Repeated range expansions and inter-/postglacial recolonization routes of Sargentodoxa cuneata (Oliv.) Rehd. et Wils. (Lardizabalaceae) in subtropical China revealed by chloroplast phylogeography

Molecular Phylogenetics and Evolution

Volumn 85, Issue , 2015, Pages 238-246

  Tian, Shuang ^a,b   Lei, Shu Qing ^a   Hu, Wan ^a   Deng, Ling Li ^a   Li, Bo ^a   Meng, Qing Lin ^a   Soltis, Douglas E ^c,d   Soltis, Pamela S ^d   Fan, Deng Mei ^a   Zhang, Zhi Yong ^a  

^a JIANGXI AGRICULTURAL UNIVERSITY   (China)

^b Jiangdezhen College   (China)

^c UNIVERSITY OF FLORIDA   (United States)

^d UNIVERSITY OF FLORIDA   (United States)

Author keywords

Chloroplast; Phylogeography; Range expansion; Recolonization

Indexed keywords

LARDIZABALACEAE; SARGENTODOXA CUNEATA;

CHLOROPLAST DNA; PLANT DNA; RIBOSOMAL SPACER DNA;

ANGIOSPERM; BAYES THEOREM; CHINA; CLASSIFICATION; DNA SEQUENCE; EVOLUTION; GENETIC VARIABILITY; GENETICS; HAPLOTYPE; PHYLOGENY; PHYLOGEOGRAPHY;

ANGIOSPERMS; BAYES THEOREM; BIOLOGICAL EVOLUTION; CHINA; DNA, CHLOROPLAST; DNA, PLANT; DNA, RIBOSOMAL SPACER; GENETIC VARIATION; HAPLOTYPES; PHYLOGENY; PHYLOGEOGRAPHY; SEQUENCE ANALYSIS, DNA;

EID: 84924744128     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2015.02.016     Document Type: Article

References (62)

1. Bandelt H.J., Forster P., Röhl A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 1999, 16:37-48.
2. Chen Z.D., Tatemi S. Lardizabalaceae. Flora of China 2001, vol. 6:440-454. Missouri Botanical Garden Press, St. Louis.
3. Chen D., Zhang X., Kang H., Sun X., Yin S., Du H., Yamanaka N., Gapare W., Wu H.X., Liu C. Phylogeography of Quercus variabilis based on chloroplast DNA sequence in East Asia: multiple glacial refugia and mainland-migrated island populations. PloS One 2012, 7:e47268.
4. Chen Y., Compton S.G., Liu M., Chen X.Y. Fig trees at the northern limit of their range: the distribution of cryptic pollinators indicated multiple glacial refugia. Mol. Ecol. 2012, 21:1687-1701.
5. Chou Y.W., Thomas P.I., Ge X.J., LePage B.A., Wang C.N. Refugia and phylogeography of Taiwania in East Asia. J. Biogeogr. 2011, 38:1992-2005.
6. 2. Quaternary Sci. Rev. 2006, 25:3150-3184.
7. Cui Z.J., Chen Y.X., Zhang W., Zhou S.Z., Zhou L.P., Zhang M., Li C.C. Research history, glacial chronology and origins of Quaternary glaciations in China. Quaternary Sci. 2011, 31:749-764.
8. Davis M.B., Shaw R.G. Range shifts and adaptive responses to Quaternary climate change. Science 2001, 5517:673-679.
9. Ding L., Gan X.N., He S.P., Zhao E.M. 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. 2011, 20:1905-1922.
10. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
11. Dutton A., Lambeck K. Ice volume and sea level during the last interglacial. Science 2012, 337:216-219.
12. Emerson K.J., Merz C.R., Catchen J.M., Hohenlohe P.A., Cresko W.A., Bradshaw W.E., Holzapfel C.M. Resolving postglacial phylogeography using high-throughput sequencing. Proc. Natl. Acad. Sci. USA 2010, 107:16196-16200.
13. Excoffier, L., Laval, G., Schneider, S., 2006. Arlequin ver. 3.1: an Integrated Software for Population Genetic Data Analysis. University of Bern, Switzerland. Available at: <>. http://cmpg.unibe.ch/software/arlequin3.
14. Frantz L.A.F., Schraiber J.G., Madsen O., et al. Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus. Genome Biol. 2013, 14:R107.
15. Fu Y.X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 1997, 147:915-925.
16. Gao L.M., Moller M., Zhang X.M., Hollingsworth M.L., Liu J., Mill R.R., Gibby M., Li D.Z. High variation and strong phylogeographic pattern among cpDNA haplotypes in Taxus wallichiana (Taxaceae) in China and North Vietnam. Mol. Ecol. 2007, 16:4684-4698.
17. Gavin D.G., Fitzpatrick M.C., Gugger P.F., et al. Climate refugia: joint inference from fossil records, species distribution models and phylogeography. New Phylot. 2014, 204:37-54.
18. Gong W., Chen C., Dobes C., Fu C.X., Koch M.A. Phylogeography of a living fossil: Pleistocene glaciations forced Ginkgo biloba L. (Ginkgoaceae) into two refuge areas in China with limited subsequent postglacial expansion. Mol. Phylogenet. Evol. 2008, 48:1094-1105.
19. Groenen M.A.M., Archibald A.L., Uenishi H., et al. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 2012, 491:393-398.
20. Harrison S.P., Yu G., Takahara H., Prentice I.C. Palaeovegetation (Communications arising): Diversity of temperate plants in east Asia. Nature 2001, 413:129-130.
21. Hewitt G.M. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol. J. Linn. Soc. 1996, 58:247-276.
22. Hewitt G.M. The genetic legacy of the quaternary ice ages. Nature 2000, 405:907-913.
23. Jacques F.M.B., De Franceschi D. Endocarps of Menispermaceae from Le Quesnoy outcrop (Sparnacian facies, Lower Eocene, Paris Basin). Rev. Palaeobot. Palyno. 2005, 135:61-70.
24. Jacques F.M.B., Guo S.X. Palaeoskapha sichuanensis gen. et sp. nov. (Menispermaceae) from the Eocene Relu Formation in western Sichuan, West China. Acta Phytotaxon. Sin. 2007, 45:576-582.
25. Knobloch E., Mai D.H. Monographie der Fruchte und Samen in der Kreide von Mitteleuropa. Rozpravy Ustrednihoustavu geolog ickeho 1986, 47:1-279.
26. Kukla G.J., De Beaulieu J.L., Bond G., et al. Last interglacial climates. Quaternary Res. 2002, 58:2-13.
27. Lei M., Wang Q., Wu Z.J., López-Pujol J., Li D.Z., Zhang Z.Y. Molecular phylogeography of Fagus engleriana (Fagaceae) in subtropical China: limited admixture among multiple refugia. Tree Genet. Genomes 2012, 8:1203-1212.
28. Li J., Jin Z., Tan T. Genetic diversity and differentiation of Sinocalycanthus chinensis populations revealed by chloroplast microsatellite (cpSSRs) markers. Biochem. Syst. Ecol. 2012, 41:48-54.
29. Li X.H., Shao J.W., Lu C., Zhang X.P., Qiu Y.X. Chloroplast phylogeography of a temperate tree Pteroceltis tatarinowii (Ulmaceae) in China. J. Syst. Evol. 2012, 50:325-333.
30. Liu J.Q., Sun Y.S., Ge X.J., Gao L.M., Qiu Y.X. Phylogeographic studies of plants in China: Advances in the past and directions in the future. J. Syst. Evol. 2012, 50:267-275.
31. Ni J., Yu G., Harrison S.P., Prentice I.C. Palaeovegetation in China during the late Pleistocene: Biome reconstructions based on a global scheme of plant functional types. Palaeogeogr. Palaeoclim. Palaecol. 2010, 289:44-61.
32. Niu, X.Y., 2013. The Palaeo-Climate and Palaeo-Vegetation of XH-2 Core in Subei Basin Since the Mid-Pleistocene. MA Dissertation, Nanjing Normal University, Nanjing.
33. Pons O., Petit R.J. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 1996, 144:1237-1245.
34. Posada D., Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 1:817-818.
35. Qi X.S., Chen C., Comes H.P., Sakaguchi S., Liu Y.H., Tanaka N., Sakio H., Qiu Y.X. Molecular data and ecological niche modelling reveal a highly dynamic evolutionary history of the East Asian Tertiary relict Cercidiphyllum (Cercidiphyllaceae). New Phytol. 2012, 196:617-630.
36. Qian H., Ricklefs R.E. Diversity of temperate plants in East Asia - reply. Nature 2001, 413:130.
37. Qiu Y.X., Guan B.C., Fu C.X., Comes H.P. Did glacials and/or interglacials promote allopatric incipient speciation in East Asian temperate plants? Phylogeographic and coalescent analyses on refugial isolation and divergence in Dysosma versipellis. Mol. Phylogenet. Evol. 2009, 2009(51):281-293.
38. Qiu Y.X., Fu C.X., Comes H.P. Plant molecular phylogeography in China and adjacent regions: tracing the genetic imprints of Quaternary climate and environment change in the world's most diverse temperate flora. Mol. Phylogenet. Evol. 2011, 59:225-244.
39. Rogers A.R. Genetic evidence for a Pleistocene population explosion. Evolution 1995, 49:608-615.
40. Rogers A.R., Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 1992, 9:552-569.
41. Shafer A., Cullingham C.I., CÔTÉ S.D., Coltman D.W. Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Mol. Ecol. 2010, 19:4589-4621.
42. Shaw J., Lickey E.B., Schilling E.E., Small R.L. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in Angiosperms: the tortoise and the hare III. Am. J. Bot. 2007, 94:275-288.
43. Shi Y. Evolution of the cryosphere in the Tibetan Plateau, China, and its relationship with the global change in the Mid Quaternary. J. Glaciol. Geocryol. 1998, 20:197-208.
44. Shi M.M., Michalski S.G., Welk E., Chen X.Y., Durka W. Phylogeography of a widespread Asian subtropical tree: genetic east-west differentiation and climate envelope modelling suggest multiple glacial refugia. J. Biogeogr. 2014, 41:1710-1720.
45. Soltis D.E., Morris A.B., McLachlan J.S., Manos P.S., Soltis P.S. Comparative phylogeography of unglaciated eastern North America. Mol. Ecol. 2006, 15:4261-4293.
46. Stapf O. Sargentodoxa cuneata. Curtis's Bot. Mag. 1926, 151:9111-9112.
47. Sun Y., Moore M.J., Yue L., Feng T., Chu H., Chen S., Ji Y., Wang H., Li J. Chloroplast phylogeography of the East Asian Arcto-Tertiary relict Tetracentron sinense (Trochodendraceae). J. Biogeogr. 2014, 41:1721-1732.
48. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123:585-595.
49. Tzedakis P.C., Raynaud D., Mcmanus J.F., Berger A., Brovkin V., Kiefer T. Interglacial diversity. Nature Geosci. 2009, 2:751-755.
50. Wang H.W., Ge S. Phylogeography of the endangered Cathaya argyrophylla (Pinaceae) inferred from sequence variation of mitochondrial and nuclear DNA. Mol. Ecol. 2006, 15:4109-4122.
51. Wang F., Li D.-Z., Yang J.-B. Molecular phylogeny of the Lardizabalaceae based on TrnL-F sequences and combined chloroplast data. Acta Bot. Sinica 2002, 44:971-977.
52. Wang H.F., Kirchoff B.K., Qin H.N., Zhu Q.X. Reproductive morphology of Sargentodoxa cuneata (Lardizabalaceae) and its systematic implications. Plant Syst. Evol. 2009, 280:207-217.
53. Wang J., Gao P.X., Kang M., Lowe A.J., Huang H.W. Refugia within refugia: the case study of a canopy tree (Eurycorymbus cavaleriei) in subtropical China. J. Biogeogr. 2009, 36:2156-2164.
54. Wu C.Y. Vegetation of China 1980, Science Press, Beijing.
55. Xiong D., Xiong Y., Xi Z., Mei J. High-yield cultivation technique of Akebia trifoliata (Thunb) Koidz. J. Hunan Agr. Univ. (Nat. Sci.) 2007, 33:156-159.
56. Yi S., Saito Y., Zhao Q., Wang P. Vegetation and climate changes in the Changjiang (Yangtze River Delta), China, during the past 13,000 years inferred from pollen records. Quaternary Sci. Rev. 2003, 22:1501-1519.
57. Ying T.S., Zhang Y.L., Boufford D.E. The Endemic Genera of Seed Plants of China 1993, Science Press, Beijing.
58. Yu G., Chen X., Ni J., Cheddadi R., et al. Palaeovegetation of China: a pollen data-based synthesis for the mid-Holocene and Last Glacial Maximum. J. Biogeogr. 2000, 27:635-664.
59. Zhan A., Fu J. Past and present: Phylogeography of the Bufo gargarizans species complex inferred from multi-loci allele sequence and frequency data. Mol. Phylogenet. Evol. 2011, 61:136-148.
60. Zhang Z.Y., Wu R., Wang Q., Zhang Z.R., Fan D.M., López-Pujol J., Li D.Z. Comparative phylogeography of two sympatric beeches in subtropical China: species-specific geographic mosaic of lineages. Ecol. Evol. 2013, 3:4461-4472.
61. Zhao S.Q. Physical Geography of China 1986, Science Press, Beijing.
62. Zhou T.H., Li S., Qian Z.Q., Su H.L., Huang Z.H., Guo Z.G., Dai P.F., Liu Z.L., Zhao G.F. Strong phylogeographic pattern of cpDNA variation reveals multiple glacial refugia for Saruma henryi Oliv. (Aristolochiaceae), an endangered herb endemic to China. Mol. Phylogenet. Evol. 2010, 57:176-188.