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Phylogeography of the Hong Kong Whipping Frog (Polypedates megacephalus) throughout Hainan Island, China

Feiyun Tu, Longhui Zhao, Robert W. Murphy, Xiaofei Zhai, Jichao Wang


The Hong Kong Whipping Frog (Polypedates megacephalus) is widespread on Hainan Island and yet nothing is known about its history. To investigate this, we use sequences of a partial fragment of mitochondrial ND1 and its flanking region from 248 individuals taken from 30 localities. Analyses reveal low genetic diversity and commonly shared haplotypes. Montane areas exhibit a significantly greater genetic diversity than lowland areas (P < 0.01). The origin of P. megacephalus on Hainan Island dates to 1.06 Ma in the Pleistocene. Population expansion events were associated with the transition from the last interglacial period to the last glacial maximum. The matrilineal history indicates dispersal from the montane to the lowland. Bidirectional dispersion occurs between northeastern and southwestern parts of the island. Low FCT values for the northeastern and the southwestern areas associate with rivers, whereas the highest values occur among two geographical groups. Thus, mountains and rivers appear to have effected dispersal. Pleistocene climatic cooling and the creation of a landbridge with mainland China owing to lowered sea levels best explains the occurrence of P. megacephalus on Hainan Island. The analyses provide insights into the effects of Pleistocene climatic fluctuations on an amphibian on Hainan Island.


mitochondrial DNA; climatic fluctuations; population expansion; Hainan Island

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Akaike H. (1974), «A new look at the statistical model identification», IEEE T. Automat. Contrib., 19(6), 716 – 723.

Beerli P. and Felsenstein J. (2001), «Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach», PNAS, 98(8), 4563 – 4568.

Bernardo P. H., Sanchez-Ramirez S., Sanchez-Pacheco S., Alvarez-Castañeda S. T., Aguilera-Miller E. F., Mendez-de-la-Cruz F. R., and Murphy R. W. (2019), «Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection, and climate», Heredity, 123(3), 359 – 370.

Blair C., Davy C. M., Ngo A., Orlov N. L., Shi H. T., Lu S. Q., Gao L., Rao D. Q., and Murphy R. W. (2013), «Genealogy and demographic history of a widespread amphibian throughout Indochina», J. Hered., 104(1), 72 – 85.

Carstens B. C., Brunsfeld S. J., Demboski J. R., Good J. M., and Sullivan J. (2005), «Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem: hypothesis testing within a comparative phylogeographic framework», Evolution, 59(8), 1639 – 1652.

Chen J. M., Prendini E., Wu Y. H., Zhang B. L., Suwannapoom C., Chen H. M., Jin J. Q., Lemmon E. M., Lemmon A. R., Stuart B. L., Raxworthy C. J., Murphy R. W., Yuan Z. Y., and Che J. (2020), «An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frog (Anura: Rhacophoridae)», Mol. Phylogen. Evol., 145(2020), 106724.

Ding L., He S. P., Gan X. N., and Zhao E. M. (2011), «A phylogeographic, demographic and historical analysis of the short-tailed pit viper (Gloydius brevicaudus): evidence for early divergence and late expansion during the Pleistocene», Mol. Ecol., 20(9), 1905 – 1922.

Duellman W. E. and Trueb L. (eds.), (1994), Biology of Amphibians, McGraw-Hill, New York.

Dupanloup I., Schneider S., and Excoffier L. (2002), «A simulated annealing approach to define the genetic structure of populations», Mol. Ecol., 11(12), 2571 – 2581.

Dutta S. K. and Manamendra-Arachchi K. (eds.), (1996), The Amphibian Fauna of Sri Lanka, Wildlife Heritage Trust of Sri Lanka, Columbo.

Drummond A. J. and Rambaut A. (2007), «BEAST: Bayesian evolutionary analyses by sampling trees», BMC Evol. Biol., 7, 214.

Drummond A. J. and Rambaut A. (2008), BEAST website. BEAST ver. 1.7.1. Page (accessed on May 7, 2012).

Excoffier L., Laval G., and Schneider S. (2005), «Arlequin ver. 3.0: an integrated software package for population genetics data analysis», Evol. Bioinf. Online, 1(47), 47 – 50.

Fan Z. X., Liu S. Y., Liu Y., Liao L. H., Zhang X. Y., and Yue B. S. (2012), «Phylogeography of the South China field mouse (Apodemus draco) on the southeastern Tibetan Plateau reveals high genetic diversity and glacial refugia», PLoS ONE, 7(5), e38184.

Fu Y. X. (1997), «Statistical test of neutrality of mutations against population growth, hitchhiking and background selection», Genetics, 147(2), 915 – 925.

Godbout J., Jaramillo-Correa J. P., and Beaulieu J. (2005), «A mitochondrial DNA minisatellite reveals the postglacial history of jack pine (Pinus banksiana), a broad-range North American conifer», Mol. Ecol., 14(11), 3497 – 3512.

Gong S. P., Shi H. T., Mo Y. M., Auer M., Vargas-Ramírez M., Hundsdörfer A. K., and Fritz U. (2009), «Phylogeography of the endangered black-breasted leaf turtle (Geoemy daspengleri) and conservation Implications for other chelonians», Amphibia–Reptilia, 30(1), 57 – 62.

Guindon S., Dufayard J. F., Lefort V., Anisimova M., Hordijk W., and Gascuel O. (2010), «New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0», Syst. Biol., 59(3), 307 – 321.

Harpending H. C. (1994), «Signature of ancient population growth in a low resolution mitochondrial DNA mismatch distribution», Human Biol., 66(4), 591 – 600.

Hewitt G. M. (2000), «The genetic legacy of the quaternary ice ages», Nature, 405(6789), 907 – 913.

Hewitt G. M. (2004), «Genetic consequences of climatic oscillations in the Quaternary», Phil. Trans. Roy. Soc. B, 359(1442), 183 – 195.

Hoffman E. A. and Blouin M. S. (2004), «Evolutionary history of the northern leopard frog: reconstruction of phylogeny, phylogeography, and historical changes in population demography from mitochondrial DNA», Evolution, 58(1), 145 – 159.

Hou G. L. and Fang X. Q. (2011), «Characteristics of Holocene temperature change in China», Progr. Geogr., 30(9), 1075 – 1080 [in Chinese with English abstract].

Huelsenbeck J. P. and Hillis D. M. (1993), «Success of phylogenetic methods in the four-taxon case», Syst. Biol., 42(3), 247 – 264.

Huelsenbeck J. P. and Rannala B. (2004) «Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models», Syst. Biol., 53(6), 904 – 913.

Inger R. F. (2003) «Sampling biodiversity in Bornean frogs», Nat. Hist. J. Chulalongkorn Univ., 3(1), 9 – 15.

Knowles L. L. (2000), «Tests of Pleistocene speciation in montane grasshoppers (genus Melanoplus) from the sky islands of western North America», Evolution, 54(4), 1337 – 1348.

Knowles L. L. (2001), «Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshoppers», Mol. Ecol., 10(3), 691 – 701.

Kvist L., Viiri K., Dias P. C., Rytkönen S., and Orell M. (2004), «Glacial history and colonization of Europe by the blue tit Parus caeruleus», J. Avian Biol., 35(4), 352 – 359.

Lambeck K., Esat T. M., and Potter E. K. (2002), «Links between climate and sea levels for the past three million years», Nature, 419(6903), 199 – 206.

Li J. T., Che J., Bain R. H., Zhao E. M., and Zhang Y. P. (2008), «Molecular phylogeny of Rhacophoridae (Anura): a framework of taxonomic reassignment of species within the genera Aquixalus, Chiromantis, Rhacophorus, and Philautus», Mol. Phylogen. Evol., 48(1), 302 – 312.

Li J. T., Che J., Murphy R. W., Zhao H., Zhao E. M., Rao D. Q., and Zhang Y. P. (2009), «New insights to the molecular phylogenetics and generic assessment in the Rhacophoridae (Amphibia: Anura) based on five nuclear and three mitochondrial genes, with comments on the evolution of reproduction», Mol. Phylogen. Evol., 53(2), 509 – 522.

Li S. H., Yeung C. K. L., Feinstein J., Han L. X., Le M. H., Wang C. X., and Ding P. (2009), «Sailing through the Late Pleistocene: unusual historical demography of an East Asian endemic, the Chinese hwamei (Leucodioptron canorum canorum), during the last glacial period», Mol. Ecol., 18(4), 622 – 633.

Li Y. L., Wang X. G., Fu L., Shu X. X., Wang B., and Jiang J. P. (2017) «Morphological variation of Microhyla fissipes on Hainan Island», Chin. J. Appl. Environ. Biol., 23(6) 1135 – 1141 [in Chinese with English abstract].

Liao P. H. (2014), Studies on Population Divergence and Molecular Phylogenetics of Fejervarya limnocharis and Bufo gargarizans in Zhoushan Archipelago, China Jiliang University, Hangzhou, pp. 62 – 68 [in Chinese with English abstract].

Librado P. and Rozas J. (2009), «DnaSP v. 5: a software for comprehensive analysis of DNA polymorphism data», Bioinformatics, 25(11), 1451 – 1452.

Liu Q., Chen P., He K., Kilpatrick C. W., Liu S. Y., Yu F. H., Jiang X. L., and Hofreiter M. (2012), «Phylogeographic study of Apodemus ilex (Rodentia: Muridae) in Southwest China», PLoS ONE, 7(2), e31453.

Liu Q. C., Zhai X. F., Wang T. L., and Wang J. C. (2018), «Morphological identification and diversity of Polypedates species (Rhacophoridae, Anura, Amphibia) on Hainan Island», Sichuan J. Zool., 37(5), 490 – 496 [in Chinese with English abstract].

Maddison W. P. and McMahon M. (2000), «Divergence and reticulation among montane populations of a jumping spider (Habronattus pugillis Griswold)», Syst. Biol., 49(3), 400 – 421.

Magri D., Vendramin G. G., Comps B., Dupanloup I., Geburek T., Gömöry D., Latałowa M., Litt T., Paule L., Roure J. M., Tantau I., van der Knaap W. O., Petit R. J., and de Beaulieu J. L. (2006), «A new scenario for the quaternary history of European beech populations: palaeobotanical evidence and genetic consequences», New Phytol., 171(1), 199 – 221.

Martínez-Freiría F., Velo-Antön G., and Brito J. C. (2014), «Trapped by climate: interglacial refuge and recent population expansion in the Iberian adder Vipera seoanei», Divers. Distrib., 21(3), 1 – 14.

Matsui M., Shimada T., and Sudin A. (2014) «First record of the tree-frog genus Chiromantis from Borneo with the description of a new species (Amphibia: Rhacophoridae)», Zool. Sci., 31(1), 45 – 51.

Masta S. E. (2000), «Phylogeography of the jumping spider Habronattus pugillis (Araneae: Salticidae): recent vicariance of sky island populations?» Evolution, 54(5), 1699 – 1711.

Mekonnen A., Rueness E. K., Stenseth N. C., Fashing P. J., Bekele A., Hernandez-Aguilar R. A., Missbach R., Haus T., Zinner D., and Roos C. (2018), «Population genetic structure and evolutionary history of Bale monkeys (Chlorocebus djamdjamensis) in the southern Ethiopian Highlands», BMC Evol. Biol., 18(1), 106 – 121.

Milä B., Smith T. B., and Wayne R. K. (2006), «Postglacial population expansion drives the evolution of long-distance migration in a songbird», Evolution, 60(11), 2403 – 2409.

Nylander J. A. A. (2004), MrModeltest v. 2, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

Pauls S. U., Nowak C., Balint M., and Pfenninger M. (2013), «The impact of global climate change on genetic diversity within populations and species», Mol. Ecol., 22(4), 925 – 946.

Phillips S. J., Anderson R. P., and Schapire R. E. (2006), «Maximum entropy modeling of species geographic distributions», Ecol. Model., 190(3 – 4), 231 – 259.

Qian H. and Ricklefs R. E. (2000), «Large-scale processes and the Asian bias in temperate plant species diversity», Nature, 407(6801), 180 – 182.

Qing N., Ma T. F., Liang X. X., Lin H. D., Lu W. H., and Lazell J. (2011), «Population genetics and biogeography of Bufo melanostictus (Anura, Bufonidae) in south China», Acta Zootaxon. Sin., 36(2), 356 – 367 [in Chinese with English abstract].

Ronquist F. R. and Huelsenbeck J. P. (2003), «MrBayes 3: Bayesian inference of phylogeny», Bioinformatics, 19(12), 1572 – 1574.

Rambaut A. (2008), Molecular Evolution, Phylogenetics and Epidemiology Website. FigTree ver. 1.3.1. (accessed on May 7, 2012).

Rambaut A. and Drummond A. J. (2007), Molecular Evolution, Phylogenetics and Epidemiology Website. Tracer ver. 1.5. (accessed on April 8, 2020)

Ramirez-Soriano A., Ramos-Onsins S. E., Rozas J., Calafell F., and Navarro A. (2008), «Statistical power analysis of neutrality tests under demographic expansions, contractions and bottlenecks with recombination», Genetics, 179(1), 555 – 567.

Ramos-Onsins S. E. and Rozas J. (2002), «Statistical properties of new neutrality tests against population growth», Mol. Biol. Evol., 19(12), 2092 – 2100.

Rogers A. and Harpending H. M. (1992), «Population growth makes waves in the distribution of pairwise genetic differences», Mol. Biol. Evol., 9(3), 552 – 569.

Shi Y. F., Cui Z. J., and Su Z. (2006), The Quaternary Glaciations and Environmental Variations in China, Hebei Science and Technology Press, Shijiazhuang [in Chinese].

Slatkin M. and Hudson R. R. (1991), «Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations», Genetics, 129(2), 555 – 562.

Smith C. I. and Farrell B. D. (2005), «Phylogeography of the longhorn cactus beetle Moneilema appressum LeConte (Coleoptera: Cerambycidae): was the differentiation of the Madrean sky islands driven by Pleistocene climate changes?» Mol. Ecol., 14(10), 3049 – 3065.

Song G., Qu Y. H., Yin Z. H., Li S. S., Liu N. F., and Lei F. M. (2009), «Phylogeography of the Alcippe morrisonia (Aves: Timaliidae): long population history beyond late Pleistocene glaciations», BMC Evol. Biol., 9(1), 143.

Wang W. J., McKay B. D., Dai C. Y., Zhao N., Zhang R. Y., Qu Y. H., Song G., Li S. H., Liang W., Yang X. J., Pasquet E., and Lei F. M. (2013), «Glacial expansion and diversification of an East Asian montane bird, the green-backed tit (Parus monticolus)», J. Biogeogr., 40(6), 1156 – 1169.

Wang X. H., Li J., Zhang L. M., He Z. W., Mei Q. M., Gong X., Jian S. G. (2019), «Population differentiation and demographic history of the Cycas taiwaniana complex (Cycadaceae) endemic to south China as indicated by DNA sequences and microsatellite markers», Front. Gen., 10, 1238.

Wilkinson J. A., Drewes R. C., and Tatum O. L. (2002), «A molecular phylogenetic analysis of the family Rhacophoridae with an emphasis on the Asian and African genera», Mol. Phylogen. Evol., 24(2), 265 – 273.

Wright S. (1931), «Evolution in Mendelian populations», Genetics, 16(2), 97 – 159.

Wright S. (1978), Evolution and the genetics of populations. Vol. 4, Univ. of Chicago Press, Edmonton, Chicago.

Xia X. and Xie Z. (2001), «DAMBE: data analysis in molecular biology and evolution», J. Hered., 92(4), 371 – 373.

Yang Y., Duke N. C., Peng F., Li J., Yang S., Zhong C., Zhou R., and Shi S. (2016), «Ancient geographical barriers drive differentiation among Sonneratia caseolaris populations and recent divergence from S. lanceolata», Front. Plant Sci., 7, 1618 – 1632.

Zeisset I. and Beebee T. J. C. (2008), «Amphibian phylogeography: a model for understanding historical aspects of species distributions», Heredity, 101(2), 109 – 119.

Zhang R. Z. (2004), «Relict distribution of land vertebrates and Quaternary glaciation in China», Acta Zool. Sin., 50(5), 841 – 851 [in English with Chinese abstract].

Zhang H., Yan J., Zhang G. Q., and Zhou K. Y. (2008), «Phylogeography and demographic history of Chinese black-spotted frog populations (Pelophylax nigromaculata): Evidence for independent refugia expansion and secondary contact», BMC Evol. Biol., 8(1), 21.

Zhang R. Z. (2011), Zoogeography of China, Science Press, Beijing [in Chinese].

Zhao H. T., Wang L. R., and Yuan J. Y. (2007), «Origin and time of Qiongzhou Strait», Marine Geol. Quatern. Geol., 27(2), 33 – 40 [in Chinese with English abstract].



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