Using a mega-phylogeny of seed plants to test for non-random patterns of areal-types across the Chinese tree of life

doi:10.1016/j.pld.2016.08.003

Abstract

Abstract: The species composition of plant assemblages can in large part be explained by a long history of biogeographic and evolutionary events. Over the past decade, botanists and plant ecologists have increasingly sought to quantify phylogenetic signal in ecological traits to help inform their inferences regarding the mechanisms driving plant assemblages. However, most studies with a test of phylogenetic signal in the ecological traits have focused on a local scale, while comparatively few studies have been carried out on a regional scale. In this study, I presented a family-level phylogeny and a genus-level phylogeny that included all families and genera of extant seed plants in China, and use both phylogenies to examine whether areal-types or distribution patterns of families and genera of seed plants are non-randomly distributed across the Chinese tree of life. My study shows that the areal-types of families and genera of seed plants exhibit significant phylogenetic signal across the family- or genus-level phylogeny of seed plants in China.

Key words: Areal-types, Biogeography, Evolution, Flora, Phylogenetic signal

Rong Li. Using a mega-phylogeny of seed plants to test for non-random patterns of areal-types across the Chinese tree of life[J]. Plant Diversity, 2016, 38(06): 283-288.

References

Alexander, I.J., 1989. Mycorrhizas in tropical forests. In: Proctor, J. (Ed.), Mineral Nutrients in Tropical Forest and Savanna Ecosystems. Blackwell, Oxford, pp. 169-188.
APG IV, 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1-20.
Ashton, P.S., 1982. Dipterocarpaceae. ser. 1, vol. 9(2). In: van Steenis, C.G.G.J. (Ed.), Flora MalesianaMartinus Nijhoff, The Hague, pp. 237-552.
Baldeck, C.A., Kembel, S.W., Harms, K.E., et al., 2013. A taxonomic comparison of local habitat niches of tropical trees. Oecologia 173, 1491-1498.
Beaulieu, J.M., Tank, D.C., Donoghue, M.J., 2013. A Southern Hemisphere origin for campanulid angiosperms, with traces of the break-up of Gondwana. BMC Evol.Biol. 13, 80.
Bell, C.D., Donoghue, M.J., 2005. Dating the Dipsacales: comparing models, genes, and evolutionary implications. Am. J. Bot. 92, 284-296.
Burns, J.H., Strauss, S.Y., 2011. More closely related species are more ecologically similar in an experimental test. Proc. Natl. Acad. Sci. U.S.A. 108, 5302-5307.
Cavender-Bares, J., Ackerly, D.D., Baum, D., et al., 2004. Phylogenetic overdispersion in Floridian oak communities. Am. Nat. 163, 823-843.
Cavender-Bares, J., Kozak, K.H., Fine, P.V., et al., 2009. The merging of community ecology and phylogenetic biology. Ecol. Lett. 12, 693-715.
Cooper, N., Jetz, W., Freckleton, R.P., 2010. Phylogenetic comparative approaches for studying niche conservatism. J. Evol. Biol. 23, 2529-2539.
Crisp, M.C., Cook, L., Steane, D., 2004. Radiation of the Australian flora: what can comparisons of molecular phylogenies across multiple taxa tell us about the evolution of diversity in presenteday communities? Philos. Trans. R. Soc. Lond.B. Biol. Sci. 359, 1551-1571.
Darwin, C., 1859. On the Origin of Species. John Murray, London.
Donoghue, M.J., Eriksson, T., Reeves, P.A., et al., 2001. Phylogeny and phylogenetic taxonomy of Dipsacales, with special reference to Sinadoxa and Tetradoxa(Adoxaceae). Harv. Pap. Bot. 6, 459-479.
Du, Y., Mao, L., Queenborough, S.A., et al., 2015. Phylogenetic constraints and trait correlates of flowering phenology in the angiosperm flora of China. Glob. Ecol.Biogeogr. 24, 928-938.
Dutta, S., Tripathi, S.M., Mallick, M., et al., 2011. Eocene out-of-India dispersal of Asian dipterocarps. Rev. Palaeobot. Palynol. 166, 63-68.
Graham, C.H., Fine, P.V.A., 2008. Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time. Ecol. Lett. 11, 1265-1277.
Hardy, O.J., Couteron, P., Munoz, F., et al., 2012. Phylogenetic turnover in tropical tree communities: impact of environmental filtering, biogeography and mesoclimatic niche conservatism. Glob. Ecol. Biogeogr. 21, 1007-1016.
Huang, H.W., Oldfield, S., Qian, H., 2013. Global significance of plant diversity in China. In: Hong, D.Y., Blackmore, S. (Eds.), Plants of China, a Companion to the Flora of China. Science Press, Beijing, pp. 7-34.
Kamilar, J.M., Cooper, N., 2013. Phylogenetic signal in primate behaviour, ecology and life history. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 368, 20120341.
Kembel, S.W., Cowan, P.D., Helmus, M.R., et al., 2010. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26, 1463-1464.
Li, R., Dao, Z.L., Ji, Y.H., et al., 2007. A floristic study on the seed plants of the northern Gaoligong mountains in western Yunnan, China. Acta Bot Yunnanica 29, 601-615.
Li, R., Kraft, N.J.B., Yang, J., et al., 2015a. A phylogenetically informed delineation of floristic regions within a biodiversity hotspot in Yunnan. China. Sci. Rep. 5, 9396.
Li, R., Kraft, N.J.B., Yu, H.Y., et al., 2015b. Seed plant phylogenetic diversity and species richness in conservation planning within a global biodiversity hotspot in eastern Asia. Conserv. Biol. 29, 1552-1562.
Li, X.W., Li, J., 1997. The Tanaka-Kaiyong line e an important floristic line for the study of the flora of East Asia. Ann. Mo. Bot. Gard. 84, 888-892.
Losos, J.B., 2008. Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecol. Lett. 11, 995-1003.
Maddison, W.P., Slatkin, M., 1991. Null models for the number of evolutionary steps in a character on a phylogenetic tree. Evolution 45, 1184-1197.
Mayfield, M.M., Levine, J.M., 2010. Opposing effects of competitive exclusion on the phylogenetic structure of communities. Ecol. Lett. 13, 1085-1093.
Moore, B.R., Donoghue, M.J., 2007. Correlates of diversification in the plant clade Dipsacales: geographic movement and evolutionary innovations. Am. Nat. 170, S28-S55.
Münkemüller, T., Lavergne, S., Bzeznik, B., et al., 2012. How to measure and test phylogenetic signal. Methods Ecol. Evol. 3, 743-756.
Pei, N., Lian, J.Y., Erickson, D.L., et al., 2011. Exploring tree-habitat associations in a Chinese subtropical forest plot using a molecular phylogeny generated from DNA barcode loci. PLoS One 6, e21273.
Qian, H., Jin, Y., 2015. An updated megaphylogeny of plants, a tool for generating plant phylogenies, and an analysis of phylogenetic community structure. J. Plant Ecol. http://dx.doi.org/10.1093/jpe/rtv047.
Qian, H., Ricklefs, R.E., 1999. A comparison of the taxonomic richness of vascular plants in China and the United States. Am. Nat. 154, 160-181.
Qian, H., Ricklefs, R.E., 2000. Large-scale processes and the Asian bias in species diversity of temperate plants. Nature 407, 180-182.
Qian, H., Zhang, J., 2014. Using an updated time-calibrated family-level phylogeny of seed plants to test for non-random patterns of life forms across the phylogeny.J. Syst. Evol. 52, 423-430.
Qian, H., Zhang, J., 2016. Are phylogenies derived from family-level supertrees robust for studies on macroecological patterns along environmental gradients? J. Syst. Evol. 54, 29-36.
R Development Core Team, 2013. R: a Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
Revell, L.J., 2012. Phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217-223.
Schliep, K.P., 2011. Phangorn: phylogenetic analysis in R. Bioinformatics 27, 592-593.
Schreeg, L.A., Kress, W.J., Erickson, D.L., et al., 2010. Phylogenetic analysis of local-scale tree soil associations in a lowland moist tropical forest. PLoS One 5, e13685.
Shukla, A., Guleria, J.S., Mehrotra, R.C., 2012. A fruit wing of Shorea Rocb. from the Early Miocene sediments of Kachchh, Gujarat and its bearing of palaeoclimatic interpretation. J. Earth Syst. Sci. 121, 195-201.
Silvertown, J., McConway, K., Gowing, D., et al., 2006. Absence of phylogenetic signal in the niche structure of meadow plant communities. Proc. R. Soc. Lond. B 273, 39-44.
Swenson, N.G., 2011. The role of evolutionary processes in producing biodiversity patterns, and the interrelationships between taxonomic, functional and phylogenetic biodiversity. Am. J. Bot. 98, 472-480.
Swenson, N.G., 2013. The assembly of tropical tree communities e the advances and shortcomings of phylogenetic and functional trait analyses. Ecography 36, 264-276.
Tsumura, Y., Kado, T., Yoshida, K., et al., 2011. Molecular database for classifying Shorea species (Dipterocarpaceae) and techniques for checking the legitimacy of timber and wood products. J. Plant Res. 124, 35-48.
Violle, C., Nemergut, D.R., Pu, Z., et al., 2011. Phylogenetic limiting similarity and competitive exclusion. Ecol. Lett. 14, 782-787.
Webb, C.O., 2000. Exploring the phylogenetic structure of ecological communities:an example for rain forest trees. Am. Nat. 156, 145-155.
Webb, C.O., Ackerly, D.D., McPeek, M.A., et al., 2002. Phylogenies and community ecology. Annu. Rev. Ecol. Evol. Syst. 33, 475-505.
Wu, Z.Y., 1965. On the tropical affinities of Chinese flora. Chin. Sci. Bull. 1, 25-33.
Wu, Z.Y., 1979. The regionalization of Chinese flora. Acta Bot. Yunnanica 1, 1-22.
Wu, Z.Y., 1983. On the significance of Pacific intercontinental discontinuity. Ann.Mo. Bot. Gard. 70, 577-590.
Wu, Z.Y., 1991. Areal-types of Chinese genera of seed plants. Acta Bot. Yunnanica 1-139. Suppl. IV.
Wu, Z.Y., Raven, P.H., Hong, D.Y., 1994-2013. Flora of China. Science Press, Beijing and Missouri Botanical Garden Press, St. Louis.
Wu, Z.Y., Sun, H., Zhou, Z.K., et al., 2005. Origin and differentiation of endemism in the flora of China. Acta Bot. Yunnanica 27, 577-604.
Wu, Z.Y., Sun, H., Zhou, Z.K., et al., 2010. Floristics of Seed Plants from China. Science Press, Beijing.
Wu, Z.Y., Zhou, Z.K., Li, D.Z., et al., 2003. The areal-types of the world families of seed plants. Acta Bot. Yunnanica 25, 245-257.
Wu, Z.Y., Zhou, Z.K., Sun, H., et al., 2006. The Areal-types of Seed Plants and Their Origin and Differentiation. Yunnan Science and Technology Press, Kunming.
Yang, J., Ci, X.Q., Lu, M.M., et al., 2014a. Functional traits of tree species with phylogenetic signal co-vary with environmental niches in two large forest dynamics plots. J. Plant Ecol. 7, 115-125.
Yang, J., Zhang, G.C., Ci, X.Q., et al., 2014b. Functional and phylogenetic assembly in a Chinese tropical tree community across size classes, spatial scales and habitats.Funct. Ecol. 28, 520-529.
Yulita, K.S., Bayer, R.J., West, J.G., 2005. Molecular phylogenetic study of Hopea and Shorea (Dipterocarpaceae): evidence from the trnL-trnF and internal transcribed spacer regions. Plant Spec. Biol. 20, 167-182.
Zanne, A.E., Tank, D.C., Cornwell, W.K., et al., 2014. Three keys to the radiation of angiosperms into freezing environments. Nature 506, 89-92.
Zar, J.H., 1984. Biostatistical Analysis, second ed. Prentice Hall, Englewood Cliffs.
Zhang, W.H., Chen, Z.D., Li, J.H., et al., 2003. Phylogeny of the Dipsacales s.l. based on chloroplast trnL-F and ndhF sequences. Mol. Phyl. Evol. 26, 176-189.

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