Dataset Information

Phylogeography of the South China field mouse (Apodemus draco) on the southeastern Tibetan Plateau reveals high genetic diversity and glacial refugia.

ABSTRACT: The southeastern margin of the Tibetan Plateau (SEMTP) is a particularly interesting region due to its topographic complexity and unique geologic history, but phylogeographic studies that focus on this region are rare. In this study, we investigated the phylogeography of the South China field mouse, Apodemus draco, in order to assess the role of geologic and climatic events on the Tibetan Plateau in shaping its genetic structure. We sequenced mitochondrial cytochrome b (cyt b) sequences in 103 individuals from 47 sampling sites. In addition, 23 cyt b sequences were collected from GenBank for analyses. Phylogenetic, demographic and landscape genetic methods were conducted. Seventy-six cyt b haplotypes were found and the genetic diversity was extremely high (? = 0.0368; h = 0.989). Five major evolutionary clades, based on geographic locations, were identified. Demographic analyses implied subclade 1A and subclade 1B experienced population expansions at about 0.052-0.013 Mya and 0.014-0.004 Mya, respectively. The divergence time analysis showed that the split between clade 1 and clade 2 occurred 0.26 Mya, which fell into the extensive glacial period (EGP, 0.5-0.17 Mya). The divergence times of other main clades (2.20-0.55 Mya) were congruent with the periods of the Qingzang Movement (3.6-1.7 Mya) and the Kun-Huang Movement (1.2-0.6 Mya), which were known as the most intense uplift events in the Tibetan Plateau. Our study supported the hypothesis that the SEMTP was a large late Pleistocene refugium, and further inferred that the Gongga Mountain Region and Hongya County were glacial refugia for A. draco in clade 1. We hypothesize that the evolutionary history of A. draco in the SEMTP primarily occurred in two stages. First, an initial divergence would have been shaped by uplift events of the Tibetan Plateau. Then, major glaciations in the Pleistocene added complexity to its demographic history and genetic structure.

SUBMITTER: Fan Z

PROVIDER: S-EPMC3364228 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Phylogeography of the South China field mouse (Apodemus draco) on the southeastern Tibetan Plateau reveals high genetic diversity and glacial refugia.

Fan Zhenxin Z Liu Shaoying S Liu Yang Y Liao Lihuan L Zhang Xiuyue X Yue Bisong B

PloS one 20120530 5

The southeastern margin of the Tibetan Plateau (SEMTP) is a particularly interesting region due to its topographic complexity and unique geologic history, but phylogeographic studies that focus on this region are rare. In this study, we investigated the phylogeography of the South China field mouse, Apodemus draco, in order to assess the role of geologic and climatic events on the Tibetan Plateau in shaping its genetic structure. We sequenced mitochondrial cytochrome b (cyt b) sequences in 103 i ...[more]

PMID: 22666478

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Project description:Although only relatively few freshwater invertebrate families are reported from the Tibetan Plateau, the degree of endemism may be high. Many endemic lineages occur within permafrost areas, raising questions about the existence of isolated intra-plateau glacial refugia. Moreover, if such refugia existed, it might be instructive to learn whether they were associated with lakes or with more dynamic ecosystems such as ponds, wetlands, or springs. To study these hypotheses, we used pulmonate snails of the plateau-wide distributed genus Radix as model group and the Lake Donggi Cona drainage system, located in the north-eastern part of the plateau, as model site. First, we performed plateau-wide phylogenetic analyses using mtDNA data to assess the overall relationships of Radix populations inhabiting the Lake Donggi Cona system for revealing refugial lineages. We then conducted regional phylogeographical analyses applying a combination of mtDNA and nuclear AFLP markers to infer the local structure and demographic history of the most abundant endemic Radix clade for identifying location and type of (sub-)refugia within the drainage system. Our phylogenetic analysis showed a high diversity of Radix lineages in the Lake Donggi Cona system. Subsequent phylogeographical analyses of the most abundant endemic clade indicated a habitat-related clustering of genotypes and several Late Pleistocene spatial/demographic expansion events. The most parsimonious explanation for these patterns would be a scenario of an intra-plateau glacial refugium in the Lake Donggi Cona drainage system, which might have consisted of isolated sub-refugia. Though the underlying processes remain unknown, an initial separation of lake and watershed populations could have been triggered by lake-level fluctuations before and during the Last Glacial Maximum. This study inferred the first intra-plateau refugium for freshwater animals on the Tibetan Plateau. It thus sheds new light on the evolutionary history of its endemic taxa and provides important insights into the complex refugial history of a high-altitude ecosystem.

Project description:Phylogeographic studies give us the opportunity to reconstruct the historical migrations of species and link them with climatic and geographic variation. They are, therefore, a key tool to understanding the relationships among biology, geology and history. One of the most interesting biogeographical areas of the world is the Mediterranean region. However, in this area, the description of concordant phylogeographic patterns is quite scarce, which limits the understanding of evolutionary patterns related to climate. Species with one-dimensional distribution ranges, such as the strawberry tree (Arbutus unedo), are particularly useful to unravel these patterns. Here, we describe its phylogeographic structure and check for concordance with patterns seen in other Mediterranean plants: longitudinal/latitudinal clines of diversity, evidence for glacial refugia and the role of sea straits in dispersal. We also identify the most likely source for the disjunct Irish population. With this aim, we sequenced four chloroplast non-coding fragments of A. unedo from 23 populations covering its whole distribution. We determined the genetic diversity, population structure, haplotype genealogy and time to the most recent common ancestor. The genealogy revealed two clades that separated during the last 700 ky but before the last glacial maximum. One clade occupies Atlantic Iberia and North Africa, while the other occurs in the Western Mediterranean. The Eastern Mediterranean is inhabited by newer haplotypes derived from both clades, while the Irish population is closely related to Iberian demes. The straits of Sicily and Gibraltar partially restricted the gene flow. We concluded that a vicariance event during the Late Quaternary in the western end of the species' range followed by eastward migration seems a likely explanation for the observed phylogeographic pattern. The role of straits indicates an occasional communication between Europe and North Africa, suggesting that the latter was a novel refugia. The East-West genetic split in Iberia is consistent with the refugia-within-refugia model. Finally, the strawberry tree possibly reached Ireland from Iberia instead of throughout the maritime fringe of France as previously thought.

Dataset Information

Phylogeography of the South China field mouse (Apodemus draco) on the southeastern Tibetan Plateau reveals high genetic diversity and glacial refugia.

Publications

Phylogeography of the South China field mouse (Apodemus draco) on the southeastern Tibetan Plateau reveals high genetic diversity and glacial refugia.

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