Diploid hybrid origin of Ostryopsis intermedia (Betulaceae) in the Qinghai-Tibet Plateau triggered by Quaternary climate change

Molecular Ecology

Volumn 23, Issue 12, 2014, Pages 3013-3027

  Liu, Bingbing ^a,b   Abbott, Richard J ^c   Lu, Zhiqiang ^b   Tian, Bin ^b   Liu, Jianquan ^a  

^a SICHUAN UNIVERSITY   (China)

^b LANZHOU UNIVERSITY   (China)

^c UNIVERSITY OF ST ANDREWS   (United Kingdom)

Author keywords

climate change; homoploid hybrid speciation; Ostryopsis; Qinghai Tibet Plateau

Indexed keywords

BETULACEAE; OSTRYOPSIS; OSTRYOPSIS DAVIDIANA; OSTRYOPSIS NOBILIS;

CHLOROPLAST DNA; MICROSATELLITE DNA; PLANT DNA; RIBOSOMAL SPACER DNA;

ARTICLE; BAYES THEOREM; BETULACEAE; BIOLOGICAL MODEL; CLASSIFICATION; CLIMATE CHANGE; DIPLOIDY; DNA SEQUENCE; ECOSYSTEM; GENETICS; HOMOPLOID HYBRID SPECIATION; HYBRIDIZATION; MOLECULAR EVOLUTION; OSTRYOPSIS; PHYLOGENY; POPULATION GENETICS; QINGHAI-TIBET PLATEAU; SPECIES DIFFERENTIATION;

CLIMATE CHANGE; HOMOPLOID HYBRID SPECIATION; OSTRYOPSIS; QINGHAI-TIBET PLATEAU;

BAYES THEOREM; BETULACEAE; CLIMATE CHANGE; DIPLOIDY; DNA, CHLOROPLAST; DNA, PLANT; DNA, RIBOSOMAL SPACER; ECOSYSTEM; EVOLUTION, MOLECULAR; GENETIC SPECIATION; GENETICS, POPULATION; HYBRIDIZATION, GENETIC; MICROSATELLITE REPEATS; MODELS, GENETIC; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84902548031     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12783     Document Type: Article

References (88)

1. Abbott RJ, Brochmann C, (2003) History and evolution of the arctic flora: in the footsteps of Eric Hultén. Molecular Ecology, 12, 299-313.
2. Abbott RJ, Hegarty MJ, Hiscock SJ, Brennan AC, (2010) Homoploid hybrid speciation in action. Taxon, 59, 1375-1386.
3. Abbott RJ, Rieseberg LH, (2012) Hybrid Speciation. Encyclopaedia of Life Sciences (eLS). John Wiley & Sons, Chichester.
4. An ZS, Kutzbach JE, Prell WL, Port SC, (2001) Evolution of Asian monsoons and phased uplift of the Himalayan-Tibetan Plateau since late Miocene times. Nature, 411, 62-66.
5. Anton KA, Rhode Ward JM, Mitchell BC, (2013) Pollinator-mediated selection on floral morphology: evidence for transgressive evolution in derived hybrid populations. Journal of Evolutionary Biology, 26, 660-673.
6. Avise JC, (2000) Phylogeography: The History and Formation of Species. Harvard University Press, London, UK.
7. Bandelt HJ, Forster P, Röhl A, (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37-48.
8. Beaumont MA, Zhang WY, Balding DJ, (2002) Approximate Bayesian computation in population genetics. Genetics, 162, 2025-2035.
9. Beaumont LJ, Hughes L, Pitman AJ, (2008) Why is the choice of future climate scenarios for species distribution modeling important? Ecology Letters, 11, 1135-1146.
10. Bennett KD, (2004) Continuing the debate on the role of Quaternary environmental change for macroevolution. Philosophical Transactions of the Royal Society of London Series B: Biological Sciences, 359, 295-303.
11. Bryant D, Moulton V, (2004) Neighbor-Net: an agglomerative method for the construction of phylogentic networks. Molecular Biology and Evolution, 21, 255-265.
12. Clay DL, Novak SJ, Serpe MD, Tank DC, Smith JF, (2012) Homoploid hybrid speciation in a rare endemic Castilleja from Idaho (Castilleja christii, Orobanchaceae). American Journal of Botany, 99, 1976-1990.
13. Collins WD, Lee-Taylor JM, Edwards DP, Francis GL, (2006) Effects of increased near-infrared absorption by water vapor on the climate system. Journal of Geophysical Research: Atmospheres, 111, 18-27.
14. Comes HP, Kadereit JW, (1998) The effect of Quaternary climatic changes on plant distribution and evolution. Trends in Plant Science, 3, 432-438.
15. Darriba D, Taboada GL, Doallo R, Posada D, (2012) jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9, 772.
16. Development Core Team R (2011) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
17. Dice LR, (1945) Measures of the amount of ecologic association between species. Ecology, 26, 297-302.
18. Dieringer D, Schlotterer C, (2003) Microsatellite Analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3, 167-169.
19. Drummond AJ, Suchard MA, Xie D, Rambaut A, (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29, 1969-1973.
20. 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.
21. Excoffier L, Foll M, (2011) Fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics, 27, 1332-1334.
22. Excoffier L, Smouse PE, Quattro JM, (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes, application to human mitochondrial DNA restriction data. Genetics, 131, 479-491.
23. Excoffier L, Laval G, Schneider S, (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics, 1, 47-50.
24. Friis EM, Pedersen KR, Schonenberger J, (2003) Endressianthus, a new Normapolles-producing plant genus of Fagalean affinity from the Late Cretaceous of Portugal. International Journal of Plant Sciences, 164, 201-223.
25. Gao J, Wang B, 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.
26. Gaut B, Yang L, Takuno S, Eguiarte LE, (2011) The patterns and causes of variation in plant nucleotide substitution Rates. Annual Review of Ecology, Evolution, and Systematics, 42, 245-266.
27. Grimm GW, Renner SS, (2013) Harvesting Betulaceae sequences from GenBank to generate a new chronogram for the family. Botanical Journal of the Linnean Society, 172, 465-477.
28. Gross BL, Rieseberg LH, (2005) The ecological genetics of homoploid hybrid speciation. Journal of Heredity, 96, 241-252.
29. Harrison TM, Copeland P, Kidd WS, Yin A, (1992) Raising Tibet. Science, 255, 1663-1670.
30. Hasumi H, Emori S, (2004) K-1 Coupled GCM (MIROC) Description. Center for Climate System Research, University of Tokyo, Tokyo.
31. Hewitt GM, (1999) Post-glacial re-colonization of European biota. Botanical Journal of the Linnean Society, 68, 87-112.
32. Hijmans R, Guarino L, Cruz M, Rojas E, (2001) Computer tools for spatial analysis of plant genetic resources data: 1, DIVA-GIS. Plant Genetic Resources Newsletter, 127, 15-19.
33. 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.
34. Howarth DG, Baum DA, (2005) Genealogical evidence of homoploid hybrid speciation in an adaptive radiation of Scaevola (Goodeniaceae) in the Hawaiian Islands. Evolution, 59, 948-961.
35. Hudson RR, Kaplan NL, (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics, 111, 147-164.
36. Huson DH, Bryant D, (2006) Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution, 23, 254-267.
37. James JK, Abbott RJ, (2005) Recent, allopatric, homoploid hybrid speciation: the origin of Senecio squalidus (Asteraceae) in the British Isles from a hybrid zone on Mount Etna, Sicily. Evolution, 59, 2533-2547.
38. Kilian B, Özkan H, Deusch O, et al,. (2007) Independent wheat B and G genome origins in outcrossing Aegilops progenitor haplotypes. Molecular Biology and Evolution, 24, 217-227.
39. Li H, (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.
40. Li PC, Skvortsov AK, (1999) Betulaceae. Science Press and Missouri Botanical Garden Press, Beijing and Missouri.
41. Li JJ, Shi YF, Li BY, (1995) Uplift of the Qinghai-Xizang Tibet Plateau and Global Change. Lanzhou University Press, Lanzhou, China.
42. Li XX, Yang YN, Ma JT, (2009) Correlations of the Nut and Catkin Quantity Properties of Corylus heterophylla × C. avellana. Scientia Silvae Sinicae, 45, 62-66.
43. Librado P, Rozas J, (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
44. Liu JQ, Wang YJ, Wang AL, Ohba H, 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.
45. Liu BB, Tian B, Ma H, et al,. (2014) Development and characterization of EST-SSR markers in Ostryopsis (Betulaceae). Applications in Plant Sciences, 2, e1300062.
46. Ma XF, Szmidt AE, Wang XR, (2006) Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci. Molecular Biology and Evolution, 23, 807-816.
47. Ma H, Liu BB, Lu ZQ, Liu JQ, Qiu Q, (2013a) Transcriptome analyses revealed genetic mechanisms underlying the drought tolerance of Ostryopsis davidiana. Sciencepaper Online. Available from http://www.paper.edu.cn/ releasepaper/content/201304-111.
48. Ma H, Lu ZQ, Liu BB, Qiu Q, Liu JQ, (2013b) Transcriptome analyses of a Chinese hazelnut species Corylus mandshurica. BMC Plant Biology, 13, 1-10.
49. Mallet J, (2008) Hybridization, ecological races and the nature of species: empirical evidence for the ease of speciation. Philosophical Transactions of the Royal Society of London Series B: Biological Sciences, 363, 2971-2986.
50. 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.
51. McCormack JE, Zellmer AJ, Knowles LL, (2010) Does niche divergence accompany allopatric divergence in Aphelocoma jays as predicted under ecological speciation? Insights from tests with niche models. Evolution, 64, 1231-1244.
52. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GA, Kent J, (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853-858.
53. Nei M, (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
54. Nogués-Bravo D, (2009) Predicting the past distribution of species climatic niches. Global Ecology and Biogeography, 18, 521-531.
55. Nolte AW, Tautz D, (2010) Understanding the onset of hybrid speciation. Trends in Genetics, 26, 54-58.
56. Petit RJ, Hampe A, (2006) Some evolutionary consequences of being a tree. Annual Review of Ecology Evolution and Systematics, 37, 187-214.
57. Phillips SJ, Dudík M, (2008) Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography, 31, 161-175.
58. Phillips SJ, Anderson RP, Schapire RE, (2006) Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190, 231-259.
59. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
60. Provan J, Bennett KD, (2008) Phylogeographic insights into cryptic glacial refugia. Trends in Ecology and Evolution, 23, 564-571.
61. Rambaut A, (2009) FigTree v1.3.1. Available from http://tree.bio.ed.ac. uk/software/figtree/.
62. Rambaut A, Drummond AJ,. (2009) Tracer v 1.5. Available from http://beast.bio.ed.ac.uk/Tracer.
63. Rieseberg LH, Raymond O, Rosenthal DM, et al,. (2003) Major ecological transitions in wild sunflowers facilitated by hybridization. Science, 301, 1211-1216.
64. Rosenberg NA, (2004) Distruct: a program for the graphical display of population structure. Molecular Ecology Notes, 4, 137-138.
65. Salazar C, Baxter SW, Pardo-Diaz C, et al,. (2010) Genetic evidence for hybrid trait speciation in Heliconius butterflies. PLoS Genetics, 6, e1000930.
66. Schoener TW, (1968) The Anolis lizards of Bimini resource partitioning in a complex fauna. Ecology, 49, 704-726.
67. Schumer M, Rosenthal GG, Andolfatto P, (2014) How common is homoploid hybrid speciation? Evolution, doi: 10.1111/evo.12399.
68. Sheppard CS, (2013) How does selection of climate variables affect predictions of species distributions? A case study of three new weeds in New Zealand. Weed Research, 53, 259-268.
69. 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, China.
70. Smith SA, Donoghue MJ, (2008) Rates of molecular evolution are linked to life history in flowering plants. Science, 322, 86-89.
71. Soltis PS, Soltis DE, (2009) The role of hybridization in plant speciation. Annual Review of Plant Biology, 60, 561-588.
72. Stephens M, Smith NJ, Donnelly P, (2001) A new statistical method for haplotype reconstruction from population data. American Journal of Human genetics, 68, 978-989.
73. Sun YS, Abbott RJ, Li LL, Li L, Zou JB, Liu JQ, (2014) Evolutionary history of Purple cone spruce (Picea purpurea) in the Qinghai-Tibet Plateau: homoploid hybrid origin and Pleistocene expansion. Molecular Ecology, 23, 343-359.
74. 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.
75. Tian B, Liu RR, Wang LY, Qiu Q, Chen KM, Liu JQ, (2009) Phylogeographic analyses suggest that a deciduous species (Ostryopsis davidiana Decne., Betulaceae) survived in northern China during the Last Glacial Maximum. Journal of Biogeography, 36, 2148-2155.
76. Tian B, Liu T, Liu JQ, (2010) Ostryopsis intermedia, a new species of Betulaceae from Yunnan, China. Botanical Studies, 51, 257-262.
77. 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.
78. Wang B, Mao J-F, Gao J, Zhao W, Wang X-R, (2011) Colonization of the Tibetan Plateau by the homoploid hybrid pine Pinus densata. Molecular Ecology, 20, 3796-3811.
79. Wang N, Thomson M, Bodles WJ, et al,. (2013) Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers. Molecular Ecology, 22, 3098-3111.
80. Warren DL, Glor RE, Turelli M, (2008) Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution, 62, 2868-2883.
81. Warren DL, Glor RE, Turelli M, (2010) ENMTools: a toolbox for comparative studies of environmental niche models. Ecography, 33, 607-611.
82. Watterson GA, (1975) On the number of segregating sites in genetical models without recombination. Theoretical Population Biology, 7, 256-276.
83. Wegmann D, Leuenberger C, Excoffier L, (2009) Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihood. Genetics, 182, 1207-1218.
84. Wegmann D, Leuenberger C, Neuenschwander S, Excoffier L, (2010) ABCtoolbox: a versatile toolkit for approximate Bayesian computations. BMC Bioinformatics, 11, 1-7.
85. Winkler M, Tribsch A, Schneeweiss GM, et al,. (2013) Strong nuclear differentiation contrasts with widespread sharing of plastid DNA haplotypes across taxa in European purple saxifrages (Saxifraga section Porphyrion subsection Oppositifoliae). Botanical Journal of the Linnean Society, 173, 622-636.
86. Wu YH, (2008) The Vascular Plants and their Eco-Geographical Distribution of the Qinghai-Tibetan Plateau. Science Press, Beijing, China.
87. 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.
88. Zhou SZ, Li JJ, Zhang SQ, Cui JX, (2004) Quaternary glaciations in China. In: Developments in Quaternary Science (eds, Ehlers J, Gibbard PL,), pp. 105-133. Elsevier, Amsterdam.