Historical processes during the Quaternary are likely to have left a signature on the geographical distribution of intraspecific genetic variation. In particular, high genetic uniqueness could be expected within glacial refugia for multiple species. We aimed to test this for plants in China and whether multi-species hotspots of genetic diversity are good indicators of glacial refugia in this region. From chloroplast DNA haplotype data for 116 species we calculated two local genetic diversity metrics for each species: haplotype genetic richness and genetic uniqueness. From these two, only uniqueness could reliably identify refugia, whereas richness may indicate either glacial refugia or areas recolonized by genetic lineages from different refugia in the postglacial period. Our results suggest the occurrence of numerous cryptic refugia and their likely importance in the maintenance and evolution of the Chinese flora, and indicate that an approach that locates geographic hotspots of genetic diversity data can reliably identify refugia.
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Abbott R.J. , Brochmann C. 2003. History and evolution of the arctic flora: in the footsteps of Eric Hultén. Mol Ecol. 12: 299-313.
An Z.S. , Kutzbach J.E. , Warren L.P. , Porter S.C. 2001. Evolution of Asian monsoons and phased uplift of the Himalayan-Tibetan plateau since Late Miocene times. Nature. 411: 62-66.
Arbogast B.S. , Kenagy G.J. 2001. Comparative phylogeography as an integrative approach to historical biogeography. J Biogeogr. 28: 819-825.
Avise J.C. 2000. Phylogeography: the History and Formation of Species. Havard University Press, Cambridge, Massachusetts.
Avise J.C. , Arnold J. , Ball R.M. . 1987. Intraspecific phylogeography - the mitochondrial-DNA bridge between population-genetics and systematics. Annu Rev Ecol Syst. 18: 489-522.
Axelrod D.I. , Al-Shehbaz I. , Raven P.H. 1998. History of the modern flora of China. In: Zhang A.L. , Wu S.G. , eds. Floristic Characteristics and Diversity of East Asian Plants. Beijing: China Higher Education Press; p. 43-55.
Bell R.C. , MacKenzie J.B. , Hickerson M.J. , Chavarria K.L. , Cunningham M. , Williams S. , Moritz C. 2012. Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs. P Roy Soc B. 279: 991-999.
Bennett K.D. , Lawton J.H. , Gibbs A. , Williamson M.H. , Holdgate M.W. , Hamilton W.D. , Conway G.R. 1986. The rate of spread and population increase of forest trees during the postglacial. Philos T R Soc B. 314: 523-531.
Bennett K.D. , Tzedakis P.C. , Willis K.J. 1991. Quaternary refugia of North European trees. J Biogeogr. 18: 103-115.
Birks H.J.B. , Willis K.J. 2008. Alpines, trees, and refugia in Europe. Plant Ecol Divers. 1: 147-160.
Brochmann C. , Brysting A.K. 2008. The Arctic – an evolutionary freezer? Plant Ecol Divers. 1: 181-195.
Brunsfeld S.J. , Sullivan J. , Soltis D.E. , Soltis P.S. 2001. Comparative phylogeography of Northwestern North America: A synthesis. In: J.S. Silvertown, J. Antonovics, eds., Integrating Ecology and Evolution in a Spatial Context. Cambridge: Cambridge University Press, pp. 319-340.
Buckley T.R. , Marske K. , Attanayake D. 2010. Phylogeography and ecological niche modelling of the New Zealand stick insect Clitarchus hookeri (White) support survival in multiple coastal refugia. J Biogeogr. 37: 682-695.
Calsbeek R. , Thompson J.N. , Richardson J.E. 2003. Patterns of molecular evolution and diversification in a biodiversity hotspot: the California floristic province. Mol Ecol. 12: 1021-1029.
Carnaval A.C. , Hickerson M.J. , Haddad C.F.B. , Rodrigues M.T. , Moritz C. 2009. Stability predicts genetic diversity in the Brazilian Atlantic forest hotspot. Science. 323: 785-789.
Carstens B.C. , Brunsfeld S.J. , Demboski J.R. , Good J.M. , Sullivan J. 2005. Investigating the evolutionary history of the Pacific northwest mesic forest ecosystem: hypothesis testing within a comparative phylogeographic framework. Evolution. 59: 1639-1652.
Carstens B.C. , Richards C.L. 2007. Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution. 61: 1439-1454.
Chen C.D. 1998. Biodiversity of China: A Country Study. Beijing: China Environmental Science Press.
Comps B. , Gomory D. , Letouzey J. , Thiebaut B. , Petit R.J. 2001. Diverging trends between heterozygosity and allelic richness during postglacial colonization in the European beech. Genetics. 157: 389-397.
Contreras-Medina R. , Luna-Vega I. 2007. Species richness, endemism and conservation of Mexican gymnosperms. Biodivers Conserv. 16: 1803-1821.
Crisp M.D. , Laffan S. , Linder H.P. , Monro A. 2001. Endemism in the Australian flora. J Biogeogr. 28: 183-198.
Dauby G. , Duminil J. , Heuertz M. , Koffi G.K. , Stevart T. , Hardy O.J. 2014. Congruent phylogeographical patterns of eight tree species in Atlantic Central Africa provide insights into the past dynamics of forest cover. Mol Ecol. 23: 2299-2312.
Davis M.B. 1981. Quaternary history and the stability of forest communities. In: D.C. West, H.H. Shugart, D.B. Botkin, eds., Forest Succession. New York: Springer-Verlag, pp. 132-153.
Eidesen P.B. , Ehrich D. , Bakkestuen V. , Alsos I.G. , Gilg O. , Taberlet P. , Brochmann C. 2013. Genetic roadmap of the arctic: plant dispersal highways, traffic barriers and capitals of diversity. New Phytol. 200: 898-910.
Fan D.M. , Hu W. , Li B. , Morris A.B. , Zheng M. , Soltis D.E. , Soltis P.S. , Zhang Z.Y. 2016. Idiosyncratic responses of evergreen broad-leaved forest constituents in China to the late Quaternary climate changes. Sci Rep. 6: 31044.
Ferla B.L. , Taplin J. , Ockwell D. , Lovett J.C. 2002. Continental scale patterns of biodiversity: can higher taxa accurately predict African plant distributions? Bot J Linn Soc. 138: 225-235.
Fjeldsa J. , Lovett J.C. 1997. Geographical patterns of old and young species in African forest biota: The significance of specific montane areas as evolutionary centres. Biodiver Conserv. 6: 325-346.
Fouquet A. , Noonan B.P. , Rodrigues M.T. , Pech N. , Gilles A. , Gemmell N.J. 2012. Multiple quaternary refugia in the eastern guiana shield revealed by comparative phylogeography of 12 frog species. Systematic Biol. 61: 461-489.
Gutierrez-Garcia T.A. , Vazquez-Dominguez E. 2011. Comparative phylogeography: designing studies while surviving the process. BioScience. 61: 857-868.
Hampe A. , Jump A.S. 2011. Climate relicts: Past, present, future. Annu Rev Ecol Evol S. 42: 313-333.
Harrison S.P. , Yu G. , Takahara H. , Prentice I.C. 2001. Palaeovegetation: Diversity of temperate plants in east Asia. Nature. 413: 129-130.
Heuertz M. , Hausman J.F. , Hardy O.J. , Vendramin G.G. , Frascaria-Lacoste N. , Vekemans X. 2004. Nuclear microsatellites reveal contrasting patterns of genetic structure between western and southeastern European populations of the common ash (Fraxinus excelsior L.). Evolution. 58: 976-988.
Hewitt G. 2000. The genetic legacy of the Quaternary ice ages. Nature 405: 907-913.
Hewitt G.M. 1996. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol J Linn Soc. 58: 247-276.
Hewitt G.M. 1999. Post-glacial re-colonization of European biota. Biol J Linn Soc. 68: 87-112.
Hijmans R.J. , Cameron S.E. , Parra J.L. , Jones P.G. , Jarvis A. 2005. Very high resolution interpolated climate surfaces for global land areas. Int J Climatol. 25:1965-1978.
Hong D.Y. , Blackmore S. 2013. Plants of China: A Companion of the Flora of China. Beijing: Science Press.
Hsu J. 1984. Changes of the Palaeoenvironment of Southern East Asia since the Late Tertiary. Hong Kong: Centre of Asian Studies, the University of Hong Kong.
Huang J. , Chen B. , Liu C. , Lai J.S. , Zhang J.L. , Ma K.P. 2012. Identifying hotspots of endemic woody seed plant diversity in China. Divers Distrib. 18: 673-688.
Huang J. , Huang J. , Lu X. , Ma K. 2016. Diversity distribution patterns of Chinese endemic seed plant species and their implications for conservation planning. Sci Rep. 6: 33913.
Huntley B. , Birks H.J.B. 1983. An Atlas of Past and Present Pollen Maps for Europe 0–13,000 Years Ago. UK: Cambridge University Press.
Knowles L.L. , Alvarado-Serrano D.F. 2010. Exploring the population genetic consequences of the colonization process with spatio-temporally explicit models: insights from coupled ecological, demographic and genetic models in montane grasshoppers. Mol Ecol. 19: 3727-3745.
Latham R.E. , Ricklefs R.E. 1993. Continental comparisons of temperate-zone tree species diversity. In: Ricklefs R.E. , Schluter D. , eds., Species Diversity in Ecological Communities: Historical and Geographical Perspectives. Chicago: Univ. Chicago Press, p. 294-314.
Linder H.P. 2001. Plant diversity and endemism in sub-Saharan tropical Africa. J Biogeogr. 28: 169-182.
Liu J.Q. , Sun Y.S. , Ge X.J. , Gao L.M. , Qiu Y.X. 2012. Phylogeographic studies of plants in China: Advances in the past and directions in the future. J Syst Evol. 50: 267-275.
López-Pujol J. , Zhang F-M. , Sun H.Q. , Ying T.S. , Ge S. 2011. Centres of plant endemism in China: places for survival or for speciation? J Biogeogr. 38: 1267-1280.
Manchester S.R. , Chen Z-D. , Lu A-M. , Uemura K. 2009. Eastern Asian endemic seed plant genera and their paleogeographic history throughout the Northern Hemisphere. J Syst Evol. 47: 1-42.
Medail F. , Diadema K. 2009. Glacial refugia influence plant diversity patterns in the Mediterranean Basin. J Biogeogr. 36: 1333-1345.
Mee J.A. , Moore J-S. 2014. The ecological and evolutionary implications of microrefugia. J Biogeogr. 41: 837-841.
Meng H.H. , Gao X.Y. , Huang J.F. , Zhang M.L. 2015. Plant phylogeography in arid Northwest China: Retrospectives and perspectives. J Syst Evol. 53: 33-46.
Mittermeier R.A. , Gil P.R. , Hoffman M. , Pilgrim J. , Brooks T. , Mittermeier C.G. , Lamoreux J. , Fonseca G.A.B. 2005. Hotspots Revisited. Chicago: The University of Chicago Press.
Morawetz W. , Raedig C. 2007. Angiosperm biodiversity, endemism and conservation in the Neotropics. Taxon. 56: 1245-1254.
Mosblech N.A.S. , Bush M.B. , van Woesik R. 2011. On metapopulations and microrefugia: Palaeoecological insights. J Biogeogr. 38: 419-429.
Ni J. , Cao X.Y. , Jeltsch F. , Herzschuh U. 2014. Biome distribution over the last 22,000 yr in China. Palaeogeogr Palaeoecol. 409: 33-47.
Olson D.M. , Dinerstein E. 1998. The global 200: A representation approach to conserving the Earth's most biologically valuable ecoregions. Conserv Biol. 12: 502-515.
Ornelas J.F. , Sosa V. , Soltis D.E. , Daza J.M. , González C. , Soltis P.S. , Gutiérrez-Rodríguez C. , de los Monteros A.E, Castoe T.A, Bell C, Ruiz-Sanchez E. 2013. Comparative phylogeographic analyses illustrate the complex evolutionary history of threatened cloud forests of Northern Mesoamerica. PLoS One. 8: e56283.
Palme A.E. , Su Q. , Rautenberg A. , Manni F. , Lascoux M. 2003. Postglacial recolonization and cpDNA variation of silver birch, Betula pendula. Mol Ecol. 12: 201-212.
Petit R.J. , Aguinagalde I. , de Beaulieu J.L. , Bittkau C. , Brewer S. , Cheddadi R. , Ennos R. , Fineschi S. , Grivet D. , Lascoux M. , Mohanty A. , Müller-Starck G. , Demesure-Musch B. , Palmé A. , Martín J.P. , Rendell S. , Vendramin G.G. 2003. Glacial refugia: Hotspots but not melting pots of genetic diversity. Science. 300: 1563-1565.
Petit R.J. , Csaikl U.M. , Bordács S. , Burg K. , Coart E. , Cottrell J. , Dam B.V. , Deans J.D. , Dumolin-Lapègue S. , Fineschi S. 2002. Chloroplast DNA variation in European white oaks. Forest Eco Manag. 156: 5-26.
Phillips S.J. , Anderson R.P. , Schapire R.E. 2006. Maximum entropy modeling of species geographic distributions. Ecol Model. 190: 231-259.
Phillips S.J. , Dudik M. 2008. Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography. 31: 161-175.
Prendergast J.R. , Quinn R.M. , Lawton J.H. , Eversham B.C. , Gibbons D.W. 1993. Rare species, the coincidence of diversity hotspots and conservation strategies. Nature. 365: 335-337.
Provan J. , Bennett K. 2008. Phylogeographic insights into cryptic glacial refugia. Trends Ecol Evol. 23: 564-571.
Qian H. 2002. A comparison of the taxonomic richness of temperate plants in East Asia and North America. Am J Bot. 89: 1818-1825.
Qian H. , Song J.S. , Krestov P. , et al.2003. Large-scale phytogeographical patterns in East Asia in relation to latitudinal and climatic gradients. J Biogeogr. 30: 129-141.
Qiu Y.X. , Fu C.X. , Comes H.P. 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. Mol Phylogenet Evol. 59: 225-244.
Raven P.H. , Axelrod D.I. 1974. Angiosperm biogeography and past continental movements. Ann MO Bot Gard. 61: 539-673.
Riddle B.R. , Hafner D.J. , Alexander L.F. , Jaeger J.R. 2000. Cryptic vicariance in the historical assembly of a Baja California Peninsular Desert biota. P Natl Acad Sci USA . 97: 14438-14443.
Rosenzweig M.L. 1995. Species Diversity in Space and Time. Cambridge University Press, Cambridge.
Rull V. 2010. On microrefugia and cryptic refugia. J Biogeogr. 37: 1623-1625.
Shi Y.F. , Ren B.H. , Wang J.T. , Derbyshire E. 1986. Quaternary glaciation in China. Quaternary Sci Rev. 5: 503-507.
Soltis D.E. , Morris A.B. , McLachlan J.S. , Manos P.S. , Soltis P.S. 2006. Comparative phylogeography of unglaciated eastern North America. Mol Ecol. 15: 4261-4293.
Stewart J.R. , Lister A.M. 2001. Cryptic northern refugia and the origins of the modern biota. Trends Ecol Evol. 16: 608-613.
Svendsen J.I. , Alexanderson H. , Astakhov V.I. , Demidov I. , Dowdeswell J.A. , Funder S. , Gataullin V. , Henriksen M. , Hjort C. , Houmark-Nielsen M. , Hubberten H.W. , Ingolfsson O. , Jakobsson M. , Kjaer K.H. , Larsen E. , Lokrantz H. , Lunkka J.P. , Lysa A. , Mangerud J. , Matiouchkov A. , Murray A. , Moller P. , Niessen F. , Nikolskaya O. , Polyak L. , Saarnisto M. , Siegert C. , Siegert M.J. , Spielhagen R.F. , Stein R. 2004. Late quaternary ice sheet history of northern Eurasia. Quaternary Sci Rev. 23: 1229-1271.
Swenson N.G. , Howard D.J. 2005. Clustering of contact zones, hybrid zones, and phylogeographic breaks in North America. Am Nat. 166: 581-591.
Taberlet P. , Cheddadi R. 2002. Quaternary refugia and persistence of biodiversity. Science. 297: 2009-2010.
Taberlet P. , Fumagalli L. , Wust-Saucy A.G. , Cosson J.F. 1998. Comparative phylogeography and postglacial colonization routes in Europe. Mol Ecol. 7: 453-464.
Tang C.Q. 2014. Habitats of Tertiary Relict Trees in China. In: Hobohm C. , ed. Endemism in Vascular Plants. Germany: Springer.
Tang Z. , Wang Z. , Zheng C. , Fang J. 2006. Biodiversity in China's mountains. Front Ecol Environ. 4: 347-352.
Temunovic M. , Frascaria-Lacoste N. , Franjic J. , Satovic Z. , Fernandez-Manjarres J.F. 2013. Identifying refugia from climate change using coupled ecological and genetic data in a transitional Mediterranean-temperate tree species. Mol Ecol. 22: 2128-2142.
Thiel-Egenter C. , Gugerli F. , Alvarez N. , Brodbeck S. , Cieslak E. , Colli L. , Englisch T. , Gaudeul M. , Gielly L. , Korbecka G. , Negrini R. , Paun O. , Pellecchia M. , Rioux D. , Ronikier M. , Schonswetter P. , Schupfer F. , Taberlet P. , Tribsch A. , van Loo M. , Winkler M. , Holderegger R. 2009. Effects of species traits on the genetic diversity of high-mountain plants: a multi-species study across the Alps and the Carpathians. Global Ecol Biogeogr. 18: 78-87.
Tian Z. , Jiang D. 2016. Revisiting last glacial maximum climate over China and East Asian monsoon using PMIP3 simulations. Palaeogeogr Palaeoecol. 453: 115-126.
Tribsch A. 2004. Areas of endemism of vascular plants in the Eastern Alps in relation to Pleistocene glaciation. J Biogeogr. 31: 747-760.
Tribsch A. , Schönswetter P. 2003. Patterns of endemism and comparative phylogeography confirm palaeo-environmental evidence for Pleistocene refugia in the Eastern Alps. Taxon. 52: 477-497.
Tzedakis P.C. , Lawson I.T. , Frogley M.R. , Hewitt G.M. , Preece R.C. 2002. Buffered tree population changes in a quaternary refugium: Evolutionary implications. Science. 297: 2044-2047.
Waltari E. , Hijmans R.J. , Peterson A.T. , Nyari A.S. , Perkins S.L. , Guralnick R.P. 2007. Locating pleistocene refugia: Comparing phylogeographic and ecological niche model predictions. PLoS One. 2: e563.
Wang P.X. , Sun X.J. 1994. Last glacial maximum in China - comparison between land and sea. Catena. 23: 341-353.
Wang S. , Xu X. , Shrestha N. , Zimmermann N.E. , Tang Z.Y. , Wang Z.H. 2017. Response of spatial vegetation distribution in China to climate changes since the Last Glacial Maximum (LGM). PLoS One. 12: e0175742.
Wang X. , Feng Z. , Fu L. , Wu P. , Xing G. 1993. Species diversity. In: L. Chen, X. Wang, S. Wang, eds., Biodiversity in China: Status and Conservation Strategy. Beijing: Science Press, pp. 164–205.
Wang X.P. , Wang Z.H. , Fang J.Y. 2004. Mountain ranges and peaks in China. Biodivers Sci. 12: 206–212.
Webb III T. 1988. Glacial and Holocene vegetation history: Eastern North America. In: B. Huntley, T. Webb, III, eds., Vegetation History. The Netherlands: Kluwer Academic, p. 385–414.
Weiss S. , Ferrand N. eds. 2006. Phylogeography of Southern European Refugia. The Netherlands: Springer.
Williams J.W. , Shuman B.N. , Webb T. , Bartlein P.J. , Leduc P.L. 2004. Late-quaternary vegetation dynamics in north america: Scaling from taxa to biomes. Ecol Monogr. 74: 309-334.
Wu Z.Y. , Sun H. , Zhou Z.K. , Peng H. , Li D.Z. 2007. Origin and differentiation of endemism in the flora of China. Frontiers of Biology in China. 2, 125-143.
Wu Z.Y. 1980. The Vegetation of China. Beijing: Science Press.
Yang J.M. , Yang X.Y. , Liang H. 2004. The discovery of buried Metasequoia wood in Lichuan, Hubei, China, and its significance. Acta Palaeo Sinica. 43: 124-130.
Ying J.S. 2001. Species diversity and distribution pattern of seed plants in China. Biodivers Sci. 9: 393–398.
Ying T.S. , Zhang Z.S. 1984. Endemism in the flora of China—studies on the endemic genera. Acta Phytotax Sinica. 22: 259-268.
Yu G. , Chen X. , Ni J. , Cheddadi R. , Guiot J. , Han H. , Harrison S.P. , Huang C. , Ke M. , Kong Z. , Li S. , Li W. , Liew P. , Liu G. , Liu J. , Liu Q. , Liu K.B. , Prentice I.C. , Qui W. , Ren G. , Song C. , Sugita S. , Sun X. , Tang L. , Van Campo E. , Xia Y. , Xu Q. , Yan S. , Yang X. , Zhao J. , Zheng Z. 2000. Palaeovegetation of China: a pollen data-based synthesis for the mid-Holocene and last glacial maximum. J Biogeogr. 27: 635-664.
Zhang M.G. , Slik J.W.F. , Ma K.P. 2016. Priority areas for the conservation of perennial plants in China. Biol Conserv. 210: 56-63.
Zhang Y.B. , Ma K.P. 2008. Geographic distribution patterns and status assessment of threatened plants in China. Biodivers Conserv. 17: 1783-1798.
Zhuo Z. , Baoyin Y. , Petit-Maire N. 1998. Paleoenvironments in China during the last glacial maximum and the Holocene optimum. Episodes. 21: 152-158.
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Historical processes during the Quaternary are likely to have left a signature on the geographical distribution of intraspecific genetic variation. In particular, high genetic uniqueness could be expected within glacial refugia for multiple species. We aimed to test this for plants in China and whether multi-species hotspots of genetic diversity are good indicators of glacial refugia in this region. From chloroplast DNA haplotype data for 116 species we calculated two local genetic diversity metrics for each species: haplotype genetic richness and genetic uniqueness. From these two, only uniqueness could reliably identify refugia, whereas richness may indicate either glacial refugia or areas recolonized by genetic lineages from different refugia in the postglacial period. Our results suggest the occurrence of numerous cryptic refugia and their likely importance in the maintenance and evolution of the Chinese flora, and indicate that an approach that locates geographic hotspots of genetic diversity data can reliably identify refugia.
| All Time | Past Year | Past 30 Days | |
|---|---|---|---|
| Abstract Views | 1158 | 162 | 5 |
| Full Text Views | 55 | 5 | 0 |
| PDF Views & Downloads | 45 | 8 | 0 |