Volume 43 Issue 5
Sep.  2022
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Tao Luo, Sha-Sha Yan, Ning Xiao, Jia-Jun Zhou, Xing-Liang Wang, Wei-Cai Chen, Huai-Qing Deng, Bao-Wei Zhang, Jiang Zhou. Phylogenetic analysis of combined mitochondrial genome and 32 nuclear genes provides key insights into molecular systematics and historical biogeography of Asian warty newts of the genus Paramesotriton (Caudata: Salamandridae). Zoological Research, 2022, 43(5): 787-804. doi: 10.24272/j.issn.2095-8137.2022.081
Citation: Tao Luo, Sha-Sha Yan, Ning Xiao, Jia-Jun Zhou, Xing-Liang Wang, Wei-Cai Chen, Huai-Qing Deng, Bao-Wei Zhang, Jiang Zhou. Phylogenetic analysis of combined mitochondrial genome and 32 nuclear genes provides key insights into molecular systematics and historical biogeography of Asian warty newts of the genus Paramesotriton (Caudata: Salamandridae). Zoological Research, 2022, 43(5): 787-804. doi: 10.24272/j.issn.2095-8137.2022.081

Phylogenetic analysis of combined mitochondrial genome and 32 nuclear genes provides key insights into molecular systematics and historical biogeography of Asian warty newts of the genus Paramesotriton (Caudata: Salamandridae)

doi: 10.24272/j.issn.2095-8137.2022.081
#Authors contributed equally to this work
Funds:  This study was supported by the Guizhou Province Top Discipline Construction Program Project (Qianjiao Keyan Fa[2019]125), Postgraduate Education Innovation Programme of Guizhou Province (Qianjiaohe YJSKYJJ (2021) 091), Strategic Priority Research Program B of the Chinese Academy of Sciences (CAS) (XDB31000000), National Animal Collection Resource Center, China, and Application of Amphibian Natural Antioxidant Peptides as Cosmetic Raw Material Antioxidants (QKZYD [2020]4002)
More Information
  • The Paramesotriton Chang, 1935 genus of Asian warty newts is the second most diverse genus in the family Salamandridae, currently containing 14 recognized species from northern Vietnam to southwest-central and southern China. Although species of this genus have been included in previous phylogenetic studies, the origin and interspecific relationships of the genus are still not fully resolved, especially at key nodes in the phylogeny. In this study, we sequenced mitochondrial genomes and 32 nuclear genes from 27 samples belonging to 14 species to reconstruct the interspecific phylogenetic relationships within Paramesotriton and explore its historical biogeography in southern China. Both Bayesian inference and maximum-likelihood analyses highly supported the monophyly of Paramesotriton and its two recognized species groups (P. caudopunctatus and P. chinensis groups) and further identified five hypothetical phylogenetic cryptic species. Biogeographic analyses indicated that Paramesotriton originated in southwestern China (Yunnan-Guizhou Plateau/South China) during the late Oligocene. The time of origin of Paramesotriton corresponded to the second uplift of the Himalayan/Qinghai-Xizang (Tibetan) Plateau (QTP), rapid lateral extrusion of Indochina, and formation of karst landscapes in southwestern China. Principal component analysis (PCA), independent sample t-tests, and niche differentiation using bioclimatic variables based on locations of occurrence suggested that Paramesotriton habitat conditions in the three current regions (West, South, and East) differ significantly, with different levels of climatic niche differentiation. Species distribution model (SDM) predictions indicated that the most suitable distribution areas for the P. caudopunctatus and P. chinensis species groups are western and southern/eastern areas of southern China. This study increases our knowledge of the taxonomy, biodiversity, origin, and suitable distribution areas of the genus Paramesotriton based on phylogenetic, biogeographic, and species distribution models.
  • #Authors contributed equally to this work
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  • [1]
    Allouche O, Tsoar A, Kadmon R. 2006. Assessing the accuracy of species distribution models: prevalence, kappa and the true skill statistic (TSS). Journal of Applied Ecology, 43(6): 1223−1232. doi: 10.1111/j.1365-2664.2006.01214.x
    [2]
    AmphibiaChina. 2022. The database of Chinese amphibians. Yunnan, China: Kunming Institute of Zoology. http://www.amphibiachina.org/. (in Chinese)
    [3]
    An ZS, Kutzbach JE, Prell WL, Porter SC. 2001. Evolution of Asian monsoons and phased uplift of the Himalaya–Tibetan plateau since Late Miocene times. Nature, 411(6833): 62−66. doi: 10.1038/35075035
    [4]
    An ZS, Zhang PZ, Wang EQ, Wang SM, Qiang XK, Li L, et al. 2006. Changes of the monsoon-arid environment in China and growth of the Tibetan Plateau since the Miocene. Quaternary Sciences, 26(5): 678−693. (in Chinese)
    [5]
    Allen GC, Flores-Vergara MA, Krasynanski S, Kumar S, Thompson WF. 2006. A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nature Protocols, 1(5): 2320−2325. doi: 10.1038/nprot.2006.384
    [6]
    Antonelli A, Kissling WD, Flantua SGA, Bermúdez MA, Mulch A, Muellner-Riehl AN, et al. 2018. Geological and climatic influences on mountain biodiversity. Nature Geoscience, 11(10): 718−725. doi: 10.1038/s41561-018-0236-z
    [7]
    Bai DH, Unsworth M, Meju MA, Ma XB, Teng JW, Kong XR, et al. 2010. Crustal deformation of the eastern Tibetan plateau revealed by magnetotelluric imaging. Nature Geoscience, 3(5): 358−362. doi: 10.1038/ngeo830
    [8]
    Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19(5): 455−477. doi: 10.1089/cmb.2012.0021
    [9]
    Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, et al. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution, 69(2): 313−319. doi: 10.1016/j.ympev.2012.08.023
    [10]
    Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, et al. 2014. BEAST 2: a software platform for bayesian evolutionary analysis. PLoS Computational Biology, 10(4): e1003537. doi: 10.1371/journal.pcbi.1003537
    [11]
    Broennimann O, Fitzpatrick MC, Pearman PB, Petitpierre B, Pellissier L, Yoccoz NG, et al. 2012. Measuring ecological niche overlap from occurrence and spatial environmental data. Global Ecology and Biogeography, 21(4): 481−497. doi: 10.1111/j.1466-8238.2011.00698.x
    [12]
    Bureau of Geology and Mineral Guizhou Province. 1987. Regional Geology of Guizhou Province. Beijing: Geological Publishing House. (in Chinese)
    [13]
    Chan LM, Zamudio KR, Wake DB. 2001. Relationships of the salamandrid genera Paramesotriton, Pachytriton, and Cynops based on mitochondrial DNA sequences. Copeia, 2001(4): 997−1009. doi: 10.1643/0045-8511(2001)001[0997:ROTSGP]2.0.CO;2
    [14]
    Chang MLY. 1935. Note préliminaire sur la classification des salamandres d’asie orientale. Bulletin de la Société Zoologique de France, 60: 424−427.
    [15]
    Che J, Zhou WW, Hu JS, Yan F, Papenfuss TJ, Wake DB, et al. 2010. Spiny frogs (Paini) illuminate the history of the Himalayan region and Southeast Asia. Proceedings of the National Academy of Sciences of the United States of America, 107(31): 13765−13770. doi: 10.1073/pnas.1008415107
    [16]
    Che YT, Yu JZ. 1985. Karst in China. Beijing: Science Press. (in Chinese)
    [17]
    Chen JM, Poyarkov Jr NA, Suwannapoom C, Lathrop A, Wu YH, Zhou WW, et al. 2018a. Large-scale phylogenetic analyses provide insights into unrecognized diversity and historical biogeography of Asian leaf-litter frogs, genus Leptolalax (Anura: Megophryidae). Molecular Phylogenetics and Evolution, 124: 162−171. doi: 10.1016/j.ympev.2018.02.020
    [18]
    Chen JM, Prendini E, Wu YH, Zhang BL, Suwannapoom C, Chen HM, et al. 2020. An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae). Molecular Phylogenetics and Evolution, 145: 106724. doi: 10.1016/j.ympev.2019.106724
    [19]
    Chen XH, Chen Z, Jiang JP, Qiao L, Lu YQ, Zhou KY, et al. 2013. Molecular phylogeny and diversification of the genus Odorrana (Amphibia, Anura, Ranidae) inferred from two mitochondrial genes. Molecular Phylogenetics and Evolution, 69(3): 1196−1202. doi: 10.1016/j.ympev.2013.07.023
    [20]
    Chen YX, Chen YS, Shi CM, Huang ZB, Zhang Y, Li SK, et al. 2018b. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. GigaScience, 7(1): gix120.
    [21]
    Cobos ME, Peterson AT, Barve N, Osorio-Olvera L. 2019. Kuenm: an R package for detailed development of ecological niche models using Maxent. PeerJ, 7: e6281. doi: 10.7717/peerj.6281
    [22]
    Cohen KM, Finney SC, Gibbard PL, Fan JX. 2013. The ICS international chronostratigraphic chart. Episodes, 36(3): 199−204. doi: 10.18814/epiiugs/2013/v36i3/002
    [23]
    Deng M, Jiang XL, Hipp AL, Manos PS, Hahn M. 2018. Phylogeny and biogeography of East Asian evergreen oaks (Quercus section Cyclobalanopsis; Fagaceae): insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia. Molecular Phylogenetics and Evolution, 119: 170−181. doi: 10.1016/j.ympev.2017.11.003
    [24]
    Di Cola V, Broennimann O, Petitpierre B, Breiner FT, D'Amen M, Randin C, et al. 2017. ecospat: an R package to support spatial analyses and modeling of species niches and distributions. Ecography, 40(6): 774−787. doi: 10.1111/ecog.02671
    [25]
    Ding L, Spicer RA, Yang J, Xu Q, Cai FL, Li S, et al. 2017. Quantifying the rise of the Himalaya orogen and implications for the South Asian monsoon. Geology, 45(3): 215−218. doi: 10.1130/G38583.1
    [26]
    Dormann CF, Elith J, Bacher S, Buchmann C, Carl G, Carré G, et al. 2013. Collinearity: a review of methods to deal with it and a simulation study evaluating their performance. Ecography, 36(1): 27−46. doi: 10.1111/j.1600-0587.2012.07348.x
    [27]
    Dubois A, Ohler A, Pyron RA. 2021. New concepts and methods for phylogenetic taxonomy and nomenclature in zoology, exemplified by a new ranked cladonomy of recent amphibians (Lissamphibia). Megataxa, 5(1): 1−738.
    [28]
    Dubois A, Raffaëlli J. 2009. A new ergotaxonomy of the family Salamandridae Goldfuss, 1820 (Amphibia, Urodela). Alytes, 26(1–4): 1–85.
    [29]
    Estes R. 1981. Gymnophiona, Caudata: Handbuch der Paläoherpetologie. New York: Gustav Fischer.
    [30]
    Favre A, Päckert M, Pauls SU, Jähnig SC, Uhl D, Michalak I, et al. 2015. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan biotas. Biological Reviews, 90(1): 236−253. doi: 10.1111/brv.12107
    [31]
    Fei L, Hu SQ, Ye CY, Huang YZ. 2006. Fauna Sinica, Amphibia, vol. 1. Beijing: Science Press. (in Chinese)
    [32]
    Fei L, Ye CY. 2016. Amphibians of China, Volume 1. Beijing: Science Press.
    [33]
    Frost DR. 2021. Amphibian Species of the World: an Online Reference. Version 6.0. New York: American Museum of Natural History. http://research.amnh.org/herpetology/amphibia/index.html.
    [34]
    Fu XW, Zhu WL, Geng JH, Yang SY, Zhong K, Huang XT, et al. 2020. The present-day Yangtze River was established in the late miocene: evidence from detrital zircon ages. Journal of Asian Earth Sciences, 205: 104600.
    [35]
    Fujita MK, Leaché AD, Burbrink FT, McGuire JA, Moritz C. 2012. Coalescent-based species delimitation in an integrative taxonomy. Trends in Ecology & Evolution, 27(9): 480−488.
    [36]
    Goldscheider N, Chen Z, Auler AS, Bakalowicz M, Broda S, Drew D, et al. 2020. Global distribution of carbonate rocks and karst water resources. Hydrogeology Journal, 28(5): 1661−1677. doi: 10.1007/s10040-020-02139-5
    [37]
    Gu XM, Chen RR, Tian YZ, Li S, Ran JC. 2012b. A new species of Paramesotriton (Caudata: Salamandridae) from Guizhou Province, China. Zootaxa, 3510(1): 41−52. doi: 10.11646/zootaxa.3510.1.2
    [38]
    Gu XM, Wang H, Chen RR, Tian YZ, Li S. 2012a. The phylogenetic relationships of Paramesotriton (Caudata: Salamandridae) based on partial mitochondrial DNA gene sequences. Zootaxa, 3150(1): 59−68. doi: 10.11646/zootaxa.3150.1.3
    [39]
    Guisan A, Thuiller W. 2005. Predicting species distribution: offering more than simple habitat models. Ecology Letters, 8(9): 993−1009. doi: 10.1111/j.1461-0248.2005.00792.x
    [40]
    Guo P, Liu Q, Li C, Chen X. Jiang K, Wang YZ, et al. 2011. Molecular phylogeography of Jerdon’s pitviper (Protobothrops jerdonii): importance of the uplift of the Tibetan plateau. Journal of Biogeography, 38(12): 2326−2336. doi: 10.1111/j.1365-2699.2011.02566.x
    [41]
    Guo P, Liu Q, Zhu F, Zhong GH, Che J, Wang P, et al. 2019. Multilocus phylogeography of the brown-spotted pitviper Protobothrops mucrosquamatus (Reptilia: Serpentes: Viperidae) sheds a new light on the diversification pattern in Asia. Molecular Phylogenetics and Evolution, 133: 82−91. doi: 10.1016/j.ympev.2018.12.028
    [42]
    Guo P, Liu Q, Zhu F, Zhong GH, Chen X, Myers EA, et al. 2016. Complex longitudinal diversification across South China and Vietnam in Stejneger's pit viper, Viridovipera stejnegeri (Schmidt, 1925) (Reptilia: Serpentes: Viperidae). Molecular Ecology, 25(12): 2920−2936. doi: 10.1111/mec.13658
    [43]
    Guo P, Zhu F, Liu Q, Wang P, Che J, Nguyen TQ. 2020. Out of the hengduan mountains: molecular phylogeny and historical biogeography of the Asian water snake genus Trimerodytes (Squamata: Colubridae). Molecular Phylogenetics and Evolution, 152: 106927. doi: 10.1016/j.ympev.2020.106927
    [44]
    Hanley JA, McNeil BJ. 1982. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology, 143(1): 29−36. doi: 10.1148/radiology.143.1.7063747
    [45]
    Hazzi NA, Moreno JS, Ortiz-Movliav C, Palacio RD. 2018. Biogeographic regions and events of isolation and diversification of the endemic biota of the tropical Andes. Proceedings of the National Academy of Sciences of the United States of America, 115(31): 7985−7990. doi: 10.1073/pnas.1803908115
    [46]
    Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A. 2005a. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25(15): 1965−1978. doi: 10.1002/joc.1276
    [47]
    Hijmans RJ, Guarino L, Jarvis A, O’Brien R, Mathur P, Bussink C, et al. 2005b. DIVA-GIS, version 5.2.https://manualzilla.com/doc/5743142/diva-gis-manual.
    [48]
    Hoang DT, Chernomor O, Von Haeseler A, Minh BQ, Vinh LS. 2018. UFBoot2: improving the ultrafast bootstrap approximation. Molecular Biology and Evolution, 35(2): 518−522. doi: 10.1093/molbev/msx281
    [49]
    Hofmann S, Baniya CB, Litvinchuk SN, Miehe G, Li JT, Schmidt J. 2019. Phylogeny of spiny frogs Nanorana (Anura: Dicroglossidae) supports a Tibetan origin of a Himalayan species group. Ecology and Evolution, 9(24): 14498−14511. doi: 10.1002/ece3.5909
    [50]
    Hu YB, Fan HZ, Chen YH, Chang J, Zhan XJ, Wu H, et al. 2021. Spatial patterns and conservation of genetic and phylogenetic diversity of wildlife in China. Science Advances, 7(4): eabd5725. doi: 10.1126/sciadv.abd5725
    [51]
    Hudson RR, Coyne JA. 2002. Mathematical consequences of the genealogical species concept. Evolution, 56(8): 1557−1565. doi: 10.1111/j.0014-3820.2002.tb01467.x
    [52]
    IUCN. 2022[2021-01-20]. The IUCN Red List of Threatened Species. Version 2020-3. http://www.iucnredlist.org.
    [53]
    Ji RA. 1992. Evolution of quaternary natural environment in Guizhou. Geology of Guizhou, 9(1): 59−62. (in Chinese)
    [54]
    Jiang H, Ding Z. 2009. Spatial and temporal characteristics of Neogene palynoflora in China and its implication for the spread of steppe vegetation. Journal of Arid Environments, 73(9): 765−772. doi: 10.1016/j.jaridenv.2009.03.011
    [55]
    Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution, 30(4): 772−780. doi: 10.1093/molbev/mst010
    [56]
    Kieren S, Sparreboom M, Hochkirch A, Veith M. 2018. A biogeographic and ecological perspective to the evolution of reproductive behaviour in the family Salamandridae. Molecular Phylogenetics and Evolution, 121: 98−109. doi: 10.1016/j.ympev.2018.01.006
    [57]
    Kizirian D, Donnelly MA. 2004. The criterion of reciprocal monophyly and classification of nested diversity at the species level. Molecular Phylogenetics and Evolution, 32(3): 1072−1076. doi: 10.1016/j.ympev.2004.05.001
    [58]
    Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7): 1870−1874. doi: 10.1093/molbev/msw054
    [59]
    Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. 2017. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution, 34(3): 772−773.
    [60]
    Lefébure T, Douady CJ, Gouy M, Trontelj P, Briolay J, Gibert J. 2006. Phylogeography of a subterranean amphipod reveals cryptic diversity and dynamic evolution in extreme environments. Molecular Ecology, 15(7): 1797−1806. doi: 10.1111/j.1365-294X.2006.02888.x
    [61]
    Lei F, Qu YH, Song G, Alström P, Fjeldså J. 2015. The potential drivers in forming avian biodiversity hotspots in the East Himalaya Mountains of Southwest China. Integrative Zoology, 10(2): 171−181. doi: 10.1111/1749-4877.12121
    [62]
    Li JT, Li Y, Klaus S, Rao DQ, Hillis DM, Zhang YP. 2013. Diversification of rhacophorid frogs provides evidence for accelerated faunal exchange between India and Eurasia during the Oligocene. Proceedings of the National Academy of Sciences of the United States of America, 110(9): 3441−3446. doi: 10.1073/pnas.1300881110
    [63]
    Li S, Tian YZ, Gu XM. 2008a. A new species of the genus Paramesotriton (Caudata, Salamandridae). Acta Zootaxonomica Sinica, 33(2): 410−413. (in Chinese)
    [64]
    Li S, Tian YZ, Gu XM, Xiong RC. 2008b. A new species of ParamesotritonParamesotriton longliensis (Caudata: Salamandridae). Zoological Research, 29(3): 313−317. (in Chinese) doi: 10.3724/SP.J.1141.2008.00313
    [65]
    Li XZ. 2001. Evolution of karst geomorphology of Upper-Cenozoic and its influential factors in Guizhou plateau. Guizhou Geology, 18(1): 29−36. (in Chinese)
    [66]
    Liang B, Zhou RB, Liu YL, Chen B, Lee Grismer L, Wang N. 2018. Renewed classification within Goniurosaurus (Squamata: Eublepharidae) uncovers the dual roles of a continental island (Hainan) in species evolution. Molecular Phylogenetics and Evolution, 127: 646−654. doi: 10.1016/j.ympev.2018.06.011
    [67]
    Lin SJ. 1993. The main features of tectonic movement of Late Cenozoic era in Guizhou. Geology of Guizhou, 10(1): 10−17. (in Chinese)
    [68]
    López-Pujol J, Zhang FM, Sun HQ, Ying TS, Ge S. 2011. Centres of plant endemism in China: places for survival or for speciation?. Journal of Biogeography, 38(7): 1267−1280. doi: 10.1111/j.1365-2699.2011.02504.x
    [69]
    Low BW, Zeng YW, Tan HH, Yeo DCJ. 2021. Predictor complexity and feature selection affect Maxent model transferability: evidence from global freshwater invasive species. Diversity and Distributions, 27(3): 497−511. doi: 10.1111/ddi.13211
    [70]
    Lu SQ, Yuan ZG, Pang JF, Yang DT, Yu FH, McGuire P, et al. 2004. Molecular phylogeny of the genus Paramesotriton (Caudata: Salamandridae). Biochemical Genetics, 42(5): 139−148.
    [71]
    Luo T, Wen HM, Gao K, Zhou J, Zhou J. 2021. Phylogeography and cryptic species diversity of Paramesotriton caudopunctatus species group (Salamandridae: Paramesotriton) in Guizhou, China. Asian Herpetological Research, 12(2): 188−200.
    [72]
    Ma L, Zhao YH, Yang JX. 2019. Cavefish of China. In: White WB, Culver DC, Pipan T. Encyclopedia of Caves. 3rd ed. London: Academic Press.
    [73]
    Matzke NJ. 2013. BioGeoBEARS: bioGeography with Bayesian (and likelihood) Evolutionary Analysis in R Scripts. Berkeley: University of California.
    [74]
    McCulloch GA, Foster BJ, Dutoit L, Harrop TWR, Guhlin J, Dearden PK, et al. 2021. Genomics reveals widespread ecological speciation in flightless insects. Systematic Biology, 70(5): 863−876. doi: 10.1093/sysbio/syaa094
    [75]
    Miao YF, Herrmann M, Wu FL, Yan XL, Yang SL. 2012. What controlled mid–late Miocene long-term aridification in central Asia?—global cooling or Tibetan plateau uplift: a review. Earth-Science Reviews, 112(3−4): 155−172. doi: 10.1016/j.earscirev.2012.02.003
    [76]
    Minh BQ, Anh M, Nguyen T, von Haeseler A. 2013. Ultrafast approximation for phylogenetic bootstrap. Molecular Biology and Evolution, 30(5): 1188−1195. doi: 10.1093/molbev/mst024
    [77]
    Ministry of Environmental Protection. 2015. Priority areas for biodiversity conservation in China. Beijing: Ministry of Environmental Protection. (in Chinese)
    [78]
    Morales NS, Fernández IC, Baca-González V. 2017. MaxEnt’s parameter configuration and small samples: are we paying attention to recommendations? A systematic review. PeerJ, 5: e3093. doi: 10.7717/peerj.3093
    [79]
    Mulch A, Chamberlain CP. 2006. The rise and growth of Tibet. Nature, 439(7077): 670−671. doi: 10.1038/439670a
    [80]
    Myers N, Mittermeier RA, Mittermeier CG, Da Fonseca GAB, Kent J. 2000. Biodiversity hotspots for conservation priorities. Nature, 403(6772): 853−858. doi: 10.1038/35002501
    [81]
    Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32(1): 268−274. doi: 10.1093/molbev/msu300
    [82]
    Nosil P. 2012. Ecological Speciation. Oxford: Oxford University Press.
    [83]
    Oliver LA, Prendini E, Kraus F, Raxworthy CJ. 2015. Systematics and biogeography of the Hylarana frog (Anura: Ranidae) radiation across tropical Australasia, Southeast Asia, and Africa. Molecular Phylogenetics and Evolution, 90: 176−192. doi: 10.1016/j.ympev.2015.05.001
    [84]
    Pan T, Sun ZL, Lai XL, Orozcoterwengel P, Yan P, Wu GY, et al. 2019. Hidden species diversity in Pachyhynobius: a multiple approaches species delimitation with mitogenomes. Molecular Phylogenetics and Evolution, 137: 138−145. doi: 10.1016/j.ympev.2019.05.005
    [85]
    Pereira RJ, Wake DB. 2009. Genetic leakage after adaptive and nonadaptive divergence in the Ensatina eschscholtzii ring species. Evolution, 63(9): 2288−2301. doi: 10.1111/j.1558-5646.2009.00722.x
    [86]
    Peterson AT, Nakazawa Y. 2008. Environmental data sets matter in ecological niche modelling: an example with Solenopsis invicta and Solenopsis richteri. Global Ecology and Biogeography, 17(1): 135–144.
    [87]
    Phillips SJ, Anderson RP, Schapire RE. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190(3–4): 231–259.
    [88]
    Phillips SJ, Dudík M. 2008. Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography, 31(2): 161−175. doi: 10.1111/j.0906-7590.2008.5203.x
    [89]
    Radosavljevic A, Anderson RP. 2014. Making better MAXENT models of species distributions: complexity, overfitting and evaluation. Journal of Biogeography, 41(4): 629−643. doi: 10.1111/jbi.12227
    [90]
    Rahbek C, Borregaard MK, Antonelli A, Colwell RK, Holt BG, Nogues-Bravo D, et al. 2019b. Building mountain biodiversity: geological and evolutionary processes. Science, 365(6458): 1114−1119. doi: 10.1126/science.aax0151
    [91]
    Rahbek C, Borregaard MK, Colwell RK, Dalsgaard B, Holt BG, Morueta-Holme N, et al. 2019a. Humboldt’s enigma: what causes global patterns of mountain biodiversity?. Science, 365(6458): 1108−1113. doi: 10.1126/science.aax0149
    [92]
    Rambaut A. 2016. FigTree v1.4. 3. http://tree.bio.ed.ac.uk/software/figtree/.
    [93]
    Rambaut A, Drummond AJ. 2010. TreeAnnotator version 1.8. http://beast.community/programs.
    [94]
    Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. 2018. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology, 67(5): 901−904. doi: 10.1093/sysbio/syy032
    [95]
    Ren JB, Schubert BA, Lukens WE, Quan C. 2021. Low oxygen isotope values of fossil cellulose indicate an intense monsoon in East Asia during the late Oligocene. Palaeogeography, Palaeoclimatology, Palaeoecology, 577: 110556. doi: 10.1016/j.palaeo.2021.110556
    [96]
    Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, et al. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61(3): 539−542. doi: 10.1093/sysbio/sys029
    [97]
    Rundle HD, Nosil P. 2005. Ecological speciation. Ecology Letters, 8(3): 336−352. doi: 10.1111/j.1461-0248.2004.00715.x
    [98]
    Schoener TW. 1968. The anolis lizards of Bimini: resource partitioning in a complex fauna. Ecology, 49(4): 704−726. doi: 10.2307/1935534
    [99]
    Sun HL. 1997. Research of the Formation, Environment Change on Qinghai-Xizang (Tibetan) Plateau. Changsha: Hunan Science and Technology Press. (in Chinese)
    [100]
    Sun QH, Morales-Briones DF, Wang HX, Landis JB, Wen J, Wang HF. 2022. Phylogenomic analyses of the East Asian endemic Abelia (Caprifoliaceae) shed insights into the temporal and spatial diversification history with widespread hybridization. Annals of Botany, 129(2): 201−216. doi: 10.1093/aob/mcab139
    [101]
    Swets JA. 1988. Measuring the accuracy of diagnostic systems. Science, 240(4857): 1285−1293. doi: 10.1126/science.3287615
    [102]
    Tapponnier P, Lacassin R, Leloup PH, Schärer U, Dalai Z, Haiwei W, et al. 1990. The Ailao Shan/Red River metamorphic belt: tertiary left-lateral shear between Indochina and South China. Nature, 343(6257): 431−437. doi: 10.1038/343431a0
    [103]
    Tong GB, Zhang JP, Yang XD, Luo BX, Wang YZ, Chen PY. 1994. Late cenozoic palynoflora and environment changes in Yunnan-guizhou plateau. Marine Geology & Quaternary Geology, 14(3): 92−104. (in Chinese)
    [104]
    Vieites DR, Min MS, Wake DB. 2007. Rapid diversification and dispersal during periods of global warming by plethodontid salamanders. Proceedings of the National Academy of Sciences of the United States of America, 104(50): 19903−19907. doi: 10.1073/pnas.0705056104
    [105]
    Vornlocher JR, Lukens WE, Schubert BA, Quan C. 2021. Late Oligocene precipitation seasonality in East Asia based on δ13C profiles in fossil wood. Paleoceanography and Paleoclimatology, 36(4): e2021PA004229.
    [106]
    Wan SM, Li AC, Clift PD, Stuut JBW. 2007. Development of the East Asian monsoon: mineralogical and sedimentologic records in the northern South China Sea since 20 Ma. Palaeogeography, Palaeoclimatology, Palaeoecology, 254(3–4): 561–582.
    [107]
    Wang B, Huang Y, Li JT, Dai Q, Wang YZ, Yang DD. 2018b. Amphibian species richness patterns in karst regions in southwest China and its environmental associations. Biodiversity Science, 26(9): 941−950. (in Chinese) doi: 10.17520/biods.2018125
    [108]
    Wang B, Nishikawa K, Matsui M, Nguyen TQ, Xie F, Li C, et al. 2018a. Phylogenetic surveys on the newt genus Tylototriton sensu lato (Salamandridae, Caudata) reveal cryptic diversity and novel diversification promoted by historical climatic shifts. PeerJ, 6: e4384. doi: 10.7717/peerj.4384
    [109]
    Wang C, Tian YZ, Gu XM. 2013. A new species of the genus Paramesotriton (Caudata, Salamandridae). Acta Zootaxonomica Sinica, 38(2): 388−397. (in Chinese)
    [110]
    Wang J, Ai B, Kong HH, Kang M. 2017. Speciation history of a species complex of Primulina eburnea (Gesneriaceae) from limestone karsts of southern China, a biodiversity hot spot. Evolutionary Applications, 10(9): 919−934. doi: 10.1111/eva.12495
    [111]
    Wang YJ, Fan WM, Zhang YH, Peng TP, Chen XY, Xu YG. 2006. Kinematics and 40Ar/39Ar geochronology of the Gaoligong and Chongshan shear systems, western Yunnan, China: implications for early Oligocene tectonic extrusion of SE Asia. Tectonophysics, 418(3–4): 235–254.
    [112]
    Warren DL, Glor RE, Turelli M. 2008. Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution, 62(11): 2868−2883. doi: 10.1111/j.1558-5646.2008.00482.x
    [113]
    Warren DL, Glor RE, Turelli M. 2010. ENMTools: a toolbox for comparative studies of environmental niche models. Ecography, 33(3): 607−611.
    [114]
    Wen HM, Luo T, Wang YL, Wang SW, Liu T, Xiao N, et al. 2022. Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China. Integrative Zoology, 17(2): 311−325. doi: 10.1111/1749-4877.12624
    [115]
    Westerhold T, Marwan N, Drury AJ, Liebrand D, Agnini C, Anagnostou E, et al. 2020. An astronomically dated record of Earth’s climate and its predictability over the last 66 million years. Science, 369(6509): 1383−1387. doi: 10.1126/science.aba6853
    [116]
    Wu YH, Yan F, Stuart BL, Prendini E, Suwannapoom C, Dahn HA, et al. 2020. A combined approach of mitochondrial DNA and anchored nuclear phylogenomics sheds light on unrecognized diversity, phylogeny, and historical biogeography of the torrent frogs, genus Amolops (Anura: Ranidae). Molecular Phylogenetics and Evolution, 148: 106789. doi: 10.1016/j.ympev.2020.106789
    [117]
    Wu YK, Jiang K, Hanken J. 2010. A new species of newt of the genus Paramesotriton (Salamandridae) from southwestern Guangdong, China, with a new northern record of P. longliensis from western Hubei. Zootaxa, 2494(1): 45−58. doi: 10.11646/zootaxa.2494.1.3
    [118]
    Wu YK, Rovito SM, Papenfuss TJ, Hanken J. 2009. A new species of the genus Paramesotriton (Caudata: Salamandridae) from Guangxi Zhuang Autonomous Region, southern China. Zootaxa, 2060(1): 59−68. doi: 10.11646/zootaxa.2060.1.5
    [119]
    Xiang KL, Erst AS, Yang J, Peng HW, del C. Ortiz R, Jabbour F, et al. 2021. Biogeographic diversification of Eranthis (Ranunculaceae) reflects the geological history of the three great Asian plateaus. Proceedings of the Royal Society B, 288(1948): 20210281. doi: 10.1098/rspb.2021.0281
    [120]
    Xiang XG, Mi XC, Zhou HL, Li JW, Chung SW, Li DZ, et al. 2016. Biogeographical diversification of mainland Asian Dendrobium (Orchidaceae) and its implications for the historical dynamics of evergreen broad-leaved forests. Journal of Biogeography, 43(7): 1310−1323. doi: 10.1111/jbi.12726
    [121]
    Xing YJ, Zhou LZ, Zhang YY, Wang XJ. 2008. Geographical patterns based on faunal types of breeding birds and mammals in China. Integrative Zoology, 3(4): 280−289. doi: 10.1111/j.1749-4877.2008.00107.x
    [122]
    Xu W, Che J. 2019. From cryptic species to biodiversity conservation in China: status and prospects. Scientia Sinica Vitae, 49(4): 519−530. (in Chinese) doi: 10.1360/N052018-00229
    [123]
    Xu W, Dong WJ, Fu TT, Gao W, Lu CQ, Yan F, et al. 2021. Herpetological phylogeographic analyses support a Miocene focal point of Himalayan uplift and biological diversification. National Science Review, 8(9): nwaa263. doi: 10.1093/nsr/nwaa263
    [124]
    Yan F, Nneji LM, Jin JQ, Yuan ZY, Chen JM, Mi X, et al. 2021. Multi-locus genetic analyses of Quasipaa from throughout its distribution. Molecular Phylogenetics and Evolution, 163: 107218. doi: 10.1016/j.ympev.2021.107218
    [125]
    Yan Y, Yao D, Tian ZX, Huang CY, Dilek Y, Clift PD, et al. 2018. Tectonic topography changes in Cenozoic East Asia: a landscape erosion-sediment archive in the South China Sea. Geochemistry, Geophysics, Geosystems, 19(6): 1731−1750. doi: 10.1029/2017GC007356
    [126]
    Ye CY, Fei L. 2001. Phylogeny of genus Odorrana (Amphibia: Ranidae) in China. Acta Zoologica Sinica, 47(5): 528−534. (in Chinese)
    [127]
    Yu Y, Harris AJ, Blair C, He XJ. 2015. RASP (Reconstruct Ancestral State in Phylogenies): a tool for historical biogeography. Molecular Phylogenetics and Evolution, 87: 46−49. doi: 10.1016/j.ympev.2015.03.008
    [128]
    Yuan ZY, Wu YK, Zhou JJ, Che J. 2016a. A new species of the genus Paramesotriton (Caudata: Salamandridae) from Fujian, southeastern China. Zootaxa, 4205(6): 549−563. doi: 10.11646/zootaxa.4205.6.3
    [129]
    Yuan ZY, Zhang BL, Raxworthy CJ, Weisrock DW, Hime PM, Jin JQ, et al. 2018. Natatanuran frogs used the Indian Plate to step-stone disperse and radiate across the Indian Ocean. National Science Review, 6(1): 10−14. doi: 10.1093/nsr/nwy092
    [130]
    Yuan ZY, Zhao HP, Jiang K, Hou M, He LZ, Murphy RW, et al. 2014. Phylogenetic relationships of the genus Paramesotriton (Caudata: Salamandridae) with the description of a new species from Qixiling nature reserve, Jiangxi, southeastern China and a key to the species. Asian Herpetological Research, 5(2): 67−79. doi: 10.3724/SP.J.1245.2014.00067
    [131]
    Yuan ZY, Zhou WW, Chen X, Poyarkov Jr NA, Chen HM, Jang-Liaw NH, et al. 2016b. Spatiotemporal diversification of the true frogs (genus Rana): a historical framework for a widely studied group of model organisms. Systematic Biology, 65(5): 824−842. doi: 10.1093/sysbio/syw055
    [132]
    Zachos J, Pagani M, Sloan L, Thomas E, Billups K. 2001. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science, 292(5517): 686−693. doi: 10.1126/science.1059412
    [133]
    Zeng ZC, Liang D, Li JX, Lyu Z, Wang YY, Zhang P. 2020. Phylogenetic relationships of the Chinese torrent frogs (Ranidae: Amolops) revealed by phylogenomic analyses of AFLP-Capture data. Molecular Phylogenetics and Evolution, 146: 106753. doi: 10.1016/j.ympev.2020.106753
    [134]
    Zhang D, Gao FL, Jakovlić I, Zou H, Zhang J, Li WX, et al. 2020. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Molecular Ecology Resources, 20(1): 348−355. doi: 10.1111/1755-0998.13096
    [135]
    Zhang P, Papenfuss TJ, Wake MH, Qu LH, Wake DB. 2008. Phylogeny and biogeography of the family Salamandridae (Amphibia: Caudata) inferred from complete mitochondrial genomes. Molecular Phylogenetics and Evolution, 49(2): 586−597. doi: 10.1016/j.ympev.2008.08.020
    [136]
    Zhang RZ. 2011. Zoogeography of China. Beijing: Science Press. (in Chinese)
    [137]
    Zhang YY, Li SQ. 2013. Ancient lineage, young troglobites: recent colonization of caves by Nesticella spiders. BMC Evolutionary Biology, 13: 183. doi: 10.1186/1471-2148-13-183
    [138]
    Zhang ZG. 1980. Karst types in China. Geojournal, 4(6): 541−570. doi: 10.1007/BF00214219
    [139]
    Zhao HT, Che J, Zhou WW, Chen YX, Zhao HP, Zhang YP. 2008. A new species of Paramesotriton (Caudata: Salamandridae) from Guizhou Province, China. Zootaxa, 1775(1): 51−60. doi: 10.11646/zootaxa.1775.1.4
    [140]
    Zhao HT, Hu SY, Wang YB, Chen YX. 2012. The biological characteristics and protection measures of Paramesotriton zhijinensis. Sichuan Journal of Zoology, 31(5): 760–762, 850. (in Chinese)
    [141]
    Zhao JL, Paudel BR, Yu XQ, Zhang J, Li QJ. 2021. Speciation along the elevation gradient: Divergence of Roscoea species within the south slope of the Himalayas. Molecular Phylogenetics and Evolution, 164: 107292. doi: 10.1016/j.ympev.2021.107292
    [142]
    Zhao JL, Xia YM, Cannon CH, Kress WJ, Li QJ. 2016. Evolutionary diversification of alpine ginger reflects the early uplift of the Himalayan–Tibetan Plateau and rapid extrusion of Indochina. Gondwana Research, 32: 232−241. doi: 10.1016/j.gr.2015.02.004
    [143]
    Zhao YH, Zhang CG. 2009. Endemic Fishes of Sinocyclocheilus (Cypriniformes: Cyprinidae) in China: Species Diversity, Cave Adaptation, Systematics and Zoogeography. Beijing: Science Press. (in Chinese)
    [144]
    Zhao Z, Li SQ. 2017. Extinction vs. rapid radiation: the juxtaposed evolutionary histories of coelotine spiders support the Eocene–Oligocene orogenesis of the Tibetan Plateau. Systematic Biology, 66(6): 988−1006. doi: 10.1093/sysbio/syx042
    [145]
    Zheng HB. 2015. Birth of the Yangtze River: age and tectonic-geomorphic implications. National Science Review, 2(4): 438−453. doi: 10.1093/nsr/nwv063
    [146]
    Zheng HB, Clift PD, Wang P, Tada R, Jia JT, He MY, et al. 2013. Pre-miocene birth of the Yangtze River. Proceedings of the National Academy of Sciences of the United States of America, 110(19): 7556−7561. doi: 10.1073/pnas.1216241110
    [147]
    Zhou J, Wang SW, Xiao N, Luo T, Wang XL, Wang YL. 2021. Lineage diversification of the Andrias davidianus complex and classification evaluation of the Chinese giant salamander in Guizhou. Journal of Guizhou Normal University:Natural Sciences, 39(2): 1−14. (in Chinese)
    [148]
    Zhou QY, Chen PY. 1993. Lithofacies change and palaeogeographical evolution during Late Cenozoic in Guizhou and its vicinity. Geology of Guizhou, 10(3): 201−207. (in Chinese)
    [149]
    Zhou Y, Wang SR, Zhu HD, Li PP, Yang BT, Ma JZ. 2017. Phylogeny and biogeography of South Chinese brown frogs (Ranidae, Anura). PLoS One, 12(4): e0175113. doi: 10.1371/journal.pone.0175113
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