Yanhua Qu

Comparative phylogeography of five avian species: implications for Pleistocene evolutionary history in the Qinghai-Tibetan plateau.

Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. In contrast to Europe and North America where the effects of recent glacial cycles on genetic diversity have been well studied, the genetic legacy of the Pleistocene for the Qinghai‐Tibetan (Tibetan) plateau, a region where glaciation was not synchronous with the North Hemisphere ice sheet maxima, remains poorly understood. Here, we compared the phylogeographical patterns of five avian species on the Qinghai‐Tibetan plateau by three mitochondrial DNA fragments: the Tibetan snow finch (Montifringilla adamsi), the Blanford’s snow finch (Pyrgilauda blanfordi), the horned lark (Eremophila alpestris), the twite (Carduelis flavirostris) and the black redstart (Phoenicurus ochruros). Our results revealed the three species mostly distributed on the platform region of the plateau that experienced population expansion following the retreat of the extensive glaciation period (0.5–0.175 Ma). These results are at odds with the results from avian species of Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023–0.018 Ma). A single refugium was identified in a restricted semi‐continuous area around the eastern margin of the plateau, instead of multiple independent refugia for European and North American species. For the other two species distributed on the edges of the plateau (the twite and black redstart), populations were maintained at stable levels. Edge areas are located on the eastern margin, which might have had little or no ice cover during the glaciation period. Thus, milder climate may have mitigated demographic stresses for edge species relative to the extremes experienced by platform counterparts, the present‐day ranges of which were heavily ice covered during the glaciation period. Finally, various behavioural and ecological characteristics, including dispersal capacities, habitat preference and altitude specificity along with evolutionary history might have helped to shape different phylogeographical structures appearing in these five species.

Phylogeography of the Alcippe morrisonia (Aves: Timaliidae): long population history beyond late Pleistocene glaciations

BackgroundThe role of Pleistocene glacial oscillations in current biodiversity and distribution patterns varies with latitude, physical topology and population life history and has long been a topic of discussion. However, there had been little phylogeographical research in south China, where the geophysical complexity is associated with great biodiversity. A bird endemic in Southeast Asia, the Grey-cheeked Fulvetta, Alcippe morrisonia, has been reported to show deep genetic divergences among its seven subspecies. In the present study, we investigated the phylogeography of A. morrisonia to explore its population structure and evolutionary history, in order to gain insight into the effect of geological events on the speciation and diversity of birds endemic in south China.ResultsMitochondrial genes cytochrome b (Cytb) and cytochrome c oxidase I (COI) were represented by 1236 nucleotide sites from 151 individuals from 29 localities. Phylogenetic analysis showed seven monophyletic clades congruent with the geographically separated groups, which were identified as major sources of molecular variance (90.92%) by AMOVA. TCS analysis revealed four disconnected networks, and that no haplotype was shared among the geographical groups. The common ancestor of these populations was dated to 11.6 Mya and several divergence events were estimated along the population evolutionary history. Isolation by distance was inferred by NCPA to be responsible for the current intra-population genetic pattern and gene flow among geographical groups was interrupted. A late Pleistocene demographic expansion was detected in the eastern geographical groups, while the expansion time (0.2–0.4 Mya) was earlier than the Last Glacial Maximum.ConclusionIt is proposed that the complicated topology preserves high genetic diversity and ancient lineages for geographical groups of A. morrisonia in China mainland and its two major islands, and restricts gene exchange during climate oscillations. Isolation by distance seems to be an important factor of genetic structure formation within geographical populations. Although glacial influence to population fluctuation was observed in late Pleistocene, it seems that populations in eastern China were more susceptible to climate change, and all geographical groups were growing stably through the Last Glacial Maximum. Coalescence analysis suggested that the ancestor of A. morrisonia might be traced back to the late Miocene, and the current phylogeographical structure of A. morrisonia is more likely to be attributable to a series geological events than to Pleistocene glacial cycles.

Conservation on diversity and distribution patterns of endemic birds in China

The diversity and distribution patterns of endemic species of birds inChina have been studied on the basis of the distribution database of specimencollections and published references. One hundred and two endemic species ofbirds in China, belonging to 53 genera, 16 families and 8 orders are recognized.They account for 8.1% of the total species of China. The distribution patternswere studied and three centers of endemism were found, includingHengduanshan Mountains, mountain areas of western Qinling, north Sichuan Province andSouth Gansu Province, as well as Taiwan Island, which are suggested as conservationpriorities based on endemism. Twenty-four endemics are rare and endangered, listedin the China Red Data Book of Endangered Animals. Among them, 15 species are in rankI and 9 species are in rank II. The study results are to be beneficial tofurther study on both the processing mechanism of the distribution patterns andon the priority of the diversity and endemism conservation.

Incomplete lineage sorting or secondary admixture: Disentangling historical divergence from recent gene flow in the Vinous-throated parrotbill (Paradoxornis webbianus)

Although Pleistocene glaciations had a major impact on the population genetic patterns of many species in North America and Europe, it remains unclear how these climatic fluctuations contributed to species diversification in East Asia. One reason for this is the difficulty of distinguishing genetic admixture following secondary contact from incomplete lineage sorting, both of which can generate similar patterns of genetic variation. Using a combination of multilocus analyses and coalescent simulation, we explore how these two processes occurred in the Pleistocene evolutionary history of a widespread East Asian bird, the Vinous‐throated parrotbill, Paradoxornis webbianus. Maximum likelihood (ML) tree identified two major mitochondrial lineages, which are geographically separated in most parts of its range, but are sympatric at a few sampling sites. NJ tree and Structure analysis of microsatellite data set revealed an extensive level of admixture and little population structure, suggesting recent admixture between two formerly separated groups. Networks from nuclear DNA data sets, however, did not indicate any geographically isolated groups but rather a panmictic population, thus support incomplete lineage sorting. By using coalescent simulation approaches, we show that both processes did occur, although at different temporal scales. During the Pleistocene glaciations, probably around 0.1–0.5 Ma (the Marine Isotope Stage 6, MIS6), P. webbianus contracted into two separate refugia, and subsequently accumulated genetic divergence. During the interglacial MIS5, the species expanded into previously glaciated areas allowing the once separated groups to come into contact and become admixed. Taken together, our results indicate the current genetic variation within P. webbianus is a combination pattern of widespread distribution in pre‐Pleistocene, then contraction and fragmentation into separated refugia during glacial advance, followed by recently postglacial expansion and admixture.

Long‐term isolation and stability explain high genetic diversity in the Eastern Himalaya

Chinas Southwest Mountainous Region in Eastern Himalaya is a ‘biodiversity hotspot’ of global interest for conservation. Yet little is known about what has driven this unique diversity. The dramatic topography of the Southwest Mountainous Region resulting from the tectonic uplift during the late Pliocene leads to dramatic ecological stratification, which creates physical barriers to migration and isolates organisms into different subregions and mountain systems. This agrees with the observation that the phylogeographical patterns found in four species of birds (Alcippe morrisonia, Stachyridopsis ruficeps, Parus monticolus and Aegithalos concinnus) distributed in this region are characterized by deep splits between lineages that coalesce between 0.8 and 2.1 Ma. Unlike other regions at this latitude, the Southwest Mountainous Region was largely unaffected by the Pleistocene glaciations. Genetically isolated populations of these birds could thus be maintained throughout the Pleistocene in these rather stable montane environments. In comparison, we found radically different phylogeographical patterns in populations of the same four species distributed in the adjacent lowland, the Central China region. This region has a distinctly different geological history with dramatic, climate‐induced shifts in vegetation during the Pleistocene. Here, we found a considerably less geographical structure in the genetic variation and a much younger coalescence time (0.3–0.7 Ma). We also found evidence of genetic bottlenecks during the glacial periods and gene flow during the interglacial expansions. We conclude that the high genetic diversity in the Southwest Mountainous Region results from a long‐term in situ diversification within these evolutionary isolated and environment stable montane habitats.

Comparative phylogeography of two endemic birds of the Tibetan plateau, the white-rumped snow finch (Onychostruthus taczanowskii) and the Hume's ground tit (Pseudopodoces humilis)

Postglacial colonization has created the main phylogeographical structures in the endemic species of the Tibetan plateau; however, patterns of diversification are species idiosyncratic and indicative of variations in geographic divergence. Here we compare the phylogeographical structures of two endemic birds of the Tibetan plateau, the white-rumped snow finch (Onychostruthus taczanowskii) and the Humes ground tit (Pseudopodoces humilis), both of which are commonly associated with alpine meadow habitats. Our results suggested that these two species experienced rapid population expansion at times estimated as 0.05-0.16 million years ago (Ma). These expansion periods were congruent with the retreat of the last extensive glacial period (0.5-0.175 Ma). Whereas O. taczanowskii populations were derived from a single more widely distributed refugium that existed along the east margin of the Tibetan plateau, P. humilis expanded from independent refugia that were located within both the northeast and southeast margin of the Tibetan plateau. While both birds experienced similar colonization events, their phylogeographical structures are quite contrasting. No trace of geographical divergence is found in O. taczanowskii, suggesting that considerable gene flow occurred after the postglacial colonization. In contrast, a geographic separation can be detected between two refugia populations of P. humilis, specifically the higher altitude platform and lower altitude edge regional groups. The gene flow between these two regions is restricted (M = 0.43). We estimate the divergence time as approximately 0.361 Ma, dating to the extensive glacial period. Potential explanations for the different phylogeographical structures of these two sympatric birds may include variance in dispersal ability, altitude specific and independent or semicontinuous refugia. While a combination of high flight ability and semicontinuous refugium may have promoted gene flow in O. taczanowskii populations, weak dispersal coupled with separated refugia may have sufficiently isolated populations such to facilitate genetic divergence in P. humilis.

Interpreting the Process behind Endemism in China by Integrating the Phylogeography and Ecological Niche Models of the Stachyridopsis ruficeps

An area of endemism (AOE) is a complex expression of the ecological and evolutionary history of a species. Here we aim to address the principal drivers of avian diversification in shaping patterns of endemism in China by integrating genetic, ecological, and distributional data on the Red-headed Tree Babbler (Stachyridopsis ruficeps), which is distributed across the eastern Himalayas and south China. We sequenced two mtDNA markers from 182 individuals representing all three of the primary AOEs in China. Phylogenetic inferences were used to reconstruct intraspecific phylogenetic relationships. Divergence time and population demography were estimated to gain insight into the evolutionary history of the species. We used Ecological niche modeling to predict species’ distributions during the Last Glacial Maximum (LGM) and in the present. Finally, we also used two quantitative tests, an identity test and background test to assess the similarity of ecological niche preferences between adjacent lineages. We found five primary reciprocally monophyletic clades, typically separated approximately 0.2–2.27 MYA, of which three were deeply isolated endemic lineages located in the three AOEs. All phylogroups were detected to have undergone population expansion during the past 0.3 MY. Niche models showed discontinuous habitats, and there were three barriers of less suitable habitat during the LGM and in modern times. Ecoclimatic niches may diverge significantly even over recent timescales, as each phylogroup had a unique distribution, and unique niche characteristics. Vicariant events associated with geographical and ecological barriers, glacial refuges and ecological differentiation may be the main drivers forming the pattern of endemism in China.

Priorities for the conservation of avian biodiversity in China based on the distribution patterns of endemic bird genera

Ten endemic Chinese bird genera are currently recognized: Nipponia, Tetraophasis, Chrysolophus, Crossoptilon, Ithaginis, Pseudopodoces, Rhopophilus, Kozlowia, Urocynchramus and Latoucheornis. Of these genera, Nipponia, Ithaginis, Pseudopodoces, Rhopophilus, Kozlowia, Urocynchramus and Latoucheornis are monotypic, while Tetraophasis, Chrysolophus and Crossoptilon are polytypic. In this paper, we first set up a database of the geographic distribution and suitable habitat requirements for each species of these endemic genera. Secondly we produced a modified habitat-based prediction of their distribution using GIS (ArcView 3.1) software overlap analysis. We then explored the spatial–temporal distribution patterns of different genera. By comparing the richness of the endemic genera in distributed areas, we identified centers of endemic avian biodiversity. These are: the northern and eastern Hengduanshan Mountains, and the Qinling, Dabashan and Minshan Mountain regions. Finally, we identified conservation ‘hotspots’ with a higher priority based on these centers. These results may provide a valuable tool for identifying and conserving areas with high endemic biodiversity and methods for researching the biogeography of endemic genera, the evolutionary history of fauna and species differentiation.

Evolutionary genomics of the pandemic 2009 H1N1 influenza viruses (pH1N 1v)

BackgroundA new strain of human H1N1 influenza A viruses was broken out in the April 2009 and caused worldwide pandemic emergency. The present study is trying to estimate a temporal reassortment history of 2009 H1N1 viruses by phylogenetic analysis based on a total 394 sequences of H1N1viruses isolated from swine, human and avian.ResultsPhylogenetic trees of eight gene segments showed that viruses sampled from human formed a well-supported clade, whereas swine and avian lineages were intermixed together. A new divergence swine sublineage containing gene segments of 2009 H1N1 viruses was characterized, which were closely related with swine viruses collected from USA and South Korea during 2004 to 2007 in six segments (PB2, PB1, PA, HA, NP and NS), and to swine viruses isolated from Thailand during 2004 to 2005 in NA and M. Substitution rates were varied drastically among eight segments and the average substitution rate was generally higher in 2009 H1N1 than in swine and human viruses (F2,23 = 5.972, P < 0.01). Similarly, higher dN/dS substitution ratios were identified in 2009 H1N1 than in swine and human viruses except M2 gene (F2, 25 = 3.779, P < 0.05). The ages of 2009 H1N1 viruses were estimated around 0.1 to 0.5 year, while their common ancestors with closest related swine viruses existed between 9.3 and 17.37 years ago.ConclusionOur results implied that at least four reassortments or transmissions probably occurred before 2009 H1N1 viruses. Initial reassortment arose in 1976 and avian-like Eurasian swine viruses emerged. The second transmission happened in Asia and North America between 1988 and 1992, and mostly influenced six segments (PB2, PB1, PA, HA, NP and NS). The third reassortment occurred between North American swine and avian viruses during 1998 to 2000, which involved PB2 and PA segments. Recent reassortments occurred among avian-to-swine reassortant, Eurasian and classical swine viruses during 2004 to 2005. South Korea, Thailand and USA, were identified as locations where reassortments most likely happened. The co-circulation of multiple swine sublineages and special lifestyle in Asia might have facilitated mixing of diverse influenza viruses, leading to generate a novel virus strain.

Comparative phylogeography of two widespread magpies: Importance of habitat preference and breeding behavior on genetic structure in China

Historical geological events and climatic changes are believed to have played important roles in shaping the current distribution of species. However, sympatric species may have responded in different ways to such climatic fluctuations. Here we compared genetic structures of two corvid species, the Azure-winged Magpie Cyanopica cyanus and the Eurasian Magpie Pica pica, both widespread but with different habitat dependence and some aspects of breeding behavior. Three mitochondrial genes and two nuclear introns were used to examine their co-distributed populations in East China and the Iberian Peninsula. Both species showed deep divergences between these two regions that were dated to the late Pliocene/early Pleistocene. In the East Chinese clade of C. cyanus, populations were subdivided between Northeast China and Central China, probably since the early to mid-Pleistocene, and the Central subclade showed a significant pattern of isolation by distance. In contrast, no genetic structure was found in the East China populations of P. pica. We suggest that the different patterns in the two species are at least partly explained by ecological differences between them, especially in habitat preference and perhaps also breeding behavior. These dissimilarities in life history traits might have affected the dispersal and survival abilities of these two species differently during environmental fluctuations.