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      Phylogeography and allopatric divergence of cypress species ( Cupressus L.) in the Qinghai-Tibetan Plateau and adjacent regions

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          Abstract

          Background

          Although allopatric speciation is viewed as the most common way in which species originate, allopatric divergence among a group of closely related species has rarely been examined at the population level through phylogeographic analysis. Here we report such a case study on eight putative cypress ( Cupressus) species, which each have a mainly allopatric distribution in the Qinghai-Tibetan Plateau (QTP) and adjacent regions. The analysis involved sequencing three plastid DNA fragments ( trnD- trnT, trnS- trnG and trnL- trnF) in 371 individuals sampled from populations at 66 localities.

          Results

          Both phylogenetic and network analyses showed that most DNA haplotypes recovered or haplotype-clustered lineages resolved were largely species-specific. Across all species, significant phylogeographic structure ( N ST > G ST, P < 0.05) implied a high correlation between haplotypes/lineages and geographic distribution. Two species, C. duclouxiana and C. chengiana, which are distributed in the eastern QTP region, contained more haplotypes and higher diversity than five species with restricted distributions in the western highlands of the QTP. The remaining species, C. funebris, is widely cultivated and contained very little cpDNA diversity.

          Conclusions

          It is concluded that the formation of high mountain barriers separating deep valleys in the QTP and adjacent regions caused by various uplifts of the plateau since the early Miocene most likely promoted allopatric divergence in Cupressus by restricting gene flow and fixing local, species-specific haplotypes in geographically isolated populations. The low levels of intraspecific diversity present in most species might stem from population bottlenecks brought about by recurrent periods of unfavorable climate and more recently by the negative impacts of human activities on species' distributions. Our findings shed new light on the importance of geographical isolation caused by the uplift of the QTP on the development of high plant species diversity in the QTP biodiversity hotspot.

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          Most cited references27

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          Arlequin (version 3.0): An integrated software package for population genetics data analysis

          Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
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            Universal primers for amplification of three non-coding regions of chloroplast DNA.

            Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.
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              Evolution of Asian monsoons and phased uplift of the Himalaya-Tibetan plateau since Late Miocene times.

              The climates of Asia are affected significantly by the extent and height of the Himalayan mountains and the Tibetan plateau. Uplift of this region began about 50 Myr ago, and further significant increases in altitude of the Tibetan plateau are thought to have occurred about 10-8 Myr ago, or more recently. However, the climatic consequences of this uplift remain unclear. Here we use records of aeolian sediments from China and marine sediments from the Indian and North Pacific oceans to identify three stages of evolution of Asian climates: first, enhanced aridity in the Asian interior and onset of the Indian and east Asian monsoons, about 9-8 Myr ago; next, continued intensification of the east Asian summer and winter monsoons, together with increased dust transport to the North Pacific Ocean, about 3.6-2.6 Myr ago; and last, increased variability and possible weakening of the Indian and east Asian summer monsoons and continued strengthening of the east Asian winter monsoon since about 2.6 Myr ago. The results of a numerical climate-model experiment, using idealized stepwise increases of mountain-plateau elevation, support the argument that the stages in evolution of Asian monsoons are linked to phases of Himalaya-Tibetan plateau uplift and to Northern Hemisphere glaciation.
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                Author and article information

                Journal
                BMC Evol Biol
                BMC Evolutionary Biology
                BioMed Central
                1471-2148
                2010
                22 June 2010
                : 10
                : 194
                Affiliations
                [1 ]Division of Molecular Ecology, Key Laboratory of Arid and Grassland Ecology, School of Life Science, Lanzhou University, Lanzhou, 730000, China
                [2 ]School of Biology, Mitchell Building, University of St Andrews, St Andrews, Fife KY16 9TH, UK
                [3 ]Institute of Molecular Plant Sciences, The University of Edinburgh, Daniel Rutherford Building, King's Buildings, Mayfield Road, Edinburgh EH9 3JH, UK
                [4 ]Department of Life Science, Tibet University, Lasha, Tibet, China
                [5 ]Faculty of Geography, University of Marburg, Deutschhaustr.10 35032 Marburg, Germany
                Article
                1471-2148-10-194
                10.1186/1471-2148-10-194
                3020627
                20569425
                954a32a0-2b6c-4e8a-b102-243249116b93
                Copyright ©2010 Xu et al; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Categories
                Research Article

                Evolutionary Biology
                Evolutionary Biology

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