Pliocene intraspecific divergence and Plio-Pleistocene range expansions within Picea likiangensis (Lijiang spruce), a dominant forest tree of the Qinghai-Tibet Plateau

Molecular Ecology

Volumn 22, Issue 20, 2013, Pages 5237-5255

  Li, Long ^a   Abbott, Richard J ^b   Liu, Bingbing ^a   Sun, Yongshuai ^a   Li, Lili ^a   Zou, Jiabin ^a   Wang, Xi ^a   Miehe, Georg ^c   Liu, Jianquan ^a  

^a LANZHOU UNIVERSITY   (China)

^b UNIVERSITY OF ST ANDREWS   (United Kingdom)

^c PHILIPPS UNIVERSITY MARBURG   (Germany)

Author keywords

glaciation; intraspecific divergence; Picea likiangensis; plateau uplift; Qinghai Tibet Plateau; range expansion

Indexed keywords

CHLOROPLAST DNA; MITOCHONDRIAL DNA; PLANT DNA;

ARTICLE; BIODIVERSITY; BIOLOGICAL MODEL; CELL NUCLEUS; CHINA; CLIMATE CHANGE; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GLACIATION; INTRASPECIFIC DIVERGENCE; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PICEA LIKIANGENSIS; PLATEAU UPLIFT; POPULATION GENETICS; QINGHAI-TIBET PLATEAU; RANGE EXPANSION; SPRUCE; STATISTICAL MODEL; TREE;

GLACIATION; INTRASPECIFIC DIVERGENCE; PICEA LIKIANGENSIS; PLATEAU UPLIFT; QINGHAI-TIBET PLATEAU; RANGE EXPANSION;

BIODIVERSITY; CELL NUCLEUS; CHINA; CLIMATE CHANGE; DNA, CHLOROPLAST; DNA, MITOCHONDRIAL; DNA, PLANT; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENETICS, POPULATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PICEA; SEQUENCE ANALYSIS, DNA; TREES;

EID: 84885642816     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12466     Document Type: Article

References (110)

1. Anderson RP, Lew D, Peterson AT, (2003) Evaluating predictive models of species' distributions: criteria for selecting optimal models. Ecological Modeling, 162, 211-232.
2. Anderson LL, Hu FS, Nelson DM, Petit RJ, Paige KN, (2006) Ice-age endurance: DNA evidence of a white spruce refugium in Alaska. Proceedings of the National Academy of Sciences, USA, 103, 12447-12450.
3. Bandelt HJ, Forster P, Röhl A, (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37-48.
4. Bouillé M, Bousquet J, (2005) Trans-species shared polymorphism at orthologous nuclear gene loci among distant species in the conifer Picea (Pinaceae): implications for the long-term maintenance of genetic diversity in trees. American Journal of Botany, 92, 63-73.
5. Carling MD, Lovette IJ, Brumfield RT, (2010) Historical divergence and gene flow: coalescent analyses of mitochondrial, autosomal and sex-linked loci in Passerina buntings. Evolution, 64, 1762-1772.
6. Chen J, Källman T, Gyllenstrand N, Lascoux M, (2010) New insights on the speciation history and nucleotide diversity of three boreal spruce species and a Tertiary relict. Heredity, 104, 3-14.
7. Chung SL, Lo C, Lee TY, et al,. (1998) Diachronomous uplift of the Tibet plateau starting 40 Myr ago. Nature, 394, 769-773.
8. Conover W, (1999) Practical Nonparametric Statistics. Wiley, New York.
9. Cornuet JM, Santos F, Beaumont MA, Robert CP, Marin JM, Balding DJ, (2008) Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation. Bioinformatics, 24, 2713-2719.
10. Cornuet JM, Ravigné A, Estoup A, (2010) Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v. 1.0). BMC Bioinformatics, 11, 401.
11. Coyne JA, (1992) Genetics and speciation. Nature, 355, 511-515.
12. Depaulis F, Veuille M, (1998) Neutrality tests based on the distribution of haplotypes under an infinite-site model. Molecular Biology and Evolution, 15, 1788-1790.
13. Depaulis F, Mousset S, Veuille M, (2001) Haplotype tests using coalescent simulations conditional on the number of segregating sites. Molecular Biology and Evolution, 18, 1136-1138.
14. Doyle JJ, Doyle JL, (1990) Isolation of plant DNA from plant tissue. Focus, 12, 13-15.
15. Du KF, Peng LX, Liu JQ, Lascoux M, Hu FS, Petit RJ, (2011) Direction and extent of organelle DNA introgression between two spruce species in the Qinghai-Tibetan Plateau. New Phytologist, 192, 1024-1033.
16. Ebihara A, Nitta JH, Ito M, (2010) Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan. PLoS ONE, 5, e15136.
17. Elith J, Graham CH, Anderson RP, et al,. (2006) Novel methods improve prediction of species' distributions from occurrence data. Ecography, 29, 129-151.
18. Evanno G, Regnaut S, Goudet J, (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology, 14, 2611-2620.
19. Ewing B, Green P, (1998) Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Research, 8, 186-194.
20. Ewing B, Hillier L, Wendl M, Green P, (1998) Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Research, 8, 175-185.
21. Excoffier L, Laval G, Schneider S, (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics, 1, 47-50.
22. Fay JC, Wu CI, (2000) Hitchhiking under positive Darwinian selection. Genetics, 131, 479-491.
23. Fielding AH, Bell JF, (1997) Areview of methods for the assessment of prediction errors in conservation presence/absence models. Environmental Conservation, 24, 38-49.
24. Fu YX, (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915-925.
25. Fu YX, Li WH, (1993) Statistical tests of neutrality of mutations. Genetics, 133, 693-709.
26. Fu L, Li N, Mill RR, (1999) Flora of China. Science Press, Beijing.
27. Gao J, Wang BS, Mao JF, Ingvarsson P, Zeng QY, Wang XR, (2012) Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau. Molecular Ecology, 21, 4811-4827.
28. Giovanni R, Siqueira M, Sutton T, et al,. (2011) openModeller: a generic approach to species potential distribution modelling. GeoInformatica, 15, 111-135.
29. Guo ZT, Ruddiman WF, Hao QZ, et al,. (2002) Onset of Asian desertification by 22 Myr ago inferred from loess deposits in China. Nature, 416, 159-163.
30. Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD, (2009) Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genetics, 5, e1000695.
31. Haddrill PR, Thornton KR, Charlesworth B, Andolfatto P, (2005) Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Gemome Research, 15, 790-799.
32. Hamilton M, (1999) Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology, 8, 521-523.
33. Harrison TM, Copeland P, Kidd WSF, Yin A, (1992) Raising Tibet. Science, 255, 1663-1670.
34. Heuertz M, Paoli ED, Källman T, et al,. (2006) Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway Spruce [Piceaabies (L.) Karst]. Genetics, 174, 2095-2105.
35. Hey J, (2010a) The divergence of Chimpanzee species and subspecies as revealed in multipopulation isolation-with-migration analyses. Molecular Biology and Evolution, 27, 921-933.
36. Hey J, (2010b) Isolation with migration models for more than two populations. Molecular Biology and Evolution, 27, 905-920.
37. Hey J, Nielsen R, (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics, 167, 747-760.
38. Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A, (2005) Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25, 1965-1978.
39. Hijmans RJ, Guarino L, Jarvis A, O'Brien R, Mathur P, (2009) DIVA-GIS, pp. A geographic information system for the analysis of species distribution data. Manual available at: http://www.diva-gis.org.
40. Hubisz MJ, Falush D, Stephens M, Pritchard JK, (2009) Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources, 9, 1322-1332.
41. Hudson RR, Kaplan NL, (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetic, 111, 147-164.
42. Hudson RR, Kreitman M, Aguadé M, (1987) A test of neutral molecular evolution based on nucleotide data. Genetics, 116, 153-159.
43. Jia DR, Liu TL, Wang LY, Zhou DW, Liu JQ, (2011) Evolutionary history of an alpine shrub Hippophae tibetana (Elaeagnaceae): allopatric divergence and regional expansion. Biological Journal of the Linnean Society, 102, 37-50.
44. Jia DR, Abbott RJ, Liu TL, Mao KS, Bartish IV, Liu JQ, (2012) Out of the Qinghai-Tibet Plateau: evidence for the origin and dispersal of Eurasian temperate plants from a phylogeographic study of Hippophaë rhamnoides (Elaeagnaceae). New Phytologist, 194, 1123-1133.
45. Kumar S, Nei M, Dudley J, Tamura K, (2008) MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequence. Briefings in Bioinformatics, 9, 299-306.
46. Li HP, (2011) A new test for detecting recent positive selection that is free from the confounding impacts of demography. Molecular Biology and Evolution, 28, 365-375.
47. Li JJ, Shi YF, Li BY, (1995) Uplift of the Qinghai-Xizang (Tibet) Plateau and Global Change. Lanzhou University Press, Lanzhou.
48. Li Y, Stocks M, Hemmilä S, et al,. (2010) Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci. Molecular Biology and Evolution, 27, 1001-1014.
49. Li ZH, Zou JB, Mao KS, et al,. (2012) Population genetic evidence for complex evolutionary histories of four high altitude juniper species in the Qinghai-Tibetan Plateau. Evolution, 66, 831-845.
50. Librado P, Rozas J, (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
51. Liu JQ, Tian B, (2007) Origin, evolution, and systematic of Himalaya endemic genera. News letter of Himalayan Botany, 40, 20-27.
52. Liu JQ, Gao TG, Chen ZD, Lu AM, (2002) Molecular phylogeny and biogeography of the Qinghai-Tibetan Plateau endemic Nannoglottis (Asteraceae). Molecular Phylogenetics and Evolution, 23, 307-325.
53. Liu JQ, Wang YJ, Wang AL, Hideaki O, Abbott RJ, (2006) Radiation and diversification within the Ligularia-Cremanthodium-Parasenecio complex (Asteraceae) triggered by uplift of the Qinghai-Tibetan Plateau. Molecular Phylogenetics and Evolution, 38, 31-49.
54. Liu JQ, Sun YS, Ge XJ, Gao LM, Qiu YX, (2012) Phylogeographic studies of plants in China: advances in the past and directions in the future. Journal of Systematic and Evolution, 50, 267-275.
55. Liu J, Moller M, Provan J, Gao LM, Poudel RM, Li DZ, (2013) Geological and ecological factors drive cryptic speciation of yews in a biodiversity hotspot. New Phytologist, 199, 1093-1108.
56. Lobo JM, Jiménez-Valverde A, Real R, (2008) AUC: a misleading measure of the performance of predictive distribution models. Global Ecology and Biogeography, 17, 145-151.
57. Mao JF, Wang XR, (2011) Distinct niche divergence characterizes the homoploid hybrid speciation of Pinus densata on the Tibetan Plateau. American Naturalist, 177, 424-439.
58. Marcott SA, Shakun JD, Clark PU, Mix AC, (2013) Reconstruction of regional and global temperature for the past 11,300 years. Science, 339, 1198-1201.
59. Mayr E, (1963) Animal Species and Evolution. Harvard University Press, Cambridge.
60. Meng LH, Yang R, Abbott RJ, George M, Hu TH, Liu JQ, (2007) Mitochondrial and chloroplast phylogeography of Picea crassifolia Kom (Pinaceae) in the Qinghai-Tibetan Plateau and adjacent highlands. Molecular Ecology, 16, 4128-4137.
61. Mittermeier RA, Gil PR, Hoffmann M, et al,. (2004) Hotspots Revisited. Mexico City, Mexico, Cemex.
62. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J, (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853-858.
63. Nadachowska K, Babik W, (2009) Divergence in the face of gene flow: the case of two newts (Amphibia: Salamandridae). Molecular Biology and Evolution, 26, 829-841.
64. Nei M, (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences, USA, 70, 3321-3323.
65. Nei M, (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
66. Nielsen R, Wakeley J, (2001) Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics, 158, 885-896.
67. Nosil P, (2008) Speciation with gene flow could be common. Molecular Ecology, 17, 2103-2106.
68. Oksanen J, Blanchet FG, Kindt R, et al,. (2010) Vegan: community ecology package. R package, version 1.17-0. http://CRAN.R-project.org/packagepvegan.
69. Opgenoorth L, Vendramin GG, Mao K, et al,. (2010) Tree endurance on the Tibetan Plateau marks the world's highest known tree line of the last glacial maximum. New Phytologist, 185, 332-342.
70. Peng XL, Zhao CM, Wu GL, Liu JQ, (2007) Genetic variation and phylogeographic history of Picealikiangensis revealed by RAPD markers. Trees-Structure and Function, 21, 457-464.
71. Peterson AT, Nyári ÁS, (2007) Ecological niche conservatism and Pleistocene refugia in the Thrush-like Mourner, Schiffornis sp., in the Neotropics. Evolution, 62, 173-183.
72. Peterson AT, Papeş M, Soberõn J, (2008) Rethinking receiver operating characteristic analysis applications in ecological niche modelling. Ecological Modelling, 213, 63-72.
73. Petit RJ, Excoffier L, (2009) Gene flow and species delimitation. Trends in Ecology & Evolution, 24, 386-393.
74. Phillips SJ, Dudík M, (2008) Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography, 31, 161-175.
75. Phillips SJ, Anderson RP, Schapire RE, (2006) Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190, 231-259.
76. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
77. Pyhäjärvi T, García-Gil MR, Knürr T, Mikkonen M, Wachowiak W, Savolainen O, (2007) Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations. Genetics, 177, 1713-1724.
78. Qiu YX, Cheng X, 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. Molecular Phylogenetics and Evolution, 59, 225-244.
79. Rice WR, Hostert EE, (1993) Laboratory experiments on speciation: what have we learned in 40 years. Evolution, 47, 1637-1653.
80. Rosenberg N, (2004) Distruct: a program for the graphical display of population structure. Molecular Ecology Notes, 4, 137-138.
81. Ross-Ibarra J, Tenaillon M, Gaut BS, (2009) Historical divergence and gene flow in the genus Zea. Genetics, 181, 1399-1413.
82. Schoener TW, (1968) The Anolis lizards of Bimini: resource partitioning in a complex fauna. Ecology, 49, 704-726.
83. Shi YF, (2002) Characteristics of Late Quaternary monsoonal glaciation on the Tibetan Plateau and in East Asia. Quaternary International, 97, 79-91.
84. Shi YF, Li JJ, Li BY, (1998) Uplift and Environmental Changes of Qinghai-Tibetan Plateau in the Late Cenozoic. Guangdong Science and Technology Press, Guangzhou.
85. Shimono A, Ueno S, Gu S, Zhao X, Tsumura Y, Tang Y, (2010) Range shifts of Potentilla fruticosa on the Qinghai-Tibetan Plateau during glacial and interglacial periods revealed by chloroplast DNA sequence variation. Heredity, 104, 534-542.
86. Spicer RA, Harris NB, Widdowson WM, et al,. (2003) Constant elevation of southern Tibet over the past 15 million years. Nature, 421, 622-624.
87. Stewart JR, Lister AM, Barnes I, Dale L, (2010) Refugia revisited: individualistic responses of species in space and time. Proceedings of the Royal Society B: Biological Sciences, 277, 661-671.
88. Syring J, Farrell K, Businský R, Cronn R, Liston A, (2007) Widespread genealogical nonmonophyly in species of Pinus subgenus strobus. Systematic Biology, 56, 163-181.
89. Taberlet P, Gielly L, Pautou G, Bouvet J, (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology, 17, 1105-1109.
90. Tajima F, (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics, 105, 437-460.
91. Tajima F, (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
92. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, (2011) MEGA5: Molecular Evolutionary Genetics Analysis Using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731-2739.
93. 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 Research, 25, 4876-4882.
94. Wakeley J, Hey J, (1997) Estimating ancestral population parameters. Genetics, 145, 847-855.
95. Wang LY, Abbott RJ, Zheng W, Chen P, Wang YJ, Liu JQ, (2009) History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae). Molecular Ecology, 18, 709-721.
96. Wang B, Mao JF, Gao J, Zhao W, Wang XR, (2011) Colonization of the Tibetan Plateau by the homoploid hybrid pine Pinus densata. Molecular Ecology, 20, 3796-3811.
97. Warren DL, Glor RE, Turelli M, (2008) Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution, 62, 2868-2883.
98. Watterson GA, (1975) On the number of segregating sites in the genetical models without recombination. Theoretical Population Biology, 7, 256-276.
99. Willyard A, Ann W, Syring J, Gernandt DS, Liston A, Cronn R, (2007) Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for Pinus. Molecular Biology and Evolution, 24, 90-101.
100. Willyard A, Cronn R, Liston A, (2009) Reticulate evolution and incomplete lineage sorting among the Ponderosa pines. Molecular Phylogenetics and Evolution, 52, 498-511.
101. Woerner AE, Cox MP, Hammer MF, (2007) Recombination-filtered genomic datasets by information maximization. Bioinformatics, 23, 1851-1853.
102. Wright S, (1951) The genetical structure of populations. Annals of Human Genetics, 15, 323-354.
103. Wu CY, (1987) Flora of Tibet. Science Press, Beijing.
104. Wu ZY, Wu SG, (1996) A proposal for a new floristic kingdom (realm)-the E. Asiatic kingdom, its delimitation and characteristics. In: Proceedings of the First International Symposium on Floristic Characteristics and Diversity of East Asian Plants (eds, Zhang AL, Wu SG,), pp. 3-42. China Higher Education Press/Springer-Verlag, Beijing, Berlin.
105. Xu TT, Abbott RJ, Milne RI, et al,. (2010) Phylogeography and allopatric divergence of cypress species (Cupressus L.) in the Qinghai-Tibetan Plateau and adjacent regions. BMC Evolutionary Biology, 10, 194-203.
106. 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 Quaternary climate change. Molecular Ecology, 17, 5135-5145.
107. Zhang Q, Chiang TY, George M, Liu JQ, Abbott RJ, (2005) Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation. Molecular Ecology, 14, 3513-3524.
108. Zheng XM, Ge S, (2010) Ecological divergence in the presence of gene flow in two closely related Oryza species (Oryza rufipogon and O. nivara). Molecular Ecology, 19, 2439-2454.
109. Zhou WW, Wen Y, Fu J, et al,. (2012) Speciation in the Rana chensinensis species complex and its relationship to the uplift of the Qinghai-Tibetan Plateau. Molecular Ecology, 21, 960-973.
110. Zou JB, Peng XL, Li L, Liu JQ, Miehe G, Opgenoorth L, (2012) Molecular phylogeography and evolutionary history of Picea likiangensis in the Qinghai-Tibetan Plateau inferred from mitochondrial and chloroplast DNA sequence variation. Journal of Systematics and Evolution, 50, 341-350.