the Amolops mantzorum species group: cryptic species and plateau uplift. Mol Phylogenet Evol. 73:40–52.
   PubMed Web of Science ®Google Scholar
• Miracle AL, Campton DE. 1995. Tandem repeat sequence variation and length heteroplasmy in the mitochondrial DNA D-loop of the threatened Gulf of Mexico sturgeon, Acipenser oxyrhynchus desotoi. J Hered. 86:22–27.
   PubMed Web of Science ®Google Scholar
• Paggi L, Nascetti G, Webb SC, Mattiucci S, Cianchi R, Bullini L. 1998. A new species of Anisakis Dujardin, 1845 (Nematoda, Anisakidae) from beaked whales (Ziphiidae)-allozyme and morphological evidence. Syst Parasitol. 40:161–174.
   Web of Science ®Google Scholar
• Roxo FF, Ochoa LE, Costa-Silva GJ, Oliveira C. 2015. Species delimitation in Neoplecostomus (Siluriformes: Loricariidae) using morphologic and genetic approaches. DNA Barcodes. 3:110–117.
   Google Scholar
• Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: a laboratory manual. New York, USA: Cold Spring Harbor Laboratory Press.
   Google Scholar
• Smith MA, Fisher BL, Hebert PDN. 2005. DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar. Philos Trans R Soc B. 360:1825–1834.
   PubMed Web of Science ®Google Scholar
• Sun P, Shi Z, Yin F, Peng S. 2012. Genetic variation analysis of Mugil cephalus in China Sea based on mitochondrial COI gene sequences. Biochem Genet. 50:180–191.
   PubMed Web of Science ®Google Scholar
• Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123:585–595.
   PubMed Web of Science ®Google Scholar
• Tamura K, Stecher G, Peterson D, Fiipski A, Kumar S. 2011. MEGA6: molecular evolutionary genetics analysis using evolutionary distance. Mol Biol Evol. 28:2725–2729.
   Web of Science ®Google Scholar
• Tavares ES, Gonçalves P, Miyaki CY, Baker AJ. 2011. DNA barcode detects high genetic structure within neotropical bird species. PLoS One. 6:e28543.
   PubMed Web of Science ®Google Scholar
• Wang B, Xie F, Li JN, Wang G, Li C, Jiang JP. 2017. Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau. PeerJ. 5:e3770. DOI: 10.7717/peerj.3770.
   PubMed Web of Science ®Google Scholar
• Weiss S, Marić S, Snoj A. 2011. Regional structure despite limited mtDNA sequence diversity found in the endangered Huchen, Hucho hucho (Linnaeus, 1758). Hydrobiologia. 658:103–110.
   Web of Science ®Google Scholar