Published November 30, 2020
| Version v1
Journal article
Open
Phylogeography of Triplophysa stenura (Nemacheilidae): Responded to the Mid-Pleistocene Climate Transition in the Qinghai-Tibetan Plateau
Authors/Creators
- 1. The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China. *Correspondence: E-mail: hedekui@ihb.ac.cn (He) E-mail: hujiaxin@ihb.ac.cn (Hu) & University of Chinese Academy of Sciences, Beijing, China
- 2. Yangtze River Fisheries Research Institute of Chinese Academy of Fishery Science, Scientific Observing and Experimental Station of Fishery and Environment in the Upper and Middle Reaches of the Yangtze River, Ministry of Agriculture, Wuhan, Hubei 430223, China. *Correspondence: E-mail: liumd@yfi.ac.cn (Liu)
- 3. The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China. *Correspondence: E-mail: hedekui@ihb.ac.cn (He) E-mail: hujiaxin@ihb.ac.cn (Hu)
Description
Hu, Jiaxin, Liu, Mingdian, He, Dekui (2020): Phylogeography of Triplophysa stenura (Nemacheilidae): Responded to the Mid-Pleistocene Climate Transition in the Qinghai-Tibetan Plateau. Zoological Studies 59 (67): 1-13, DOI: 10.6620/ZS.2020.59-67, URL: http://dx.doi.org/10.5281/zenodo.12823176
Files
source.pdf
Files
(31.6 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:3e6c7d27c1fabfcd64a32d4d112cd6db
|
31.6 MB | Preview Download |
Linked records
Additional details
Identifiers
- LSID
- urn:lsid:plazi.org:pub:3E6C7D27FFFAFFCDFFA32D4D112CFFDB
References
- Avise JC, Nelson WS, Bowen BW, Walker D. 2000. Phylogeography of colonially nesting seabirds, with special reference to global matrilineal patterns in the sooty tern (Sterna fuscata). Mol Ecol 9(11):1783-1792. doi:10.1046/j.1365-294x.2000.01068.x.
- Bouckaert R, Heled J, Kuehnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ. 2014. BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. PLoS Comput Biol 10(4):e1003537. doi:10.1371/journal. pcbi.1003537.
- Chen CA, Ablan MCA, McManus JW, Bell JD, Tuan VS, Cabanban AS, Shao KT. 2004. Population structure and genetic variability of six bar wrasse (Thallasoma hardwicki) in northern South China sea revealed by mitochondrial control region sequences. Mar Biotechnol 6(4):312-326. doi:10.1007/s10126-003-0028-2.
- Chen GJ, Liao W, Lei XQ. 2015. First fossil cobitid (Teleostei: Cypriniformes) from Early-Middle Oligocene deposits of South China. Vertebrat Palasiatic 53(4):299-309.
- Clement M, Posada D, Crandall KA. 2000. TCS: a computer program to estimate gene genealogies. Mol Ecol 9(10):1657-1659. doi:10.1046/j.1365-294x.2000.01020.x.
- Cui ZJ, Wu YQ, Liu GN, Ge DK, Pang QQ, Xu QH. 1998. On Kunlun Yellow River tectonic movement. Sci China Ser D Earth Sci 41(6):592-600. doi:10.1007/bf02878741.
- Cun YZ, Wang XQ. 2010. Plant recolonization in the Himalaya from the southeastern Qinghai-Tibetan Plateau: Geographical isolation contributed to high population differentiation. Mol Phylogenet Evol 56(3):972-982. doi:10.1016/j.ympev.2010.05.007.
- De Macedo-Soares PHM, Petry AC, Farjalla VF, Caramaschi EP. 2010. Hydrological connectivity in coastal inland systems: lessons from a Neotropical fish metacommunity. Ecol Freshw Fish 19(1):7-18. doi:10.1111/j.1600-0633.2009.00384.x.
- Dinca V, Dapporto L, Vila R. 2011. A combined genetic-morphometric analysis unravels the complex biogeographical history of Polyommatus icarus and Polyommatus celina Common Blue butterflies. Mol Ecol 20(18):3921-3935. doi:10.1111/j.1365- 294X.2011.05223.x.
- Ding L, Liao J. 2019. Phylogeography of the Tibetan hamster Cricetulus kamensis in response to uplift and environmental change in the Qinghai-Tibet Plateau. Ecol Evol 9(12):7291- 7306. doi:10.1002/ece3.5301.
- Doadrio I, Perdices A. 2005. Phylogenetic relationships among the Ibero-African cobitids (Cobitis, Cobitidae) based on cytochrome b sequence data. Mol Phylogenet Evol 37(2):484-493. doi:10.1016/j.ympev.2005.07.009.
- Dong G, Yi C, Chen L. 2010. An introduction to the physical geography of the Qiangtang Plateau: a frontier for future geoscience research on the Tibetan Plateau. Phys Geogr 31(6):475-492. doi:10.2747/0272-3646.31.6.475.
- Dupanloup I, Schneider S, Excoffier L. 2002. A simulated annealing approach to define the genetic structure of populations. Mol Ecol 11(12):2571-2581. doi:10.1046/j.1365-294X.2002.01650.x.
- Elderfield H, Ferretti P, Greaves M, Crowhurst S, McCave IN, Hodell D, Piotrowski AM. 2012. Evolution of ocean temperature and ice volume through the mid-Pleistocene climate transition. Science 337:704-709. doi:10.1126/science.1221294.
- Excoffier L. 2004. Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infiniteisland model. Mol Ecol 13(4):853-864. doi:10.1046/j.1365- 294X.2003.02004.x.
- Fan Q, Ma H, Hou G. 2012. Late Pleistocene lake and glaciation evolution on the northeastern Qinghai-Tibetan Plateau: a review. Environ Earth Sci 66(2):625-634. doi:10.1007/s12665-011- 1271-x.
- Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147(2):915-925. doi:10.1017/S0016672397002966.
- Funk VA, Wagner WL. 1995. Biogeographic patterns in the Hawaiian Islands. In: Hawaiian biogeography: evolution on a hot spot archipelago, Smithsonian Institution Press, Washington, USA, pp. 379-419.
- Guo X, Liu L, Wang Y. 2012. Phylogeography of the Phrynocephalus vlangalii Species Complex in the Upper Reaches of the Yellow River Inferred from mtDNA ND4-tRNA LEU Segments. Asian Herpetol Res 3(1):52-68. doi:10.3724/sp.j.1245.2012.00052.
- Hall T, Biosciences I, Carlsbad C. 2011. BioEdit: an important software for molecular biology. GERF Bull Biosci 2(1):60-61.
- He D, Chen Y. 2006. Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei: Cyprinidae) in China inferred from cytochrome b sequences. J Biogeogr 33(8):1448-1460. doi:10.1111/j.1365-2699.2006.01510.x.
- He D, Chen Y. 2007. Molecular phylogeny and biogeography of the highly specialized grade schizothoracine fishes (Teleostei: Cyprinidae) inferred from cytochrome b sequences. Chin Sci Bull 52(6):777-788. doi:10.1007/s11434-007-0123-2.
- He D, Chen Y, Liu C, Tao J, Ding C, Chen Y. 2016. Comparative phylogeography and evolutionary history of schizothoracine fishes in the Changtang Plateau and their implications for the lake level and Pleistocene climate fluctuations. Ecol Evol 6(3):656-674. doi:10.1002/ece3.1890.
- He D, Sui X, Sun H, Tao J, Ding C, Chen Y, Chen Y. 2020. Diversity, pattern and ecological drivers of freshwater fish in China and adjacent areas. Rev Fish Biol Fish 30:387-404. doi:10.1007/ s11160-020-09600-4.
- Hewitt G. 2000. The genetic legacy of the Quaternary ice ages. Nature 405(6789):907-913. doi:10.1038/35016000.
- Hewitt GM. 2004. Genetic consequences of climatic oscillations in the Quaternary. Philos T Roy Soc B 359(1442):183-195. doi:10.1098/rstb.2003.1388.
- 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. Mol Biol Evol 34(3):772-773. doi:10.1093/molbev/ msw260.
- Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and clustal X version 2.0. Bioinformatics 23(21):2947-2948. doi:10.1093/bioinformatics/btm404.
- Lehmkuhl F, Owen LA. 2005. Late Quaternary glaciation of Tibet and the bordering mountains: a review. Boreas 34(2):87-100. doi:10.1080/03009480510012908.
- Leigh JW, Bryant D. 2015. POPART: full-feature software for haplotype network construction. Methods Ecol Evol 6(9):1110- 1116. doi:10.1111/2041-210x.12410.
- Lemey P, Salemi M, Vandamme AM. 2009. The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing. Cambridge University Press, New York, USA, pp. 1-723.
- Li Y, Ludwig A, Peng Z. 2017. Geographical differentiation of the Euchiloglanis fish complex (Teleostei: Siluriformes) in the Hengduan Mountain Region, China: Phylogeographic evidence of altered drainage patterns. Ecol Evol 7(3):928-940. doi:10.1002/ece3.2715.
- Liang Y, He D, Jia Y, Sun H, Chen Y. 2017. Phylogeographic studies of Schizothoracine fishes on the central Qinghai-Tibet Plateau reveal the highest known glacial microrefugia. Sci Rep 7(1):10983. doi:10.1038/s41598-017-11198-w.
- Lv X, Cheng J, Meng Y, Chang Y, Xia L, Wen Z, Ge D, Liu S, Yang Q. 2018. Disjunct distribution and distinct intraspecific diversification of Eothenomys melanogaster in South China. BMC Evol Biol 18(1):50. doi:10.1186/s12862-018-1168-3.
- Miller MA, Pfeiffer W, Schwartz T. 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: 2010 gateway computing environments workshop (GCE): Ieee. pp. 1-8. doi:10.1109/GCE.2010.5676129.
- Maniatis T, Fritsch EF, Sambrook J. 1982. Molecular cloning: a laboratory manual: Cold spring harbor laboratory press, New York. pp. 721-722. doi:10.2307/1309366.
- Nei M, Kumar S, Nei M. 2000. Molecular evolution and phylogenetics. Oxford university press, New York, USA, pp. 1-333.
- Prokofiev A. 2007. Redescription of a fossil loach Triplophysa opinata (Yakowlew, 1959) from the Miocene of Kirgizia (Balitoridae: Nemacheilinae). J Ichthyol 47(1):26-31. doi:10.1134/ S0032945207010031.
- Qu Y, Lei F, Zhang R, Lu X. 2010. Comparative phylogeography of five avian species: implications for Pleistocene evolutionary history in the Qinghai-Tibetan plateau. Mol Ecol 19(2):338-351. doi:10.1111/j.1365-294X.2009.04445.x.
- Rambaut A. 2012. FigTree v1. 4. 3. Available at http://tree.bio.ed.ac. uk/software/figtree/.
- Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. 2018. Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7. Syst Biol 67(5):901-904. doi:10.1093/sysbio/syy032.
- Rana SK, Luo D, Rana HK, O'Neill AR, Sun H. 2019. Geoclimatic factors influence the population genetic connectivity of Incarvillea arguta (Bignoniaceae) in the Himalaya-Hengduan Mountains biodiversity hotspot. J Syst Evol (Published online). doi:10.1111/jse.12521.
- Ren Q, Yang JX, Chen XY. 2018. Phylogeographical and morphological analyses of Triplophysa stenura (Cypriniformes: Nemacheilidae) from the three Parallel Rivers region, China. Zool Stud 57:26. doi:10.6620/zs.2018.57-26.
- Renner SS. 2016. Available data point to a 4-km-high Tibetan Plateau by 40 Ma, but 100 molecular-clock papers have linked supposed recent uplift to young node ages. J Biogeogr 43(8):1479-1487. doi:10.1111/jbi.12755.
- Roach KA, Thorp JH, Delong MD. 2009. Influence of lateral gradients of hydrologic connectivity on trophic positions of fishes in the Upper Mississippi River. Freshw Biol 54(3):607-620. doi:10.1111/j.1365-2427.2008.02137.x.
- Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Syst Biol 61(3):539-542. doi:10.1093/sysbio/sys029.
- Rozas J, Ferrer MA, Carlos SDJ, Guirao RS, Librado P, Ramos OSE, Sanchez GA. 2017. DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Mol Biol Evol 34(12):3299-3302. doi:10.1093/molbev/msx248.
- Schmidt D, Pool J. 2002. The effect of population history on the distribution of the Tajima's D statistic. Population English Edition. pp. 1-8. doi:10.1677/joe.0.0330211.
- Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312-1313. doi:10.1093/bioinformatics/btu033.
- Taberlet P, Cheddadi R. 2002. Quaternary refugia and persistence of biodiversity. Science 297(5589):2009-2010. doi:10.1126/ science.297.5589.2009.
- Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123(3):585-595.
- Thompson LG, Mosley TE, Davis ME, Mashiotta TA, Henderson KA, Lin PN, Yao T. 2006. Ice core evidence for asynchronous glaciation on the Tibetan Plateau. Quat Int 154:3-10. doi:10.1016/j.quaint.2006.02.001.
- Wang H, Qiong L, Sun K, Lu F, Wang Y, Song Z, Wu Q, Chen J, Zhang W. 2010. Phylogeographic structure of Hippophae tibetana (Elaeagnaceae) highlights the highest microrefugia and the rapid uplift of the Qinghai-Tibetan Plateau. Mol Ecol 19(14):2964-2979. doi:10.1111/j.1365-294X.2010.04729.x.
- Wiens JJ, Donoghue MJ. 2004. Historical biogeography, ecology and species richness. Trends Ecol Evol 19(12):639-644. doi:10.1016/ j.tree.2004.09.011.
- Xia M, Tian Z, Zhang F, Khan G, Gao Q, Xing R, Zhang Y, Yu J, Chen S. 2018. Deep Intraspecific Divergence in the Endemic Herb Lancea tibetica (Mazaceae) Distributed Over the Qinghai-Tibetan Plateau. Front Genet 9:492. doi:10.3389/ fgene.2018.00492.
- Xu W, Yin W, Chen A, Li J, Lei G, Fu C. 2014. Phylogeographical analysis of a cold-temperate freshwater fish, the Amur sleeper (Perccottus glenii) in the Amur and Liaohe River basins of Northeast Asia Zoolog Sci 31(10):671-679. doi:10.2108/ zs130046.
- Yang FS, Li YF, Ding X, Wang XQ. 2008. Extensive population expansion of Pedicularis longiflora (Orobanchaceae) on the Qinghai-Tibetan Plateau and its correlation with the Quaternary climate change. Mol Ecol 17(23):5135-5145. doi:10.1111/ j.1365-294X.2008.03976.x.
- Yao T, Thompson L, Yang W, Yu W, Gao Y, Guo X, Yang X, Duan K, Zhao H, Xu B, Pu J, Lu A, Xiang Y, Kattel DB, Joswiak D. 2012. Different glacier status with atmospheric circulations in Tibetan Plateau and surroundings. Nat Clim Chang 2(9):663-5667. doi:10.1038/nclimate1580.
- Ye Z, Yuan J, Li M, Damgaard J, Chen P, Zheng C, Yu H, Fu S, Bu W. 2018. Geological effects influence population genetic connectivity more than Pleistocene glaciations in the water strider Metrocoris sichuanensis (Insecta: Hemiptera: Gerridae). J Biogeogr 45(3):690-701. doi:10.1111/jbi.13148.
- Yu G, Zhang M, Rao D, Yang J. 2013. Effect of Pleistocene climatic oscillations on the phylogeography and demography of red knobby newt (Tylototriton shanjing) from southwestern China. PLoS ONE 8(2):e56066. doi:10.1371/journal.pone.0056066.
- Zhang F, Zhu L, Zhang L, Wang W, Sun G. 2017. Phylogeography of freshwater fishes of the Qilian Mountains area (Triplophysa leptosoma, Cobitidae: Cypriniformes). Environ Biol Fishes 100(11):1383-1396. doi:10.1007/s10641-017-0650-x.
- Zhao M, Chang Y, Kimball RT, Zhao J, Lei F, Qu Y. 2019. Pleistocene glaciation explains the disjunct distribution of the Chestnutvented Nuthatch (Aves, Sittidae). Zool Scr 48(1):33-45. doi:10.1111/zsc.12327.
- Zheng BX, Xu QQ, Shen YP. 2002. The relationship between climate change and Quaternary glacial cycles on the Qinghai-Tibetan Plateau: review and speculation. Quat Int 97:93-101. doi:10.1016/s1040-6182(02)00054-x.
- Zhu S. 1989. The loaches of the subfamily Nemacheilinae in China (Cypriniformes: Cobitidae). Jiangsu Science and Technology Publishing House, Nanjing, China.