Articles

Visualizing Patterns of Genetic Landscapes and Species Distribution of Taxus wallichiana (Taxaceae), Based on GIS and Ecological Niche Models

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  • 1 Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing 100101, China;
    2 University of Chinese Academy of Sciences, Beijing 100049, China

Received date: 2014-03-07

  Revised date: 2014-07-03

  Online published: 2014-09-10

Supported by

National Basic Research Program of China (No. 2010CB951704), and National Natural Science Foundation of China (No. 41271068).

Abstract

The Chinese yew (Taxus wallichiana), which is widely distributed in the Himalayas and in southern China, is now on the edge of extinction. In order to understand the evolutionary processes that control the current diversity within this species at the genetic and ecological levels, its genetic patterns and range dynamics must first be identified and mapped. This knowledge can then be applied in the development of an effective conservation strategy. Based on molecular data obtained from 48 populations of T. wallichiana, we used GIS-based interpolation approach for the explicit visualization of patterns of genetic divergence and diversity, and a number of potential evolutionary hotspots have been specifically identified within the genetic landscape maps. Within the maps of genetic divergence and diversity, five areas of high inter-population genetic divergence and six areas of high intra-population genetic diversity have been highlighted in a number of separate mountain regions, and these evolutionary hotspots should have the priority to be protected. Furthermore, four geographical barriers have been identified: the eastern Himalayas, the Yunnan Plateau, the Hengduan Mountains and the Taiwan Strait. According to ecological niche modeling (ENM), the populations of T. wallichiana within the Sino-Himalayan Forest floristic subkingdom experienced westward expansion from the periods of Last Inter-glacial to Last Glacial Maximum (LGM). Following the LGM, the distribution range overall became reduced and fragmented. These findings challenge the classic mode of contraction-expansion in response to the last glaciation. In conclusion, our findings suggest that the changes in geographical landscapes and climate that occurred during the Quaternary resulted in current genetic landscape patterns.

Cite this article

YU Haibin, ZHANG Yili, GAO Jungang, QI Wei . Visualizing Patterns of Genetic Landscapes and Species Distribution of Taxus wallichiana (Taxaceae), Based on GIS and Ecological Niche Models[J]. Journal of Resources and Ecology, 2014 , 5(3) : 193 -202 . DOI: 10.5814/j.issn.1674-764x.2014.03.001

References

Avise J C. 2000. Phylogeography: the history and formation of species. Cambridge, Massachusetts: Harvard University Press.

Bittkau C and H P Comes. 2008. Molecular inference of a Late Pleistocene diversification shift in Nigella s. lat. (Ranunculaceae) resulting from increased speciation in the Aegean archipelago. Journal of Biogeography, 36: 1346-1360.

Carstens B C and C L Richards. 2007. Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution, 61: 1439-1454.

Chan L M, J L Brown, A D Yoder. 2011. Integrating statistical genetic and geospatial methods brings new power to phylogeography. Molecular Phylogenetics and Evolution, 59: 523-537.

Chen SY, Wu G L, Zhang D J, et al. 2008. Potential refugium on the Qinghai-Tibet Plateau revealed by the chloroplast DNA phylogeography of the alpine species Metagentiana striata (Gentianaceae). Biological Journal of the Linnean Society, 157: 125-140.

Chou Y W, P I Thomas, Ge X J, et al. 2011. Refugia and phylogeography of Taiwania in East Asia. Journal of Biogeography, 38: 1992-2005.

Cun Y Z and Wang X Q. 2010. Plant recolonization in the Himalaya from the southeastern Qinghai-Tibetan Plateau: Geographical isolation contributed to high population differentiation. Molecular Phylogenetics and Evolution, 56: 972-982.

Excoffier L, G Laval, S Schneider. 2005. Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1: 47.

Gao J, Wang B S, Mao J F, et al. 2012. Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau. Molecular Ecology, 21:4811-4827.

Gao L M, M Möller, Zhang X M, et al. 2007. High variation and strong phylogeographic pattern among cpDNA haplotypes in Taxus wallichiana (Taxaceae) in China and North Vietnam. Molecular Ecology, 16: 4684-4698.

Gong W, Chen C, C Dobeš, et al. 2008. Phylogeography of a living fossil: Pleistocene glaciations forced Ginkgo biloba L. (Ginkgoaceae) into two refuge areas in China with limited subsequent postglacial expansion. Molecular Phylogenetics and Evolution, 48: 1094-1105.

Hewitt G. 2000. The genetic legacy of the Quaternary ice ages. Nature, 405: 907-913.

Hewitt G M. 2004. Genetic consequences of climatic oscillations in the Quaternary.Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 359: 183-195.

Hickerson M J, B C Carstens, J Cavender-Bares, et al. 2010. Phylogeography's past, present, and future: 10 years after Avise, 2000. Molecular Phylogenetics and Evolution, 54: 291-301.

Hijmans R J, S E Cameron, J L Parra, et al. 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25: 1965-1978.

Huang S, Chiang Y, B A Schaal, et al. 2001. Organelle DNA phylogeography of Cycas taitungensis, a relict species in Taiwan. Molecular Ecology, 10: 2669-2681.

Hwang S Y, Lin T P, Ma C S, et al. 2003. Postglacial population growth of Cunninghamia konishii (Cupressaceae) inferred from phylogeographical and mismatch analysis of chloroplast DNA variation. Molecular Ecology, 12: 2689-2695.

Jensen J L, A J Bohonak, S T Kelley. 2005. Isolation by distance, web service. BMC Genetics, 6: 13.

Keppel G, Van Niel KP, G W Wardell Johnson, et al. 2011. Refugia: Identifying and understanding safe havens for biodiversity under climate change. Global Ecology and Biogeography, 21: 393-404.

Kidd D M and M G Ritchie. 2006. Phylogeographic information systems: Putting the geography into phylogeography. Journal of Biogeography, 33: 1851-1865.

Kozak K H, C H Graham, J J Wiens. 2008. Integrating GIS-based environmental data into evolutionary biology. Trends in Ecology & Evolution, 23: 141-148.

Lehmkuhl F and F Haselein. 2000. Quaternary paleoenvironmental change on the Tibetan Plateau and adjacent areas (Western China and Western Mongolia). Quaternary International, 65: 121-145.

Li G D, Yue L L, Sun H, et al. 2012a. Phylogeography of Cyananthus delavayi (Campanulaceae) in Hengduan Mountains inferred from variation in nuclear and chloroplast DNA sequences. Journal of Systematics and Evolution, 50: 305-315.

Li L, R J Abbott, Liu B, et al. 2013. Pliocene intraspecific divergence and Plio-Pleistocene range expansions within Picea likiangensis (Lijiang spruce), a dominant forest tree of the Qinghai-Tibet Plateau. Molecular Ecology, 22: 5237-5255.

Li X H, Shao J W , Lu C, et al. 2012b. Chloroplast phylogeography of a temperate tree Pteroceltis tatarinowii (Ulmaceae) in China. Journal of Systematics and Evolution, 50: 325-333.

Li Y, Zhai S N, Qiu Y X, et al. 2011. Glacial survival east and west of the ‘Mekong-Salween Divide' in the Himalaya-Hengduan Mountains region as revealed by AFLPs and cpDNA sequence variation in Sinopodophyllum hexandrum (Berberidaceae). Molecular Phylogenetics and Evolution, 59: 412-424.

Manel S and G Segelbacher. 2009. Perspectives and challenges in landscape genetics. Molecular Ecology, 18: 1821-1822.

Manel S, M K Schwartz, G Luikart, et al. 2003. Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology & Evolution, 18: 189-197.

Manni F, E Guerard, E Heyer. 2004. Geographic patterns of (genetic, morphologic, linguistic) variation: How barriers can be detected by using Monmonier's algorithm. Human Biology, 76: 173-190.

Meng L, Yang R, R J Abbott, et al. 2007. Mitochondrial and chloroplast phylogeography of Picea crassifolia Kom. (Pinaceae) in the Qinghai-Tibetan Plateau and adjacent highlands. Molecular Ecology, 16: 4128-4137.

Nei M and Li W. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences, 76: 5269-5273.

Noss R F. 1990. Indicators for monitoring biodiversity: A hierarchical approach. Conservation Biology, 4: 355-364.

Opgenoorth L, G G Vendramin, 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.

Phillips S J, R P Anderson, R E Schapire. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190: 231-259.

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. Molecular Phylogenetics and Evolution, 59: 225-244.

Qiu Y X, Sun Y, Zhang X P, et al. 2009. Molecular phylogeography of East Asian Kirengeshoma (Hydrangeaceae) in relation to Quaternary climate change and landbridge configurations. New Phytologist, 183: 480-495.

Richards C L, B C Carstens, L L Knowles. 2007. Distribution modelling and statistical phylogeography: An integrative framework for generating and testing alternative biogeographical hypotheses. Journal of Biogeography, 34: 1833-1845.

Schönswetter P, I Stehlik, R Holderegger, et al. 2005. Molecular evidence for glacial refugia of mountain plants in the European Alps. Molecular Ecology, 14: 3547-3555.

Schorr G, N Holstein, P B Pearman, et al. 2012. Integrating species distribution models (SDMs) and phylogeography for two species of Alpine Primula. Molecular Ecology, 2:1260-1277.

Soltis D E, A B Morris, J S McLachlan, et al. 2006. Comparative phylogeography of unglaciated eastern North America. Molecular Ecology, 15: 4261-4293.

Taberlet P, L Fumagalli, A G Wust, et al. 1998. Comparative phylogeography and postglacial colonization routes in Europe. Molecular Ecology, 7: 453-464.

Tamura K and Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10: 512-526.

Thomassen H A, Z A Cheviron, A H Freedman, et al. 2010. Spatial modelling and landscape-level approaches for visualizing intra-specific variation. Molecular Ecology, 19: 3532-3548.

Vandergast A G, A J Bohonak, S A Hathaway, et al. 2008. Are hotspots of evolutionary potential adequately protected in southern California? Biological Conservation, 141: 1648-1664.

Vandergast A G, W M Perry, R V Lugo, et al. 2011. Genetic landscapes GIS Toolbox: tools to map patterns of genetic divergence and diversity. Molecular Ecology Resources, 11: 158-161.

Wang F Y, Gong X, Hu C M, et al. 2008. Phylogeography of an alpine species Primula secundiflora inferred from the chloroplast DNA sequence variation. Journal of Systematics and Evolution, 46: 13-22.

Wood D A, A G Vandergast, K R Barr, et al. 2012. Comparative phylogeography reveals deep lineages and regional evolutionary hotspots in the Mojave and Sonoran Deserts. Diversity and Distribution, 19: 722-737.

Wu Z Y and Wu S G. 1998. A proposal for a new floristic kingdom (realm): The E. Asiatic Kingdom, its delineation and characteristics. In: Zhang A L, Wu S G (Eds.). Proceedings of the First International Symposium of Floristic Characteristics and Diversity of East Asian Plants. Berlin/ Beijing: Springer Verlag/China Higher Education Press, 3-42.

Yu G, Chen X, Ni J, et al. 2000. Palaeovegetation of China: A pollen data-based synthesis for the mid-Holocene and last glacial maximum. Journal of Biogeography, 27: 635-664.

Yu H B and Zhang Y L. 2013. Advances in Phylogeography of alpine plants in the Tibetan Plateau and adjacent regions. Acta Botany Boreal –Occident Sinica, 33: 1268-1278. (in Chinese)

Yuan Q J, Zhang Z Y, Peng H, et al. 2008. Chloroplast phylogeography of Dipentodon (Dipentodontaceae) in southwest China and northern Vietnam. Molecular Ecology, 17: 1054-1065.

Zhang J P, Zhang Y L, Liu L S, et al. 2011a. Predicting potential distribution of Tibetan spruce (Picea smithiana) in Qomolangma (Mount Everest) National Nature Preserve using maximum entropy niche-based model. Chinese Geographical Sciences, 21: 417-426.

Zhang Q, Chiang T Y, George M, et al. 2005. Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation. Molecular Ecology, 14: 3513-3524.

Zhang T C, Comes H P, Sun H. 2011b. Chloroplast phylogeography of Terminalia franchetii (Combretaceae) from the eastern Sino-Himalayan region and its correlation with historical river capture events. Molecular Phylogenetics and Evolution, 60: 1-12.
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