title: Chloroplast DNA phylogeography reveals repeated range expansion in a widespread aquatic herb Hippuris vulgaris in the Qinghai-Tibetan Plateau and adjacent areas.
abstract: BACKGROUND
  The Qinghai-Tibetan Plateau (QTP) is one of the most extensive habitats for alpine plants in the world. Climatic oscillations during the Quaternary ice age had a dramatic effect on species ranges on the QTP and the adjacent areas. However, how the distribution ranges of aquatic plant species shifted on the QTP in response to Quaternary climatic changes remains almost unknown.
  
  
  RESULTS
  We studied the phylogeography and demographic history of the widespread aquatic herb Hippuris vulgaris from the QTP and adjacent areas. Our sampling included 385 individuals from 47 natural populations of H. vulgaris. Using sequences from four chloroplast DNA (cpDNA) non-coding regions, we distinguished eight different cpDNA haplotypes. From the cpDNA variation in H. vulgaris, we found a very high level of population differentiation (G ST = 0.819) but the phylogeographical structure remained obscure (N ST = 0.853>G ST = 0.819, P>0.05). Phylogenetic analyses revealed two main cpDNA haplotype lineages. The split between these two haplotype groups can be dated back to the mid-to-late Pleistocene (ca. 0.480 Myr). Mismatch distribution analyses showed that each of these had experienced a recent range expansion. These two expansions (ca. 0.12 and 0.17 Myr) might have begun from the different refugees before the Last Glacial Maximum (LGM).
  
  
  CONCLUSIONS
  This study initiates a research on the phylogeography of aquatic herbs in the QTP and for the first time sheds light on the response of an alpine aquatic seed plant species in the QTP to Quaternary climate oscillations.
authors.affiliation: Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, China.
authors.forename: Jin-Ming
authors.initials: JM
authors.lastname: Chen
authors.forename: Zhi-Yuan
authors.initials: ZY
authors.lastname: Du
authors.forename: Shan-Shan
authors.initials: SS
authors.lastname: Sun
authors.forename: Robert Wahiti
authors.initials: RW
authors.lastname: Gituru
authors.forename: Qing-Feng
authors.initials: QF
authors.lastname: Wang
mesh_terms: D002681:China; D018742:DNA, Chloroplast / Q000235:genetics*; D017753:Ecosystem; D006239:Haplotypes; D058974:Phylogeography; D010944:Plants / Q000145:classification / Q000235:genetics*
chemical_list: D018742:DNA, Chloroplast
references.citation: Plant Mol Biol. 1991 Nov;17(5):1105-9
references.pmid: 1932684
references.citation: Mol Ecol. 1998 Apr;7(4):453-64
references.pmid: 9628000
references.citation: Mol Ecol. 2004 Sep;13(9):2699-707
references.pmid: 15315682
references.citation: BMC Evol Biol. 2007 Nov 08;7:214
references.pmid: 17996036
references.citation: Mol Phylogenet Evol. 2010 Dec;57(3):1162-72
references.pmid: 20828627
references.citation: Mol Ecol. 2007 Oct;16(19):4128-37
references.pmid: 17894761
references.citation: Proc Natl Acad Sci U S A. 1987 Dec;84(24):9054-8
references.pmid: 3480529
references.citation: Mol Phylogenet Evol. 2010 Jan;54(1):291-301
references.pmid: 19755165
references.citation: Am J Bot. 2007 Mar;94(3):275-88
references.pmid: 21636401
references.citation: Mol Ecol. 2008 Dec;17(23):5135-45
references.pmid: 19017264
references.citation: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references.pmid: 7984417
references.citation: Mol Ecol. 2006 Dec;15(14):4261-93
references.pmid: 17107465
references.citation: Science. 2001 Sep 21;293(5538):2242-5
references.pmid: 11567135
references.citation: Philos Trans R Soc Lond B Biol Sci. 2004 Feb 29;359(1442):183-95; discussion 195
references.pmid: 15101575
references.citation: Science. 1975 Aug 8;189(4201):419-26
references.pmid: 17781869
references.citation: Proc Natl Acad Sci U S A. 2000 Aug 1;97(16):9115-20
references.pmid: 10922067
references.citation: J Mol Evol. 1980 Dec;16(2):111-20
references.pmid: 7463489
references.citation: Science. 2001 Nov 23;294(5547):1671-7
references.pmid: 11721044
references.citation: Nature. 2000 Jun 22;405(6789):907-13
references.pmid: 10879524
references.citation: Mol Phylogenet Evol. 2011 Jul;60(1):1-12
references.pmid: 21545839
references.citation: Am J Bot. 2005 Jan;92(1):142-66
references.pmid: 21652394
references.citation: DNA Res. 2006 Oct 31;13(5):197-204
references.pmid: 17110395
references.citation: Hum Biol. 1994 Aug;66(4):591-600
references.pmid: 8088750
references.citation: Genetics. 1999 Jul;152(3):1079-89
references.pmid: 10388826
references.citation: Mol Ecol. 2002 Dec;11(12):2571-81
references.pmid: 12453240
references.citation: Mol Ecol. 2005 Oct;14(11):3513-24
references.pmid: 16156819
references.citation: Genetics. 1993 Jul;134(3):959-69
references.pmid: 8349118
references.citation: Brief Bioinform. 2004 Jun;5(2):150-63
references.pmid: 15260895
references.citation: PLoS One. 2011;6(9):e25896
references.pmid: 21984953
references.citation: PLoS One. 2012;7(5):e37196
references.pmid: 22590654
references.citation: Genetics. 1996 Nov;144(3):1237-45
references.pmid: 8913764
references.citation: Science. 2008 Aug 22;321(5892):1054-8
references.pmid: 18719275
references.citation: Mol Ecol. 2009 Feb;18(4):709-21
references.pmid: 19175501
references.citation: Mol Ecol. 2010 Jul;19(14):2964-79
references.pmid: 20584145
references.citation: Mol Biol Evol. 1992 May;9(3):552-69
references.pmid: 1316531
references.citation: Genetics. 1992 Jun;131(2):479-91
references.pmid: 1644282
references.citation: Evolution. 1995 Aug;49(4):608-615
references.pmid: 28565146
references.citation: Bioinformatics. 2003 Aug 12;19(12):1572-4
references.pmid: 12912839
references.citation: Mol Phylogenet Evol. 2011 Apr;59(1):225-44
references.pmid: 21292014
references.citation: Heredity (Edinb). 2010 Jun;104(6):534-42
references.pmid: 19920855
references.citation: Evolution. 1985 Jul;39(4):783-791
references.pmid: 28561359
references.citation: Nature. 2001 May 3;411(6833):62-6
references.pmid: 11333976
references.citation: Science. 1992 Mar 27;255(5052):1663-70
references.pmid: 17749419
references.citation: Mol Ecol. 2004 May;13(5):1143-55
references.pmid: 15078452
references.citation: Mol Ecol. 2000 Oct;9(10):1657-9
references.pmid: 11050560
references.citation: J Integr Plant Biol. 2009 Jul;51(7):698-706
references.pmid: 19566648