Phylogeographic analyses of poplar revealed potential glacial refugia and allopatric divergence in southwest China

References

• Bai WN, Liao WJ, Zhang DY. 2010. Nuclear and chloroplast DNA phylogeography reveal two refuge areas with asymmetrical gene flow in a temperate walnut tree from East Asia. New Phytol. 188(3):892–901.
   PubMed Web of Science ®Google Scholar
• Bandelt HJ, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 16(1):37–48.
   PubMed Web of Science ®Google Scholar
• Doyle J. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 19(1):11–15.
   Google Scholar
• Du S, Wang Z, Ingvarsson PK, Wang D, Wang J, Wu Z, Tembrock LR, Zhang J. 2015. Multilocus analysis of nucleotide variation and speciation in three closely related Populus (Salicaceae) species. Mol Ecol. 24(19):4994–5005.
   PubMed Web of Science ®Google Scholar
• Earl DA, Vonholdt BM. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour. 4(2):359–361.
   Web of Science ®Google Scholar
• Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 14(8):2611–2620.
   PubMed Web of Science ®Google Scholar
• Excoffier L, Laval G, Schneider S. 2007. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online. 1(4A):47–50.
   PubMedGoogle Scholar
• Falush D, Stephens M, Pritchard JK. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 164(4):1567–1587.
   PubMed Web of Science ®Google Scholar
• Feulner PGD, Chain FJJ, Panchal M, Huang Y, Eizaguirre C, Kalbe M, Lenz TL, Samonte IE, Stoll M, Bornberg-Bauer E. 2015. Correction: genomics of divergence along a continuum of parapatric population differentiation. PLoS Genet. 11(2):e1004966.
   PubMed Web of Science ®Google Scholar
• Frankham GJ, Handasyde KA, Norton M, Murray A, Eldridge MDB. 2014. Molecular detection of intra-population structure in a threatened potoroid, Potorous tridactylus: conservation management and sampling implications. Conserv Genet. 15(3):547–560.
   Web of Science ®Google Scholar
• Fu YX, Li WH. 1993. Statistical tests of neutrality of mutations. Genetics. 133(3):693–709.
   PubMed Web of Science ®Google Scholar
• Gilbert KJ, Andrew RL, Bock DG, Franklin MT, Kane NC, Moore J-S, Moyers BT, Renaut S, Rennison DJ, Veen T. 2012. Recommendations for utilizing and reporting population genetic analyses: the reproducibility of genetic clustering using the program structure. Mol Ecol. 21(20):4925–4930.
   PubMed Web of Science ®Google Scholar
• Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 41:95–98.
   Google Scholar
• Hewitt G. 2000. The genetic legacy of the Quaternary ice ages. Nature. 405(6789):907–913.
   PubMed Web of Science ®Google Scholar
• Hewitt GM. 2004. Genetic consequences of climatic oscillations in the Quaternary. Philos Trans R Soc Lond B Biol Sci. 359(1442):183–195.
   PubMed Web of Science ®Google Scholar
• Hijmans R, Cruz M, Rojas E, Guarino L. 2001. DIVA-GIS version 1.4: a geographic information system for the analysis of biodiversity data, manual, University of California.
   Google Scholar
• Hou Z, Wang Z, Ye Z, Du S, Liu S, Zhang J. 2018. Phylogeographic analyses of a widely distributed Populus davidiana: further evidence for the existence of glacial refugia of cool-temperate deciduous trees in northern East Asia. Ecol Evol. 8(24):13014–13026.
   PubMed Web of Science ®Google Scholar
• Hwang SY, Lin TP, Ma CS, Lin CL, Chung JD, Yang JC. 2003. Postglacial population growth of Cunninghamia konishii (Cupressaceae) inferred from phylogeographical and mismatch analysis of chloroplast DNA variation. Mol Ecol. 12(10):2689–2695.
   PubMed Web of Science ®Google Scholar
• Jakob SS, Martinez-Meyer E, Blattner FR. 2009. Phylogeographic analyses and paleodistribution modeling indicate Pleistocene in situ survival of Hordeum species (Poaceae) in southern Patagonia without genetic or spatial restriction. Mol Biol Evol. 26(4):907–923.
   PubMed Web of Science ®Google Scholar
• Lewis PO, Crawford DJ. 1995. Pleistocene refugium endemics exhibit greater allozymic diversity than widespread congeners in the genus Polygonella (Polygonaceae). Am J Bot. 82(2):141–149.
   Web of Science ®Google Scholar
• Lian K, Zhang L, Zhao L, Zhang G, Zhang F. 2010. Analysis on the floristic characteristics of wild seed plants in the Zhongtiao Mountains, Shanxi. J Wuhan Bot Res. 28(2):144–152.
   Google Scholar
• Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25(11):1451–1452.
   PubMed Web of Science ®Google Scholar
• Liu C. 2013. Study on genetic structure and phylogeography of Acer mono natural populations. Northeast Forestry University, Haerbin.
   Google Scholar
• Liu JQ, Gao TG, Chen ZD, Lu AM. 2002. Molecular phylogeny and biogeography of the Qinghai-Tibet Plateau endemic Nannoglottis (Asteraceae). Mol Phylogenet Evol. 23(3):307–325.
   PubMed Web of Science ®Google Scholar
• Meng HH, Gao XY, Huang JF, Zhang ML. 2015. Plant phylogeography in arid Northwest China: retrospectives and perspectives. J Syst Evol. 53(1):33–46.
   Web of Science ®Google Scholar
• Neale DB, Antoine K. 2011. Forest tree genomics: growing resources and applications. Nat Rev Genet. 12(2):111–122.
   PubMed Web of Science ®Google Scholar
• Nei M. 1987. Molecular evolutionary genetics. Columbia University, New York.
   Google Scholar
• Nei M. 1996. Phylogenetic analysis in molecular evolutionary genetics. Annu Rev Genet. 30(1):371–403.
   PubMedGoogle Scholar
• Peakall R, Smouse PE. 2006. genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes. 6(1):288–295.
   Web of Science ®Google Scholar
• Qian H, Ricklefs RE. 1999. A comparison of the taxonomic richness of vascular plants in China and the United States. Am Nat. 154(2):160–181.
   PubMed Web of Science ®Google Scholar
• Qiu YX, Fu CX, Comes HP. 2011. Plant molecular phylogeography in China and adjacent regions: tracing the genetic imprints of Quaternary climate and environmental change in the world's most diverse temperate flora. Mol Phylogenet Evol. 59(1):225–244.
   PubMed Web of Science ®Google Scholar
• Sakaguchi S, Qiu Y-X, Liu Y-H, Qi X-S, Kim S-H, Han J, Takeuchi Y, Worth JRP, Yamasaki M, Sakurai S. 2012. Climate oscillation during the Quaternary associated with landscape heterogeneity promoted allopatric lineage divergence of a temperate tree Kalopanax septemlobus (Araliaceae) in East Asia. Mol Ecol. 21(15):3823–3838.
   PubMed Web of Science ®Google Scholar
• Soltis DE, Gitzendanner MA, Strenge DD, Soltis PS. 1997. Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America. Plant Syst Evol. 206(1–4):353–373.
   Web of Science ®Google Scholar
• Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123(3):585–595.
   PubMed Web of Science ®Google Scholar
• Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25(24):4876–4882.
   PubMed Web of Science ®Google Scholar
• Turelli M, Barton NH, Coyne JA. 2001. Theory and speciation. Trends Ecol Evol. 16(7):330–343.
   PubMed Web of Science ®Google Scholar
• Wang L, Abbott RJ, Zheng W, Chen P, Wang Y, Liu J. 2009. History and evolution of alpine plants endemic to the Qinghai-Tibetan plateau: Aconitum gymnandrum (Ranunculaceae). Mol Ecol. 18(4):709–721.
   PubMed Web of Science ®Google Scholar
• Wang H-W, Ge S. 2006. Phylogeography of the endangered Cathaya argyrophylla (Pinaceae) inferred from sequence variation of mitochondrial and nuclear DNA. Mol Ecol. 15(13):4109–4122.
   PubMed Web of Science ®Google Scholar
• Wang LY, Ikeda H, Liu TL, Wang YJ, Liu JQ. 2009. Repeated range expansion and glacial endurance of Potentilla glabra (Rosaceae) in the Qinghai-Tibetan plateau. J Integr Plant Biol. 51(7):698–706.
   PubMed Web of Science ®Google Scholar
• Wang H, Kang M, Liu W, Liu Q. 2004. Advance in studies on flora and vegetation in Zhongtiao mountain. J Beijing Normal Univ (Nat Sci). 40(5):676–683.
   Google Scholar
• Wang Y, Qin Y, Du Z, Yan G. 2012. Genetic diversity and differentiation of the endangered tree Elaeagnus mollis Diels (Elaeagnus L.) as revealed by simple sequence repeat (SSR) markers. Biochem Syst Ecol. 40(2):25–33.
   Google Scholar
• Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 7(2):256–276.
   PubMed Web of Science ®Google Scholar
• Widmer A, Lexer C. 2001. Glacial refugia: sanctuaries for allelic richness, but not for gene diversity. Trends Ecol Evol. 16(6):267.
   PubMed Web of Science ®Google Scholar
• Zawko G, Krauss SL, Dixon KW, Sivasithamparam K. 2001. Conservation genetics of the rare and endangered Leucopogon obtectus (Ericaceae). Mol Ecol. 10(10):2389–2396.
   PubMed Web of Science ®Google Scholar
• Zeng YF, Wang WT, Liao WJ, Wang HF, Zhang DY. 2015. Multiple glacial refugia for cool-temperate deciduous trees in northern East Asia: the Mongolian oak as a case study. Mol Ecol. 24(22):5676–5691.
   PubMed Web of Science ®Google Scholar
• Zhang M, Kang Y, Zhou L, Podlech D. 2009. Phylogenetic origin of Phyllolobium with a further implication for diversification of Astragalus in China. J Integr Plant Biol. 51(9):889–899.
   PubMed Web of Science ®Google Scholar
• Zhang ML, Uhink CH, Kadereit JW. 2007. Phylogeny and biogeography of Epimedium/Vancouveria (Berberidaceae): Western North American-East Asian disjunctions, the origin of European mountain plant taxa, and East Asian species diversity. Syst Bot. 32(1):81–92.
   Web of Science ®Google Scholar
• Zhu R. 2016. Phylogeography of Xanthoceras sorbifolium Bunge, an endemic plant to China. Northwest A&F University, Haerbin.
   Google Scholar
• Zhuo Z, Baoyin Y, Petit-Maire N. 1998. Paleoenvironments in China during the last glacial maximum and the Holocene Optimum. Episodes. 21(3):152–158.
   Web of Science ®Google Scholar
• Zink RM. 1996. Comparative phylogeography in North American birds. Evolution. 50(1):308–317.
   PubMed Web of Science ®Google Scholar