Phylogeographic study of Apodemus ilex (Rodentia: Muridae) in Southwest China

Mitochondrial phylogeography of grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) endemic to the Qinghai-Tibetan plateau

Grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) are the most damaging pests to alpine meadows in the Qinghai-Tibetan Plateau (QTP). Here, we conducted extensive sampling from 39 geographic populations covering almost the entire distribution of the eight QTP Gynaephora (Hübner) species to investigate phylogeographic patterns and speciation based on two mitochondrial genes (COI and ND5). A total of 40 haplotypes were detected in the 39 populations, with >70% of all haplotypes not shared between populations. The monophyletic QTP Gynaephora migrated from non-QTP regions during the Pliocene, corresponding to the uplift of the QTP, suggesting a mode of transport into the QTP. Among the eight QTP Gynaephora species described by morphological characteristics, two species (G. alpherakii and G. menyuanensis) were recovered as monophyletic groups (Clades B and C), while the remaining six formed two monophyletic clades: Clade A (G. qinghaiensis, G. jiuzhiensis, and G. qumalaiensis) and Clade D (G. aureata, G. ruoergensis, and G. minora). These results suggested that the number of the QTP Gynaephora species may be overestimated and further studies based on both morphological and nuclear gene data are needed. Genetic differentiation and speciation of the QTP Gynaephora were likely driven by the QTP uplifts and associated climate fluctuations during the Pleistocene, indicated by divergence time estimation, suggesting that isolation and subsequent divergence was the dominant mode of speciation. The Sanjiangyuan region (i.e., Clade A, characterized by high genetic diversity) may have been a glacial refugium of the QTP Gynaephora, as supported by analyses of gene flow and biogeography. High levels of genetic diversity were found in QTP Gynaephora, without population expansion, which may explain the high-altitude adaptation and outbreaks of grassland caterpillars in alpine meadows of the QTP. This study provides the largest phylogeographic analysis of QTP Gynaephora and improves our understanding of the diversity and speciation of QTP insects.

Ecological Niche Characteristics of the Diets of Three Sympatric Rodents in the Meili Snow Mountain, Yunnan

Understanding the dietary preferences and ecological niche characteristics of mammals not only reveals their adaptive strategies under environmental changes but also reveals the interspecific relationships and coexistence mechanisms among sympatric species. Nevertheless, such data are scarce for rodents inhabiting areas spanning a wide altitude range. This study employed DNA metabarcoding technology to analyze the stomach contents of Apodemus ilex, Apodemus chevrieri, and Niviventer confucianus, aiming to investigate their dietary compositions and diversity in the Meili Snow Mountain in Yunnan Province, China. Levins's and Pianka's indices were used to compare the interspecific niche breadth and niche overlaps. The results revealed the following: (1) Insecta (relative abundance: 59.4-78.4%) and Clitellata (relative abundance: 5.2-25.5%) were the primary animal food sources for the three species, while Magnoliopsida (relative abundance: 90.3-99.9%) constitutes their main plant food source. Considerable interspecific differences were detected in the relative abundance of primary animal and plant foods among the three species; (2) There was partial overlap in the genus-level animal food between A. ilex and N. confucianus (Ojk = 0.4648), and partial overlap in plant food between A. ilex and A. chevrieri (Ojk = 0.3418). However, no overlap exists between A. chevrieri and N. confucianus, either in animal or plant food; (3) There were no significant interspecific differences in the α-diversity of animal and plant foods among the three species. The feeding strategies and ecological niche variations of these rodents support the niche differentiation hypothesis, indicating that they have diversified in their primary food sources. This diversification may be a strategy to reduce competition and achieve long-term coexistence by adjusting the types and proportions of primary foods consumed.

Impacts of Quaternary glaciation, geological history and geography on animal species history in continental East Asia: A phylogeographic review

Continental East Asia has a mild Pleistocene climate and a complex recent geological history. Phylogeographic studies of animals over the last 30 years have produced several distinctive patterns. Glaciation refugia are numerous and are not restricted to any particular regions. Most of them are localized and species-specific, although several large refugia, for example the mountains of SW China, are shared by multiple species and have refugia-within-refugia. Furthermore, postglaciation range expansion events vary greatly in time, scale and direction. Large-scale south-to-north post-LGM expansions are few and mostly occurred in the northern regions. Additionally, several unique geographic features, including the three-step terrain of China and the northern arid belt, have significant impacts on many species histories. Overall, the impacts of Pleistocene glaciations, particularly the LGM, on species history vary drastically from nondetectable to significant. The impacts are the least for species from the southwestern region and are most dominant for species from the north. Geological events play a more significant role in shaping species history than Pleistocene climatic changes. Phylogeographic patterns among animals species are highly consistent with those of plants. Future phylogeographic endeavour in East Asia should be hypothesis-driven and seek processes that underlie common patterns. The wide use of genomic data allow accurate estimates of historical population processes and exploration of older history beyond the Pleistocene.

Phylogeography of the Plateau Pika (Ochotona curzoniae) in Response to the Uplift of the Qinghai-Tibet Plateau

The evolution and current distribution of species on the Qinghai-Tibet Plateau have been significantly impacted by historical occurrences, including the uplift of the plateau and the Quaternary climate upheaval. As a remnant species, the plateau pika (Ochotona curzoniae) is a great model for researching historical events. In this study, 302 samples from 42 sample sites were utilized to analyze the impact of historical events on the evolution and distribution pattern of plateau pikas. The genetic diversity, patterns of differentiation, and historical dynamics of the plateau pika were investigated using molecular markers that included four mitochondrial genes (COI, D-loop, Cytb, and 12S rRNA) and three nuclear genes (GHR, IRBP, and RAG1). The results showed that: (1) The genetic diversity of the plateau pika was high in the Tibetan Plateau (Hd = 0.9997, π = 0.01205), and the plateau pika evolved into five lineages that occupied different geographical areas, with lineage 1 (Group 1) in the south of the Yarlung Zangbo River, lineage 2 (Group 2) in the hinterland of the plateau, lineage 3 (Group 3) in the northeastern part of the plateau, lineage 4 (Group 4) in the Hengduan Mountains, and lineage 5 (Group 5) in the eastern part of the plateau. (2) The gene flow among the five lineages was low, and the differentiation level was high (Nm < 0.25; Fst > 0.25), indicating that the geographical barriers between the five lineages, such as the Yarlung Zangbo River, the Qaidam-Ghuong-Guide Basin, and the Lancang River, effectively promoted the population differentiation of the plateau pika. (3) The plateau pika first spread from the Hengduan Mountains to the entire Qinghai-Tibet Plateau and then conducted small-scale migration and dispersal in several refuges across the plateau in response to climate changes during the glacial and interglacial periods. (4) Except for Group 1 and Group 4, all the other populations exhibited a rapid expansion between 0.06 and 0.01 Mya, but the expansion was considerably delayed or halted by the effects of climate change during the last glacial maximum (0.02 Mya). Overall, the plateau pika on the Qinghai-Tibet Plateau exhibits high genetic diversity, and topographic obstacles, including mountains, valleys, and basins, created by the uplift of the plateau and climatic changes since the Quaternary period have played an important role in the differentiation and historical dynamics of the plateau pika population.

Phylogeography and genetic diversity of the widespread katydid Ducetia japonica (Thunberg, 1815) across China

Habitat fragmentation can lower migration rates and genetic connectivity among remaining populations of native species. Ducetia japonica is one of the most widespread katydids in China, but little is known about its genetic structure and phylogeographic distribution. We combined the five-prime region of cytochrome c oxidase subunit I (COI-5P), 11 newly developed microsatellite loci coupled with an ecological niche model (ENM) to examine the genetic diversity and population structure of D. japonica in China and beyond to Laos and Singapore. Both Bayesian inference (BI) and haplotype network methods revealed six mitochondrial COI-5P lineages. The distribution of COI-5P haplotypes may not demonstrate significant phylogeographic structure (N ST > G ST, p > .05). The STRUCTURE analysis based on microsatellite data also revealed six genetic clusters, but discordant with those obtained from COI-5P haplotypes. For both COI-5P and microsatellite data, Mantel tests revealed a significant positive correlation between geographic and genetic distances in mainland China. Bayesian skyline plot (BSP) analyses indicated that the population size of D. japonica's three major mitochondrial COI-5P lineages were seemingly not affected by last glacial maximum (LGM, 0.015-0.025 Mya). The ecological niche models showed that the current distribution of D. japonica was similar to the species' distribution during the LGM period and only slightly extended in northern China. Further phylogeographic studies based on more extensive sampling are needed to identify specific locations of glacial refugia in northern China.

Ring distribution patterns-diversification or speciation? Comparative phylogeography of two small mammals in the mountains surrounding the Sichuan Basin

Studying the genetic differentiation in a unique geographical area contributes to understanding the process of speciation. Here, we explore the spatial genetic structure and underlying formation mechanism of two congeneric small mammal species (Apodemus draco and A. chevrieri), which are mainly distributed in the mountains surrounding the lowland Sichuan Basin, southwest China. We applied a set of comparative phylogeographical analyses to determine their genetic diversification patterns, combining mitochondrial (Cytb and COI) and nuclear (microsatellite loci) markers, with dense sampling throughout the range (411 A. draco from 21 sites and 191 A. chevrieri from 22 sites). Moreover, we performed three complementary statistical methods to investigate the correlation between genotype and geographical and environmental components, and predicted the potential suitable distributional range under the present and historical climate conditions. Our results suggest that both species have experienced allopatric differentiation and admixture in historical periods, resulting in a ring-shape diversification, under the barrier effect of the Sichuan Basin. We infer that the tectonic events of the Qinghai-Tibetan Plateau and climatic oscillations during the Quaternary played an important role on the genetic divergence of the two species by providing environmental heterogeneity and geographical variation. Our study reveals a case of two sympatric small mammals following a ring-shaped diversification pattern and provides insight into the process of differentiation.

Molecular and morphological evidence for a new species of the genus Typhlomys (Rodentia: Platacanthomyidae)

In this study, we reassessed the taxonomic position of Typhlomys (Rodentia: Platacanthomyidae) from Huangshan, Anhui, China, based on morphological and molecular evidence. Results suggested that Typhlomys is comprised of up to six species, including four currently recognized species ( Typhlomys cinereus, T. chapensis, T. daloushanensis, and T. nanus), one unconfirmed candidate species, and one new species ( Typhlomys huangshanensis sp. nov.). Morphological analyses further supported the designation of the Huangshan specimens found at mid-elevations in the southern Huangshan Mountains (600 m to 1 200 m a.s.l.) as a new species.

Isolated alpine habitats reveal disparate ecological drivers of taxonomic and functional beta-diversity of small mammal assemblages

The interpretation of patterns of biodiversity requires the disentanglement of geographical and environmental variables. Disjunct alpine communities are geographically isolated from one another but experience similar environmental impacts. Isolated homogenous habitats may promote speciation but constrain functional trait variation. In this study, we examined the hypothesis that dispersal limitation promotes taxonomic divergence, whereas habitat similarity in alpine mountains leads to functional convergence. We performed standardized field investigation to sample non-volant small mammals from 18 prominent alpine sites in the Three Parallel Rivers area. We estimated indices quantifying taxonomic and functional alpha- and beta-diversity, as well as beta-diversity components. We then assessed the respective importance of geographical and environmental predictors in explaining taxonomic and functional compositions. No evidence was found to show that species were more functionally similar than expected in local assemblages. However, the taxonomic turnover components were higher than functional ones (0.471±0.230 vs. 0.243±0.215), with nestedness components showing the opposite pattern (0.063±0.054 vs. 0.269±0.225). This indicated that differences in taxonomic compositions between sites occurred from replacement of functionally similar species. Geographical barriers were the key factor influencing both taxonomic total dissimilarity and turnover components, whereas functional beta-diversity was primarily explained by climatic factors such as minimum temperature of the coldest month. Our findings provide empirical evidence that taxonomic and functional diversity patterns can be independently driven by different ecological processes. Our results point to the importance of clarifying different components of beta-diversity to understand the underlying mechanisms of community assembly. These results also shed light on the assembly rules and ecological processes of terrestrial mammal communities in extreme environments.

Differences in Quaternary co-divergence reveals community-wide diversification in the mountains of southwest China varied among species

The mountains of southwest China (MSWC) is a biodiversity hotspot with highly complex and unusual terrain. However, with the majority of studies focusing on the biogeographic consequences of massive mountain building, the Quaternary legacy of biodiversity for the MSWC has long been overlooked. Here, we took a statistical comparative phylogeography approach to examine factors that shaped community-wide diversification. With data from 30 vertebrate species, the results reveal spatially concordant genetic structure, and temporally clustered co-divergence events associated with river barriers during severe glacial cycles. This indicates the importance of riverine barriers in the phylogeographic history of the MSWC vertebrate community. We conclude that the repeated glacial cycles are associated with co-divergences that are themselves structured by the heterogeneity of the montane landscape of the MSWC. This orderly process of diversification has profound implications for conservation by highlighting the relative independence of different geographical areas in which some, but not all species in communities have responded similarly to climate change and calls for further comparative phylogeographic investigations to reveal the connection between biological traits and divergence pulses in this biodiversity hotspot.

Sky islands as foci for divergence of fig trees and their pollinators in southwest China

The dynamics of populations and their divergence over time have shaped current levels of biodiversity and in the case of the "sky islands" of mountainous southwest (SW) China have resulted in an area of exceptional botanical diversity. Ficus tikoua is a prostrate fig tree subendemic to the area that displays unique intraspecific diversity, producing figs typical of different pollination modes in different parts of its range. By combining climate models, genetic variation in populations of the tree's obligate fig wasp pollinators and distributions of the different plant phenotypes, we examined how this unusual situation may have developed. We identified three genetically distinct groups of a single Ceratosolen pollinator species that have largely parapatric distributions. The complex topography of the region contributed to genetic divergence among the pollinators by facilitating geographical isolation and providing refugia. Migration along elevations in response to climate oscillations further enhanced genetic differentiation of the three pollinator groups. Their distributions loosely correspond to the distributions of the functionally significant morphological differences in the male figs of their host plants, but postglacial expansion of one group has not been matched by spread of its associated plant phenotype, possibly due to a major river barrier. The results highlight how interplay between the complex topography of the "sky island" complex and climate change has shaped intraspecies differentiation and relationships between the plant and its pollinator. Similar processes may explain the exceptional botanical diversity of SW China.

Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds

Detection of selection footprints provides insight into the evolution process and the underlying mechanisms controlling the phenotypic diversity of traits that have been exposed to selection. Selection focused on certain characters, mapping certain genomic regions often shows a loss of genetic diversity with an increased level of homozygosity. Therefore, the runs of homozygosity (ROHs), homozygosity by descent (HBD), and effective population size (N_e) are effective tools for exploring the genetic diversity, understanding the demographic history, foretelling the signature of directional selection, and improving the breeding strategies to use and conserve genetic resources. We characterized the ROH, HBD, N_e, and signature of selection of six Chinese goat populations using single nucleotide polymorphism (SNP) 50K Illumina beadchips. Our results show an inverse relationship between the length and frequency of ROH. A long ROH length, higher level of inbreeding, long HBD segment, and smaller N_e in Guangfeng (GF) goats suggested intensive selection pressure and recent inbreeding in this breed. We identified six reproduction-related genes within the genomic regions with a high ROH frequency, of which two genes overlapped with a putative selection signature. The estimated pair-wise genetic differentiation (F_ST) among the populations is 9.60% and the inter- and intra-population molecular variations are 9.68% and 89.6%, respectively, indicating low to moderate genetic differentiation. Our selection signatures analysis revealed 54 loci harboring 86 putative candidate genes, with a strong signature of selection. Further analysis showed that several candidate genes, including MARF1, SYCP2, TMEM200C, SF1, ADCY1, and BMP5, are involved in goat fecundity. We identified 11 candidate genes by using cross-population extended haplotype homozygosity (XP-EHH) estimates, of which MARF1 and SF1 are under strong positive selection, as they are differentiated in high and low reproduction groups according to the three approaches used. Gene ontology enrichment analysis revealed that different biological pathways could be involved in the variation of fecundity in female goats. This study provides a new insight into the ROHs patterns for maintenance of within breed diversity and suggests a role of positive selection for genetic variation influencing fecundity in Chinese goat.

Evolutionary history of field mice (Murinae: Apodemus), with emphasis on morphological variation among species in China and description of a new species

Mice of the genus Apodemus are widely distributed across Eurasia. Several species of this genus are hosts of important zoonotic diseases and parasites. The evolutionary history and dispersal routes of these mice remain unclear and the distribution of these species in China was poorly explored in previous studies. We here investigate the divergence times and historical geographical evolution of Apodemus and study the taxonomy of species in China by integrating molecular and morphological data. The crown age of this genus is dated to the Late Miocene, approximately 9.84 Mya. Western and Central Asia were inferred as the most likely ancestral area of this genus. Moreover, we recognize nine living species of Apodemus in China: Apodemus uralensis, A. agrarius, A. chevrieri, A. latronum, A. peninsulae, A. draco, A. ilex, A. semotus and A. nigrus sp. nov., the last from the highlands (elevation > 1984 m) of Fanjing Mountain in Guizhou Province and Jinfo Mountain in Chongqing Province. This new species diverged from A. draco, A. semotus and A. ilex approximately 4.53 Mya. The discovery of A. nigrus highlights the importance of high mountains as refugia and ‘isolated ecological islands’ for temperate species in south-eastern China.

Genetic diversity estimation of Yunnan indigenous goat breeds using microsatellite markers

BACKGROUND

To assess the genetic diversity of seven Yunnan indigenous goat populations (Fengqing hornless goat, Mile red-bone goat, Longling goat, Ninglang black goat, Black-bone goat, Yunling black goat, and Zhaotong goat), their population structures were investigated using 20 microsatellite markers.

RESULTS

The results indicated that the genetic diversity of these goats was rich. The observed heterozygosity ranged from 0.4667 ± 0.0243 to 0.5793 ± 0.0230, and the mean number of alleles ranged from 4.80 ± 1.61 and 4.80 ± 1.64 to 6.20 ± 2.93. The population structure analysis showed that these seven goat populations were separated into two clusters, consistent with the results from phylogenetic networks, pairwise differences, and STRUCTURE analyses. We speculate that this may have been caused by natural geographical isolation, human migration and economic and cultural exchanges. We suggest removing CSRD247 and ILSTS005, two loci identified to be under positive selection in the present study, from the microsatellite evaluation system of goats.

CONCLUSIONS

The present study may provide a scientific basis for the conservation and utilization of Yunnan indigenous goats.

Molecular phylogeographic analyses and species delimitations reveal that Leopoldamys edwardsi (Rodentia: Muridae) is a species complex

Leopoldamys edwardsi is a species with wide distribution ranges in southern China but is not discussed in studies on geographic variation and species differentiation. We used 2 mitochondrial (Cytb, CO1) and 3 nuclear (GHR, IRBP and RAG1) genes to clarify species phylogeography and geographical differentiation. Maximum likelihood (ML) and Bayesian phylogenetic inference (BI) trees consistently indicated that L. edwardsi is a species complex containing 3 main lineages with high Kimura-2-parameter (K2P) divergences (i.e. lineages L_N , L_S and L_HN ) found in the northern and southern China and Hainan Island, respectively. The 3 species delimitation methods, automated barcoding gap discovery, Bayesian poisson tree process analysis and Bayesian phylogenetics and phylogeography, consistently supported the existence of cryptic species. Divergence times among the main lineages were inferred to be during the Pleistocene, with L_HN /L_S split at 1.33 Ma and L_N /(L_HN +L_S ) at 2.61 Ma; the diversifications of L. edwardsi complex might be caused by the rapid uplifts of Tibetan Plateau, paleoclimate change and complex topography. The divergence between L_HN and L_S was probably related to the separation of Hainan Island from the mainland via the formation of the Qiongzhou Strait. Lineages L_N and (L_S +L_HN ) likely diverged due to the Wuyi-Nanling mountain range forming a dispersal barrier. Our results suggested that L. edwardsi complex contains at least 3 distinct species: L_HN represents L. hainanensis, endemic to Hainan Island and previously considered as a subspecies L. e. hainanensis; L_S represents a cryptic species distributed throughout the southern Chinese continent; and L_N represents the nominotypical species L. edwardsi.

Karyotypes of field mice of the genus Apodemus (Mammalia: Rodentia) from China

Karyotypes of four Chinese species of field mice of the genus Apodemus were examined, including Apodemus chevrieri (diploid chromosome number, 2n=48, fundamental number of autosomal arms, FNa=56), A. draco (2n=48, FNa=48), A. ilex (2n=48, FNa=48), and A. latronum (2n=48, FNa=48). Karyotypes of A. chevrieri, A. draco, and A. ilex are reported here for the first time, providing useful information for their species taxonomy. Determining the karyotypes of all species of Apodemus in Asia, both in this and previous studies, provides a solid overview of the chromosome evolution and species differentiation of the genus in East Asia. In addition to allopatric speciation, chromosome rearrangements likely played an important role in the formation of the four Apodemus species groups as well as speciation within each group in East Asia. For example, increased centromeric heterochromatin in A. latronum may have contributed to the post-mating reproductive isolation from the A. draco-A. ilex-A. semotus clade.

The roles of environment, space, and phylogeny in determining functional dispersion of rodents (Rodentia) in the Hengduan Mountains, China

The recently described trait-based approach is becoming widely popular for a mechanistic understanding of species coexistence. However, the greatest challenge in functional analyses is decomposing the contributions of different ecological and evolutionary processes (e.g., niche-based process, neutral process, and evolutionary process) in determining trait structure. Taking rodents (Rodentia) in the Hengduan Mountains as our study model, we aim to (1) quantify the vertical patterns of functional structure for head-body length (HL), tail/body ratio (TR), animal component in diet (ACD), and all traits; (2) disentangle the relative importance of different assembly processes (environment, space, and phylogeny) in structuring trait dispersion; and (3) assess the feasibility of Bergmann's rule and Allen's rule along elevational gradient. Our results have suggested that the vertical functional structure pattern varied across these three traits, indicating distinct functional roles in the community assembly process. These nonrandom vertical patterns of HL, TR, and terminal ACD have demonstrated these traits were dominated by different ecological process along environmental gradient. In variance partitioning, high proportion of the spatial variations in trait dispersion was explained by environmental and spatial models, which have provided supporting strong evidence for niche-based and neutral processes in leading species coexistence. Although the three traits all exhibited apparent phylogenetic signals, phylogenetic relationship within community failed to predict the spatial variations of functional dispersion, confirming the enormous inference of phylogenetic signals in predicting trait structure. By assessing the vertical patterns of HL and TR at order and family levels, we argued that functional adaptation along an environmental gradient is a surrogate of series of complex processes (e.g., environmental filtering, interspecific interaction, and neutral dispersal) acting on multiple functional axes, which results in inconsistence with the empirical rules along elevational gradient.

Population structure and historical demography of Dipteronia dyeriana (Sapindaceae), an extremely narrow palaeoendemic plant from China: implications for conservation in a biodiversity hot spot

Inferring past demography is a central question in evolutionary and conservation biology. It is, however, sometimes challenging to disentangle their roles of contemporary versus historical processes in shaping the current patterns of genetic variation in endangered species. In this study, we used both chloroplast microsatellite (cpSSR) loci and nuclear microsatellite (nSSR) loci to assess the levels of genetic differentiation, genetic effective population size, contemporary/historical levels of gene flow and demographic history for five populations sampled across the range of Dipteronia dyeriana, an endangered palaeoendemism from Southwestern China. We found that D. dyeriana had a mixed pattern of moderate genetic diversity and high inbreeding. Bayesian clustering divided D. dyeriana populations into two nSSR genetic clusters. Coalescent-based approximate Bayesian computation analyses suggest the western and eastern groups of D. dyeriana likely persisted in a long-term refuge in Southern China since the beginning of the last glacial period, whereas increasingly colder and arid climates at the onset of the last glacial maximum might have fostered the fragmentation of D. dyeriana within refugia. Following their divergence, the western group kept relatively stable effective population size, whereas the eastern group had experienced 500-fold population expansion during the Holocene. Although clear loss of genetic diversity by human activities was not suggested, recent habitat fragmentation has led to a reduction of population connectivity and increased genetic differentiation by ongoing genetic drift in isolated populations, possibly owing to decreased population size in recent dozen years. Finally, we discussed the implications of these results on conservation policies.

Developing informative microsatellite markers for non-model species using reference mapping against a model species' genome

Microsatellites have a wide range of applications from behavioral biology, evolution, to agriculture-based breeding programs. The recent progress in the next-generation sequencing technologies and the rapidly increasing number of published genomes may greatly enhance the current applications of microsatellites by turning them from anonymous to informative markers. Here we developed an approach to anchor microsatellite markers of any target species in a genome of a related model species, through which the genomic locations of the markers, along with any functional genes potentially linked to them, can be revealed. We mapped the shotgun sequence reads of a non-model rodent species Apodemus semotus against the genome of a model species, Mus musculus, and presented 24 polymorphic microsatellite markers with detailed background information for A. semotus in this study. The developed markers can be used in other rodent species, especially those that are closely related to A. semotus or M. musculus. Compared to the traditional approaches based on DNA cloning, our approach is likely to yield more loci for the same cost. This study is a timely demonstration of how a research team can efficiently generate informative (neutral or function-associated) microsatellite markers for their study species and unique biological questions.

Interglacial refugia preserved high genetic diversity of the Chinese mole shrew in the mountains of southwest China

The mountains of southwest China (MSC) harbor extremely high species diversity; however, the mechanism behind this diversity is unknown. We investigated to what degree the topography and climate change shaped the genetic diversity and diversification in these mountains, and we also sought to identify the locations of microrefugia areas in these mountains. For these purposes, we sampled extensively to estimate the intraspecific phylogenetic pattern of the Chinese mole shrew (Anourosorex squamipes) in southwest China throughout its range of distribution. Two mitochondrial genes, namely, cytochrome b (CYT B) and NADH dehydrogenase subunit 2 (ND2), from 383 archived specimens from 43 localities were determined for phylogeographic and demographic analyses. We used the continuous-diffusion phylogeographic model, extensive Bayesian skyline plot species distribution modeling (SDM) and approximate Bayesian computation (ABC) to explore the changes in population size and distribution through time of the species. Two phylogenetic clades were identified, and significantly higher genetic diversity was preserved in the southern subregion of the mountains. The results of the SDM, continuous-diffusion phylogeographic model, extensive Bayesian skyline plot and ABC analyses were congruent and supported that the Last Interglacial Maximum (LIG) was an unfavorable period for the mole shrews because of a high degree of seasonality; A. squamipes survived in isolated interglacial refugia mainly located in the southern subregion during the LIG and rapidly expanded during the last glacial period. These results furnished the first evidence for major Pleistocene interglacial refugia and a latitudinal effect in southwest China, and the results shedding light on the higher level of species richness in the southern subregion.

Molecular Phylogeny of Grassland Caterpillars (Lepidoptera: Lymantriinae: Gynaephora) Endemic to the Qinghai-Tibetan Plateau

Gynaephora (Lepidoptera Erebidae: Lymantriinae) is a small genus, consisting of 15 nominated species, of which eight species are endemic to the Qinghai-Tibetan Plateau (QTP). In this study, we employed both mitochondrial and nuclear loci to infer a molecular phylogeny for the eight QTP Gynaephora spp. We used the phylogeny to estimate divergence dates in a molecular dating analysis and to delimit species. This information allowed us to investigate associations between the diversification history of the eight QTP species and geological and climatic events. Phylogenetic analyses indicated that the eight QTP species formed a monophyletic group with strong supports in both Bayesian and maximum likelihood analyses. The low K2P genetic distances between the eight QTP species suggested that diversification occurred relatively quickly and recently. Out of the eight species, five species were highly supported as monophyletic, which were also recovered by species delimitation analyses. Samples of the remaining three species (G. aureata, G. rouergensis, and G. minora) mixed together, suggesting that further studies using extensive population sampling and comprehensive morphological approaches are necessary to clarify their species status. Divergence time estimation results demonstrated that the diversification and speciation of Gynaephora on the QTP began during the late Miocene/early Pliocene and was potentially affected by the QTP uplift and associated climate changes during this time.

Molecular phylogenetics and phylogeographic structure of Sorex bedfordiae based on mitochondrial and nuclear DNA sequences

The southeastern margin of the Tibetan Plateau is characterized by complex topography and a discontinuous landscape, creating a sky island situation. However, the way topography shapes genetic structures and demographic histories of endemic species has not been well studied. We examined the phylogeographic pattern and demographic histories of Sorex bedfordiae, a dispersal-limited small mammal, using three nuclear genes [1977bp] and two mitochondrial genes [1794bp] with comprehensive molecular approaches. We recovered five well-supported clades whose distributions are along mountain ridges and roughly subdivided by large rivers. Demographic expansions in the middle Pleistocene were strongly supported by both nuclear and mitochondrial genes. Our results support the hypothesis that sky island topography and river systems strongly affect the genetic structure of non-aquatic terrestrial species. We further clarify that S. bedfordiae and S. cylindricauda are valid sibling species, whereas S. excelsus is most likely a geographic subspecies of S. bedfordiae.

Genetic structure of Chinese indigenous goats and the special geographical structure in the Southwest China as a geographic barrier driving the fragmentation of a large population

Background

China has numerous native domestic goat breeds, however, extensive studies are focused on the genetic diversity within the fewer breeds and limited regions, the population demograogic history and origin of Chinese goats are still unclear. The roles of geographical structure have not been analyzed in Chinese goat domestic process. In this study, the genetic relationships of Chinese indigenous goat populations were evaluated using 30 microsatellite markers.

Methodology/Principal Findings

Forty Chinese indigenous populations containing 2078 goats were sampled from different geographic regions of China. Moderate genetic diversity at the population level (H_S of 0.644) and high population diversity at the species level (H_T value of 0.737) were estimated. Significant moderate population differentiation was detected (F_ST value of 0.129). Significant excess homozygosity (F_IS of 0.105) and recent population bottlenecks were detected in thirty-six populations. Neighbour-joining tree, principal components analysis and Bayesian clusters all revealed that Chinese goat populations could be subdivided into at least four genetic clusters: Southwest China, South China, Northwest China and East China. It was observed that the genetic diversity of Northern China goats was highest among these clusters. The results here suggested that the goat populations in Southwest China might be the earliest domestic goats in China.

Conclusions/Significance

Our results suggested that the current genetic structure of Chinese goats were resulted from the special geographical structure, especially in the Western China, and the Western goat populations had been separated by the geographic structure (Hengduan Mountains and Qinling Mountains-Huaihe River Line) into two clusters: the Southwest and Northwest. It also indicated that the current genetic structure was caused by the geographical origin mainly, in close accordance with the human’s migration history throughout China. This study provides a fundamental genetic profile for the conservation of these populations and better to understand the domestication process and origin of Chinese goats.

Molecular phylogeography and evolutionary history of Poropuntius huangchuchieni (Cyprinidae) in Southwest China

BACKGROUND

The evolution of the Yunnan Plateau's drainages network during the Pleistocene was dominated by the intense uplifts of the Qinghai-Tibetan Plateau. In the present study, we investigated the association between the evolutionary histories of three main drainage systems and the geographic patterns of genetic differentiation of Poropuntius huangchuchieni.

METHODOLOGY/PRINCIPAL FINDINGS

We sequenced the complete sequences of mitochondrial control region for 304 specimens and the sequences of Cytochrome b gene for 15 specimens of the species P. huangchuchieni and 5 specimens of Poropuntius opisthoptera. Phylogenetic analysis identified five major lineages, of which lineages MK-A and MK-B constrained to the Mekong River System, lineages RL and LX to the Red River System, and lineage SW to the Salween River System. The genetic distance and network analysis detected significant divergences among these lineages. Mismatch distribution analysis implied that the population of P. huangchuchieni underwent demographic stability and the lineage MK-B, sublineages MK-A1 and LX-1 underwent a recent population expansion. The divergence of the 5 major lineages was dated back to 0.73-1.57 MYA.

CONCLUSIONS/SIGNIFICANCE

Our results suggest that P. opisthoptera was a paraphyletic group of P. huangchuchieni. The phylogenetic pattern of P. huangchuchieni was mostly associated with the drainage's structures and the geomorphological history of the Southwest Yunnan Plateau. Also the differentiation of the major lineages among the three drainages systems coincides with the Kunlun-Yellow River Movement (1.10-0.60 MYA). The genetic differentiation within river basins and recent demographical expansions that occurred in some lineages and sublineages are consistent with the palaeoclimatic oscillations during the Pleistocene. Additionally, our results also suggest that the populations of P. huangchuchieni had keep long term large effective population sizes and demographic stability in the recent evolutionary history, which may be responsible for the high genetic diversity and incomplete lineages sorting of Poropuntius huangchuchieni.

Phylogeography of the Rickett's big-footed bat, Myotis pilosus (Chiroptera: Vespertilionidae): a novel pattern of genetic structure of bats in China

Background

China is characterized by complex topographic structure and dramatic palaeoclimatic changes, making species biogeography studies particularly interesting. Previous researchers have also demonstrated multiple species experienced complex population histories, meanwhile multiple shelters existed in Chinese mainland. Despite this, species phylogeography is still largely unexplored. In the present study, we used a combination of microsatellites and mitochondrial DNA (mtDNA) to investigate the phylogeography of the east Asian fish-eating bat (Myotis pilosus).

Results

Phylogenetic analyses showed that M. pilosus comprised three main lineages: A, B and C, which corresponded to distinct geographic populations of the Yangtze Plain (YTP), Sichuan Basin (SCB) and North and South of China (NSC), respectively. The most recent common ancestor of M. pilosus was dated as 0.25 million years before present (BP). Population expansion events were inferred for populations of Clade C, North China Plain region, Clade B and YunGui Plateau region at 38,700, 15,900, 4,520 and 4,520 years BP, respectively. Conflicting results were obtained from mtDNA and microsatellite analyses; strong population genetic structure was obtained from mtDNA data but not microsatellite data. The microsatellite data indicated that genetic subdivision fits an isolation-by-distance (IBD) model, but the mtDNA data failed to support this model.

Conclusions

Our results suggested that Pleistocene climatic oscillations might have had a profound influence on the demographic history of M. pilosus. Spatial genetic structures of maternal lineages that are different from those observed in other sympatric bats species may be as a result of interactions among special population history and local environmental factors. There are at least three possible refugia for M. pilosus during glacial episodes. Apparently contradictory genetic structure patterns of mtDNA and microsatellite could be explained by male-mediated gene flow among populations. This study also provides insights on the necessity of conservation of M. pilosus populations to conserve this genetic biodiversity, especially in the areas of YTP, SCB and NSC regions.

Molecular phylogeny and biogeography of percocypris (Cyprinidae, Teleostei)

Fierce predatory freshwater fishes, the species of Percocypris (Cyprinidae, Teleostei) inhabit large rivers or lakes, and have a specific distribution pattern. Only a single species or subspecies occurs in each large-scale drainage basin of the Southeastern Tibetan Plateau. In this study, the molecular phylogenetic relationships for all but one of the described subspecies/species of Percocypris were investigated based on three mitochondrial genes (16S; COI; Cyt b) and one nuclear marker (Rag2). The results of Maximum Likelihood and Bayesian Inference analyses show that Percocypris is a strongly supported monophyletic group and that it is the sister group of Schizothorax. Combined with analyses of morphological characters, our results suggest that Percocypris needs to be reclassified, and we propose that six species be recognized, with corresponding distributions in five main drainages (including one lake). In addition, based on the results of the estimation of divergence times and ancestral drainages, we hypothesize that Percocypris likely originated in the early Miocene from a paleo-connected drainage system containing the contemporary main drainages of the Southeastern Tibetan Plateau. This study suggests that vicariance (due to the uplift of the Tibetan Plateau modifying the large-scale morphologies of drainage basins in the Southeastern Tibetan Plateau) has played an important role in the speciation of the genus. Furthermore, external morphological characters (such as the length of the fins) and an internal trait (the position of pterygiophore) appear to be correlated with different habitats in rivers and the lake.

Effect of Pleistocene climatic oscillations on the phylogeography and demography of red knobby newt (Tylototriton shanjing) from southwestern China

Factors that determine the genetic structure of species in southwestern China remain largely unknown. In this study, phylogeography and demography of Tylototriton shanjing was investigated from a mitochondrial perspective to address the role of the Quaternary ice ages in shaping phylogeographic history and genetic diversity of Yunnan. A total of 146 individuals from 19 populations across the entire range of the species were collected. We detected four maternal phylogenetic lineages corresponding to four population groups, and found that major glaciation events during the Pleistocene have triggered the intra-specific divergence. Coalescent simulations indicated that the populations retreated to different refugia located in southern Yunnan, northwestern Yunnan, the border region of western Yunnan with Myanmar, and middle-western Yunnan, respectively, during previous glacial periods in the Pleistocene, and these four refugia were not retained during the Last Glacial Maximum. Population expansions occurred during the last inter-glaciation, during which ice core and pollen data indicated that the temperature and precipitation gradually increased, and declines of population sizes started after the beginning of the Last Glacial Maximum when the climate became cooler and dryer. The paleo-drainage system had no contribution to the current genetic structure and the rivers were not dispersal barriers for this salamander.

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

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 (π = 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.