Cryptic speciation in the Chinese white pine (Pinus armandii): Implications for the high species diversity of conifers in the Hengduan Mountains, a global biodiversity hotspot
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Armenise, 2012, Validation of DNA barcoding as an efficient tool for taxon identification and detection of species diversity in Italian conifers, Eur. J. Forest Res., 131, 1337, 10.1007/s10342-012-0602-0
Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170
Buschiazzo, 2012, Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms, BMC Evol. Biol., 12, 8, 10.1186/1471-2148-12-8
Christenhusz, 2011, A new classification and linear sequence of extant gymnosperms, Phytotaxa, 19, 55, 10.11646/phytotaxa.19.1.3
Critchfield, 1986, Hybridization and classification of the white pines (Pinus section Strobus), Taxon, 35, 647, 10.2307/1221606
Cun, 2010, Plant recolonization in the Himalaya from the southeastern Qinghai-Tibetan Plateau: geographical isolation contributed to high population differentiation, Mol. Phylogenet. Evol., 56, 972, 10.1016/j.ympev.2010.05.007
Cun, 2015, Phylogeography and evolution of three closely related species of Tsuga (hemlock) from subtropical eastern Asia: further insights into speciation of conifers, J. Biogeogr., 42, 315, 10.1111/jbi.12421
De La Torre, 2017, Contrasting rates of molecular evolution and patterns of selection among gymnosperms and flowering plants, Mol. Biol. Evol., 34, 1363, 10.1093/molbev/msx069
DePristo, 2011, A framework for variation discovery and genotyping using next-generation DNA sequencing data, Nat. Genet., 43, 491, 10.1038/ng.806
Dray, 2007, The ade4 package-II: two-table and K-table methods, R News, 7, 47
Elith, 2006, Novel methods improve prediction of species’ distributions from occurrence data, Ecography, 29, 129, 10.1111/j.2006.0906-7590.04596.x
Emms, 2015, OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy, Genome Biol., 16, 157, 10.1186/s13059-015-0721-2
Evanno, 2005, Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study, Mol. Ecol., 14, 2611, 10.1111/j.1365-294X.2005.02553.x
Excoffier, 2005, Arlequin (version 3.0): an integrated software package for population genetics data analysis, Evol. Bioinform., 1, 47, 10.1177/117693430500100003
Farjon, 2010
Farjon, 2013
Fu, 1993, Statistical tests of neutrality of mutations, Genetics, 133, 693, 10.1093/genetics/133.3.693
Funk, 2006, Ecological divergence exhibits consistently positive associations with reproductive isolation across disparate taxa, Proc. Natl. Acad. Sci. USA, 103, 3209, 10.1073/pnas.0508653103
Gao, 2007, High variation and strong phylogeographic pattern among cpDNA haplotypes in Taxus wallichiana (Taxaceae) in China and North Vietnam, Mol. Ecol., 16, 4684, 10.1111/j.1365-294X.2007.03537.x
Grabherr, 2011, Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nat. Biotechnol., 29, 644, 10.1038/nbt.1883
Grant, 1981, Speciation and the adaptive radiation of Darwin's finches, Am. Sci., 69, 653
Grierson, 1980, Notes relating to the flora of Bhutan: III Pinus bhutanica: a new 5-needle pine from Bhutan and India, Notes R. B. G. Edinb., 38, 297
Hall, 1999, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp. Ser., 41, 95
Hao, 2015, Molecular phylogenetics and evolutionary history of sect. Quinquefoliae (Pinus): implications for Northern Hemisphere biogeography, Mol. Phylogenet. Evol., 87, 65, 10.1016/j.ympev.2015.03.013
Hijmans, 2005, Very high resolution interpolated climate surfaces for global land areas, Int. J. Climatol., 25, 1965, 10.1002/joc.1276
Hubisz, 2009, Inferring weak population structure with the assistance of sample group information, Mol. Ecol. Res., 9, 1322, 10.1111/j.1755-0998.2009.02591.x
Hudson, 1985, Statistical properties of the number of recombination events in the history of a sample of DNA sequences, Genetics, 111, 147, 10.1093/genetics/111.1.147
Jones, 1992, The rapid generation of mutation data matrices from protein sequences, Comput. Appl. Biosci., 8, 275
Katoh, 2013, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol., 30, 772, 10.1093/molbev/mst010
Leslie, 2018, An overview of extant conifer evolution from the perspective of the fossil record, Am. J. Bot., 105, 1, 10.1002/ajb2.1143
Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324
Li, 2009, The sequence alignment/map (SAM) format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352
Li, 2013, Pliocene intraspecific divergence and Plio-Pleistocene range expansions within Picea likiangensis (Lijiang spruce), a dominant forest tree of the Qinghai-Tibet Plateau, Mol. Ecol., 22, 5237, 10.1111/mec.12466
Li, 2012, Population genetic evidence for complex evolutionary histories of four high altitude juniper species in the Qinghai-Tibetan Plateau, Evolution, 66, 831, 10.1111/j.1558-5646.2011.01466.x
Librado, 2009, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, 25, 1451, 10.1093/bioinformatics/btp187
Liu, 2013, Geological and ecological factors drive cryptic speciation of yews in a biodiversity hotspot, New Phytol., 199, 1093, 10.1111/nph.12336
Liu, 2014, Phylogeography of Pinus armandii and its relatives: heterogeneous contributions of geography and climate changes to the genetic differentiation and diversification of Chinese white pines, PLoS One, 9
López-Pujol, 2011, Centres of plant endemism in China: places for survival or for speciation?, J. Biogeogr., 38, 1267, 10.1111/j.1365-2699.2011.02504.x
Ma, 1989, Geographic variation in Pinus armandii, Silvae Genet., 38, 81
Ma, 1992
Marchese, 2015, Biodiversity hotspots: a shortcut for a more complicated concept, Global Ecol. Conserv., 3, 297, 10.1016/j.gecco.2014.12.008
Mayr, 1942
McKenna, 2010, The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res., 20, 1297, 10.1101/gr.107524.110
Meijer, 2000, Fossil woods from the late Cretaceous Aachen Formation, Rev. Palaeobot. Palynol., 112, 297, 10.1016/S0034-6667(00)00007-5
Mirarab, 2014, ASTRAL: genome-scale coalescent-based species tree estimation, Bioinformatics, 30, i541, 10.1093/bioinformatics/btu462
Mittermeier, 2011, Global biodiversity conservation: the critical role of hotspots, 3
Mutke, 2005, Patterns of vascular plant diversity at continental to global scales, Biol. Skr., 55, 521
Nosil, 2012, Genomic divergence during speciation: causes and consequences, Phil. Trans. R. Soc. B., 367, 332, 10.1098/rstb.2011.0263
Nystedt, 2013, The Norway spruce genome sequence and conifer genome evolution, Nature, 497, 579, 10.1038/nature12211
Oksanen, J., Blanchet, F. G., Kindt, R., Legendre, P., O'Hara, R. B., Simpson, G., Solymos, P., Henry, M., Stevens, W. H., 2010. vegan: community ecology package. R package, version 1.17-0. https://cran.r-project.org/web/packages/vegan/.
Peakall, 2012, GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research - an update, Bioinformatics, 28, 2537, 10.1093/bioinformatics/bts460
Phillips, 2006, Maximum entropy modeling of species geographic distributions, Ecol. Model., 190, 231, 10.1016/j.ecolmodel.2005.03.026
Pritchard, 2000, Inference of population structure using multilocus genotype data, Genetics, 155, 945, 10.1093/genetics/155.2.945
Ran, 2015, Mitochondrial introgression and complex biogeographic history of the genus Picea, Mol. Phylogenet. Evol., 93, 63, 10.1016/j.ympev.2015.07.020
Ran, 2006, Molecular phylogeny and biogeography of Picea (Pinaceae): implications for phylogeographical studies using cytoplasmic haplotypes, Mol. Phylogenet. Evol., 41, 405, 10.1016/j.ympev.2006.05.039
Ru, 2018, Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process, Mol. Ecol., 27, 4875, 10.1111/mec.14909
Saladin, 2017, Fossils matter: improved estimates of divergence times in Pinus reveal older diversification, BMC Evol. Biol., 17, 95, 10.1186/s12862-017-0941-z
Sanderson, 2003, r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock, Bioinformatics, 19, 301, 10.1093/bioinformatics/19.2.301
Schluter, 2009, Genetics and ecological speciation, Proc. Natl. Acad. Sci. USA, 106, 9955, 10.1073/pnas.0901264106
Schoener, 1968, The Anolis lizards of Bimini: resource partitioning in a complex fauna, Ecology, 49, 704, 10.2307/1935534
Stamatakis, 2014, RAxML Version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 30, 1312, 10.1093/bioinformatics/btu033
Sun, 2014, Evolutionary history of purple cone spruce (Picea purpurea) in the Qinghai-Tibet Plateau: homoploid hybrid origin and pleistocene expansion, Mol. Eol., 23, 343
Tajima, 1983, Evolutionary relationship of DNA sequences infinite populations, Genetics, 105, 437, 10.1093/genetics/105.2.437
Tajima, 1989, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, 123, 585, 10.1093/genetics/123.3.585
Tamura, 2013, MEGA6: molecular evolutionary genetics analysis version 6.0, Mol. Biol. Evol., 30, 2725, 10.1093/molbev/mst197
Thompson, 1997, The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Res., 25, 4876, 10.1093/nar/25.24.4876
Wang, 2017, Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: an example from Pedicularis section Cyathophora, Mol. Phylogenet. Evol., 107, 345, 10.1016/j.ympev.2016.11.018
Wang, 2013, Examining the full effects of landscape heterogeneity on spatial genetic variation: a multiple matrix regression approach for quantifying geographic and ecological isolation, Evolution, 67, 3403, 10.1111/evo.12134
Wang, 2014, Evolution and biogeography of gymnosperms, Mol. Phylogenet. Evol., 75, 24, 10.1016/j.ympev.2014.02.005
Warren, 2008, Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution, Evolution, 62, 2868, 10.1111/j.1558-5646.2008.00482.x
Warren, 2010, ENMTools: a toolbox for comparative studies of environmental niche models, Ecography, 33, 607, 10.1111/j.1600-0587.2009.06142.x
Watterson, 1975, On the number of segregating sites in the genetical models without recombination, Theor. Popul. Biol., 7, 256, 10.1016/0040-5809(75)90020-9
Wei, 2004, Recolonization and radiation in Larix (Pinaceae): evidence from nuclear ribosomal DNA paralogues, Mol. Ecol., 13, 3115, 10.1111/j.1365-294X.2004.02299.x
Wheeler, B., 2010. lmPerm: Permutation tests for linear models. R package version, 1.
Willyard, 2007, Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for Pinus, Mol. Biol. Evol., 24, 90, 10.1093/molbev/msl131
Xing, 2017, Uplift-driven diversification in the Hengduan Mountains, a temperate biodiversity hotspot, Proc. Natl. Acad. Sci. USA, 114, E3444, 10.1073/pnas.1616063114
Xu, 2010, Phylogeography and allopatric divergence of cypress species (Cupressus L.) in the Qinghai-Tibetan Plateau and adjacent regions, BMC Evol. Biol., 10, 194, 10.1186/1471-2148-10-194
Zhang, 2009, The 29°N latitudinal line: an important division in the Hengduan Moutains, a biodiversity hotspot in southwest China, Nord. J. Bot., 27, 405, 10.1111/j.1756-1051.2008.00235.x