A new bunting species in South China revealed by an integrative taxonomic investigation of the Emberiza godlewskii complex (Aves, Emberidae).

Species boundaries of birds across the Euro-Asian continent, especially the widely distributed passerines with multiple subspecies, are not completely resolved. The Rock Bunting complex, Emberiza cia and E. godlewskii, is subject to ongoing debate due to geographic variation in its morphology, and deep genetic splits. In this study, the phylogenetic relationships of the E. cia/godlewskii complex were evaluated based on multilocus coalescence methods combined with analyses of plumage color and morphological variation. Although the northern and southern populations of E. godlewski formed reciprocally monophyletic groups, the northern E. godlewskii clade is the sister group to E. cia, rendering E. godlewskii as currently defined paraphyletic. The significant differences in morphometry and plumage color reflectance are complementary and support the phenotypic validity of northern and southern E. godlewskii. Thus, we recommend the following taxonomic revisions: the northern and southern E. godlewskii subspecies should be recognized as different full species, such as E. godlewskii and E. yunnanensis, respectively. This resolves the issue that E. godlewskii, as currently defined, is paraphyletic. Our research provides direct evidence of cryptic species in old world buntings and highlights the underestimation of species diversity in birds in East Asia.

Deep south-north genetic divergence in Godlewski's bunting (Emberiza godlewskii) related to uplift of the Qinghai-Tibet Plateau and habitat preferences.

BACKGROUND: Geological events and climatic changes played important roles in shaping population differentiation and distribution within species. In China, populations in many species have contracted and expanded responding to environmental changes with the uplift of the Qinghai-Tibet Plateau (QTP) and glacial cycles during Pleistocene. In this study, we analysed the population structure of Godlewski's Bunting, Emberiza godlewskii, to determine the effects of major historical events, geographic barriers and past climatic changes on phylogenetic divergence and historical demographic dynamics of this species. RESULTS: A phylogeny based on concatenated mitochondrial and nuclear DNA datasets show two (northern and southern) clades approximately diverged 3.26 million years ago (Ma). The West Qinling Mountains serve as a dividing line between the two lineages. Both lineages experienced a recent demographic expansion during interglacial periods (marine isotope stages (MISs) 2-6). Bayesian skyline plots and the results of ecological niche modelling suggested a more intensive expansion of the northern lineage during the late Pleistocene, whereas the southern lineage was comparatively mild in population growth. CONCLUSIONS: Our results provide insights into the distribution patterns of avian taxa and the possible mechanisms for a south and north divergence model in China. The deep divergence may have been shaped by the uplift of the QTP. Habitat preferences might have facilitated the lineage divergence for E. godlewskii. Moreover, the West Qinling Mountains act as a dividing line between the two lineages, indicating a novel phylogeographic pattern of organisms in China. The difference in population expansion mode between two lineages resulted from different effects caused by the climate of the LGM and the subsequent habitat changes accompanying the arrival of a colder climate in northern and southern regions of China.

Intraspecific lineages of the lizard Phrynocephalus putjatia from the Qinghai-Tibetan Plateau: impact of physical events on divergence and discordance between morphology and molecular markers.

The Northeastern Qinghai-Tibetan Plateau (NQTP) contains many physical features that may have contributed to its rich biological diversity. We explored the systematics and genetic structures of the sand lizards Phrynocephalus putjatia, distributed across semi-deserts or rocky steppe habitats, and Phrynocephalus guinanensis, found only in sand dune habitats, from the NQTP using mitochondrial (ND2 and tRNAs) and nuclear (RAG-1) markers. Bayesian analyses revealed two main monophyletic mtDNA groups that separate populations of the Qinghai Lake Basin (QLB) from populations to the southeast of this basin (SEQL), but these did not correspond to the two morphological species. The QLB populations are divided into western and eastern groups. Two major groups with similar geographical structuring were also detected for the nuclear RAG-1 marker, but with some geographical discordance. A Bayesian species delimitation analysis did not support division of P. putjatia/P. guinanensis into separate species. Bayesian dating of mtDNA suggests that the earliest divergence within this group occurred less than 2 Ma, which seems to be explained by mountain uplift between the QLB and the SEQL regions. Other Pleistocene events may explain further genetic structuring. Overall, we do not detect reciprocal monophyly of markers between morphological species but note that they do appear to represent ecological forms.

Sex-specific parental care strategies via nestling age: females pay more attention to nestling demands than males do in the horned lark, Eremophila alpestris.

In many species, nestling demands vary continuously during early development and both parents have different parental care strategies at each nestling age. Sexual conflict arises when each parent expects its partner investing more in parental care. It is largely unknown how the two parents respond to the dynamics of nestling demands and resolve the sexual conflict during nestling period, especially on Qinghai-Tibetan Plateau. To address this question, we monitored parental care behaviors of horned larks (Eremophila alpestris) using video-recording systems. We found that male horned larks invested less in parental care, but had a larger body size than females, which is consistent with the parental investment hypothesis. Only the female brooded nestlings, but both parents contributed to feeding efforts. Feeding rates of males and females were negatively correlated, indicating that they used evolutionarily stable strategies. Strategies of parental care via nestling age were sex-specific. Females continuously adjusted care behaviors to follow the dynamics of nestling demands as nestling age increased, such as decreasing brood attentiveness and increasing feeding rate. By contrast, male feeding rate showed no significant correlation with nestling age, but increased with the synchrony feeding rate. We suggest the synchrony feeding behavior may act as a control measure for females to promote and assess the males' contribution. We consider low mating opportunities drive males to act as assistants for females, and correspondingly cause males to pay less attention to nestling demands than females.

Phylogeography-based delimitation of subspecies boundaries in the common pheasant (Phasianus colchicus).

To test the validity of subspecies status within the common pheasant (Phasianus colchicus), we used genetic data to assess differences among five subspecies distributed across the Loess Plateau in central China. Samples were collected from 191 individuals representing subspecies P. c. strauchi, P. c. satscheuensis, P. c. kiangsuensis, P. c. suehschanensis, and P. c. edzinensis. Analysis of mitochondrial genetic variation suggested that there were no phylogenetically distinct subspecies clades, and we could not exclude that hybridization has occurred among subspecies. A potential explanation of the observed pattern is that an increase in common pheasant rearing farms may have led to enforcement of hybridization between different subspecies. Consistent with phenotypic data, our analysis suggests that a previously identified common pheasant subspecies (P. c. strauchi) represents an intermediate form between the subspecies P. c. satscheuensis and P. c. suehschanensis.

Effects of the Qinghai-Tibetan Plateau uplift and environmental changes on phylogeographic structure of the Daurian Partridge (Perdix dauuricae) in China.

Data from eight microsatellite loci were used to assess the evolutionary demographic processes of Daurian Partridges from 285 individuals distributed among 23 populations throughout much of the species' distribution range in China. Phylogenetic analysis using microsatellite DNA data indicated that the species were geographically structured and were split into two distinctive phylogroups A and B, splitting partridges geographically from high plateaus vs. lowlands in northern China with high bootstrap support in phylogenetic trees. Each of cluster A and cluster B was comprised with two subgroups respectively. Cluster A was further subdivided into the Loess Plateau group and the Qinghai-Tibetan group. Two subgroups of cluster B corresponded to populations of Liupan Mountains and northern China, respectively. This subdivision was confirmed by Bayesian clustering and population assignment analyses of microsatellite genotypes which indicated strong isolation of these groups/populations. Our results suggested that the vicariance patterns of genetic structures of Daurian Partridge may have resulted from: (1) the uplift of the Qinghai-Tibetan Plateau and the Loess Plateau followed by the increased aridification and desertification in northern China in Middle Pleistocene, (2) the monsoon and the existence of Qinling Mountains and Liupan Mountains, and (3) the glacial cycles from the late of Middle Pleistocene to early of Late Pleistocene. In addition, BOTTLENECK analysis indicated that Daurian Partridge had been experienced recent evolutionary bottlenecks.

Seasonal changes in the genetic diversity of two rodent populations, midday gerbil (Meriones meridianus) and northern three-toed jerboa (Dipus sagitta), detected by ISSR.

Seasonal changes in genetic diversity of Meriones meridianus and Dipus sagitta populations in the Ningxia Hui Autonomous Region were monitored using inter-simple sequence repeats. There were 45 discernible DNA fragments isolated from 33 samples of M. meridianus, and 25 from 40 samples of D. sagitta. The differences in gene frequencies are statistically significant for some alleles. Nei's index revealed that the greatest genetic differentiation was distributed within the seasonal groups. Nei's and Shannon's indexes exhibited similar seasonal trends, indicating that the spring group has the highest level of genetic diversity and that genetic diversity changes with the seasons. Correlation analysis found no statistically significant correlation between genetic diversity and population density. The results suggest that the seasonal changes in genetic diversity of the two species depend mainly on reproduction and dispersal.

Phylogeography of Phrynocephalus erythrurus from the Qiangtang Plateau of the Tibetan Plateau.

Phrynocephalus erythrurus of the Qiangtang Plateau occupies the highest regions of any reptile on earth. Here, we report mitochondrial DNA haplotypes sampled throughout the distribution of P. erythrurus and analyze patterns of genetic divergence among populations. The species diverged into two major lineages/subspecies at 3.67mya corresponding to the Northern and Southern Qiangtang Plateau. The Northern Qiangtang lineage diverged into two subpopulations at 2.76mya separated by the Beilu River Region and Wulanwula Mountains. Haplotypes from the southern Qiangtang lineage diverged 0.98mya as a star-shaped pattern. Analyses of molecular variance indicated that most of the observed genetic variation occurred among populations/regions implying long-term interruptions to gene flow. There was no evidence of sudden recent range expansions within any of the clades/lineages. NCPA infers allopatric fragmentation and restricted gene flow as the most likely mechanisms of population differentiation. Our results also indicate the presence of at least three refugia since the Hongya glaciation. Mountain movement and glaciations since mid-Pliocene are considered to have shaped phylogenetic patterns of P. erythrurus. P. erythrurus parva is suggested as a valid subspecies of P. erythrurus. Using four calibration points, we estimate an evolutionary rate of 0.762% divergence per lineage per million years for a mitochondrial genomic segment comprising the genes encoding ND2, tRNA(Trp) and tRNA(Ala).

Phylogeography of Chinese bamboo partridge, Bambusicola thoracica thoracica (Aves: Galliformes) in south China: inference from mitochondrial DNA control-region sequences.

Chinese bamboo partridge (Bambusicola thoracica thoracica), an endemic subspecies of south China, distributes in mountainous areas that were affected by climate changes throughout the Pleistocene. We investigated the potential impact of cyclical Pleistocene climate changes on phylogeographic patterns using 1140 nucleotides of mitochondrial DNA (mtDNA) control-region from 180 individuals sampled from 13 populations of the partridge. We found 50 haplotypes defined by 39 polymorphic positions. Phylogenetic analyses revealed two robustly supported clades. There was a significant genetic differentiation among the populations with little gene flow. Refugia were identified in the southwestern mountains and Luoxiao Mountains in China, implying that topographic complexity played a substantial role in providing suitable habitats for the partridge during cold periods. Results from the mismatch distribution and neutrality test analysis suggested a range expansion of the two clades. The mtDNA marker suggested the existence of a geographical structure among Chinese bamboo partridge populations, resulting from the synergistic affect of Pleistocene climatic variations.

The phylogenetic position and speciation dynamics of the genus Perdix (Phasianidae, Galliformes).

The nuclear gene (c-mos) and mitochondrial genes (CYT B and ND2) sequences, representing 44 phasianid species and 26 genera (mainly distributed in China), were used to study the phylogeny of the genus Perdix, which comprises three partridge species. Maximum parsimony and Bayesian methods were employed, and the analysis of mitochondrial sequence data and the combined dataset showed that Perdix is specifically related either to typical pheasants or to Ithaginis. Phylogenetic trees also indicated that: (1) Perdix is monophyletic; (2) the Tibetan partridge (Perdix hodgsoniae) has been consistently placed as basal to all other Perdix, and the Daurian partridge (Perdix dauuricae) is placed sister to gray partridge (Perdix perdix); (3) the Daurian partridge subspecies przewalskii and Tibetan partridge subspecies hodgsoniae are basal to other subspecies in their species clade, respectively. Speciation in Perdix was likely promoted by the late Pliocene/early Pleistocene intensive uplift of the Tibetan Plateau and by Pleistocene glaciations.

The uplift of the Qinghai-Tibet Plateau and glacial oscillations triggered the diversification of Tetraogallus (Galliformes, Phasianidae).

The Qinghai-Tibet Plateau (QTP) plays an important role in avian diversification. To reveal the relationship between the QTP uplift and avian diversification since the Late Cenozoic, here, we analyzed the phylogenetic relationship and biogeographical pattern of the genus Tetraogallus (Galliformes, Phasianidae) and the probable factors of speciation in the period of the QTP uplift inferred from concatenated data of four nuclear and five mitochondrial genes using the method of the Bayesian inference. Phylogenetic analysis indicated that T. himalayensis had a close relationship with T. altaicus and conflicted with the previous taxonomy of dark-bellied and white-bellied groups. The molecular clock showed that the speciation of Tetraogallus was profoundly affected by the uplift of the QTP and glacial oscillations. Biogeographic analysis suggested that the extant snowcocks originated from the QTP, and the QTP uplift and glacial oscillations triggered the diversification of Tetraogallus ancestor. Specifically, the uplift of the mountain provided a prerequisite for the colonization of snowcocks Tetraogallus as a result of the collision between the Indian and the Arab plates and the Eurasian plate, in which ecological isolation (the glacial and interglacial periods alternate) and geographical barrier had accelerated the Tetraogallus diversification process. Interestingly, we discovered hybrids between T. tibetanus and T. himalayensis for the first time and suggested that T. tibetanus and T. himalayensis hybridized after a second contact during the glacial period. Here, we proposed that the hybrid offspring was the ancestor of the T. altaicus. In conclusion, the uplift of QTP and glacial oscillations triggered the snowcocks colonization, and then, isolation and introgression hybridization promoted diversification.

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

BACKGROUND: The 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. RESULTS: Mitochondrial 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. CONCLUSION: It 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.

Phylogeography of the ring-necked pheasant (Phasianus colchicus) in China.

The ring-necked pheasants (Phasianus colchicus) are widely distributed in China. We used mitochondrial DNA control-region data to investigate the origin and past demographic changes in 139 ring-necked pheasants (P. colchicus) sampled from the species' distribution range. A total of 1078 nucleotides from the control region of mitochondrial DNA were sequenced, and 88 polymorphic positions defined 102 haplotypes. High level of genetic diversity was detected in all populations studied which could be associated with the wide ecological distributions and niche variation. Phylogenetic analyses of all haplotypes identified five major clades. The haplotypes of Gray-rumped Pheasants existed in the three clades: A (western clade), B (eastern clade) and C (Sichuan Basin clade). Two haplotypes of Kirghiz Pheasants were in the clade B, and the rest haplotype of Kirghiz Pheasants formed the clade D. Only one haplotype from White-winged Pheasants made up clade E. The results of AMOVA showed a low gene flow (Nm=0.44) and significant genetic differentiation (Fst=0.31, P<0.001) among all populations. Based on the divergence time, we speculate that the divergence of the ring-necked pheasant occurring in the late Pleistocene may have resulted from three events: (1) the uplift of Qinghai-Tibet Plateau, (2) the existence of Qinling Mountains and Liupan Mountains, (3) the isolation of Sichuan Basin. Demographic population expansion was strongly confirmed by the non-significant mismatch distribution analysis. The described subspecies of the ring-necked pheasant could not be supported by the phylogeographical structuring.

Phylogeography of Tibetan snowcock (Tetraogallus tibetanus) in Qinghai-Tibetan Plateau.

Data from eight microsatellite loci were used to infer the evolutionary and past demographic processes in 97 Tibetan snowcocks sampled from eight different geographical locations on the Qinghai-Tibetan Plateau. Analysis of the microsatellite DNA markers indicated that Tibetan snowcock on the plateau were geographically structured, and that phylogenetic analyses identified three phylogroups, namely those from Xunhua, the Qilian Mountains and all others. The use of Bayesian Clustering and Population Assignment analyses of the microsatellite genotypes revealed clear differentiation among the eight sampled groups of Tibetan snowcock, indicating strong isolation of these sub-populations. Therefore, we suggested that the distribution pattern of Tibetan snowcock observed today resulted from adaptation to the climatic conditions and glacial cycles on the Qinghai-Tibetan Plateau. In addition, BOTTLENECK analysis indicated that Tibetan snowcock had recently passed through evolutionary bottlenecks. These results suggested that effective conservation measures should be undertaken to protect Tibetan snowcock from an increased probability of extinction.

Phylogenetic relationships of four endemic genera of the Phasianidae in China based on mitochondrial DNA control-region genes.

The taxonomic status of some genera within the Phasianidae remains controversial. To demonstrate the phylogenetic relationships of four endemic genera (Tetraophasis, Ithaginis, Crossoptilon and Chrysolophus) and other 11 genera of Phasianidae in China, a total of 1070 nucleotides of mitochondrial DNA (mtDNA) control-region genes were sequenced. There are 376 variable sites including 345 parsimony sites. The genetic distance ranged from 0.067 (Chrysolophus and Phasianus) to 0.181 (Perdix and Bambusicola) among the 15 genera. Maximum likelihood method was used to construct a phylogenetic tree, which grouped all the genera into two deeply divergent clades. Perdix was shown to be a non-partridge genus. Alternatively, it appears ancestral to either partridges or pheasants. The sibling taxa of the four endemic genera were Lophophorus, Tragopan, Lophura and Phasianus, respectively. Calibrated rates of molecular evolution suggested that the divergence time between the four genera and related taxa was 4.00-5.00 million years ago, corresponding to the Pliocene. Considering their molecular phylogenetics, fossil and geographical distribution patterns, the four endemic genera might have originated in the southwestern mountains in China.

Cladogenesis and phylogeography of the lizard Phrynocephalus vlangalii (Agamidae) on the Tibetan plateau.

Phrynocephalus vlangalii is restricted to dry sand or Gobi desert highlands between major mountain ranges in the Qinghai (Tibetan) Plateau. Mitochondrial DNA (mtDNA) sequence (partial ND2, tRNA(Trp) and partial tRNA(Ala)) was obtained from 293 Phrynocephalus sampled from 34 sites across the plateau. Partitioned Bayesian and maximum parsimony phylogenetic analyses revealed that P. vlangalii and two other proposed species (P. erythrus and P. putjatia) together form a monophyletic mtDNA clade which, in contrast with previous studies, does not include P. theobaldi and P. zetangensis. The main P. vlangalli clade comprises seven well-supported lineages that correspond to distinct geographical areas with little or no overlap, and share a most recent common ancestor at 5.06 +/- 0.68 million years ago (mya). This is much older than intraspecific lineages in other Tibetan animal groups. Analyses of molecular variance indicated that most of the observed genetic variation occurred among populations/regions implying long-term interruption of maternal gene flow. A combined approach based on tests of population expansion, estimation of node dates, and significance tests on clade areas indicated that phylogeographical structuring has been primarily shaped by three main periods of plateau uplift during the Pliocene and Pleistocene, specifically 3.4 mya, 2.5 mya and 1.7 mya. These periods corresponded to the appearance of several mountain ranges that formed physical barriers between lineages. Populations from the Qaidam Basin are shown to have undergone major demographic and range expansions in the early Pleistocene, consistent with colonization of areas previously covered by the huge Qaidam palaeolake, which desiccated at this time. The study represents one of the most detailed phylogeographical analyses of the Qinghai Plateau to date and shows how geological events have shaped current patterns of diversity.

Changes in intestinal microbiota across an altitudinal gradient in the lizard Phrynocephalus vlangalii.

High altitude is an important driving force in animal evolution. However, the effect of altitude on gut microbial communities in reptiles has not been examined in detail. Here, we investigated the intestinal microbiota of three populations of the lizard Phrynocephalus vlangalii living at different altitudes using 16S rRNA gene sequencing. Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant phyla. Bacteroides, Odoribacter, and Parabacteroides were the most abundant genera. Significant differences in the intestinal microbiota composition were found among the three populations from different altitudes. The proportions of Verrucomicrobia and Akkermansia decreased, whereas Bacteroides increased significantly with altitude. Greater abundance of Bacteroides at higher altitude led to the fractional increase in the phylum Bacteroides relative to other phyla. Hypoxia may be the main factor that caused intestinal microbiota variation in P. vlangalii along the altitude gradient. Overall, our study suggested that the community composition and structure of intestinal microbiota of the lizard P. vlangalii varied along altitudes, and such differences likely play a certain role in highland adaptation. Our findings warrant a further study that would determine whether ambient and body temperatures play a key role in the modulation of intestinal microbiota in reptiles.

Phylogeography of chukar partridge (Alectoris chukar) in China based on mtDNA control region.

The chukar partridge (Alectoris chukar) is distributed in north and northwest of China, in mountainous areas that were heavily affected by cyclic climate and landscape changes during the last Pleistocene glaciations. Some partridge populations have colonized and expanded their present ranges only after deglaciation and recent deforestation by human. Consequently, partridges from different areas could be genetically differentiated. In this study, a 1152-1154 bp portion of the mitochondrial DNA control region were analyzed for all 279 specimens collected from 28 populations through their distribution in China. A total number of 91 haplotypes were defined by 113 variable sites. The mean haplotype diversity and nucleotide diversity were 0.939 ± 0.008 and 0.0030 ± 0.0017, respectively, for chukar. Haplotype diversity among the 28 populations varied from 0.600 ± 0.215 (HH) to 1.000 ± 0.272 (SBC), and nucleotide diversity ranged from 0.0006 ± 0.0007 (HJ) to (0.0071 ± 0.0041) (HEG). The nucleotide diversity of chukar was descending from west to east and a possible historical scenario might be that A. chukar inhabited central Asia, and then dispersed eastward. Phylogenetic analyses indicated that there was no distinct phylogeographic structure in chukar populations in China. Haplotype network of chukar was star-like with some common haplotypes shared by different samples came from different populations as center. Both unstructured phylogeographic tree and star-like haplotype network are signatures of population expansion.

The geography and timing of genetic divergence in the lizard Phrynocephalus theobaldi on the Qinghai-Tibetan plateau.

The Qinghai-Tibetan Plateau (QTP) represents one of the earth's most significant physical features and there is increasing interest in the historical generation of biodiversity within this region. We hypothesized that there should be clear geographically coherent genetic structuring within one of the world's highest altitude lizards, Phrynocephalus theobaldi, due to considerable historical population fragmentation in this environment. This was tested using a major mitochondrial DNA (mtDNA) survey and sequencing of two nuclear markers (AME and RAG-1) from P. theobaldi, from across the southern QTP. A Bayesian method (BPEC) was used to detect four geographically structured mtDNA clusters. A Bayesian phylogenetic tree, together with associated dating analyses, supported four corresponding evolutionary lineages with a timing of 3.74-7.03 Ma for the most basal P. theobaldi split and Pliocene splits of 2.97-5.79 Ma and 2.40-5.39 Ma in the two daughter lineages. Himalayan uplift and changes in the Jilong basin may have contributed to these divergences, but uplift of the Gangdese mountains is rejected due to its timing. The nuclear markers appeared to be sorted between the four mtDNA groups, and species delimitation analyses supported the four phylogeographical groups as candidate species. The study contributes to our understanding of biodiversity on the QTP.

Asymmetrical introgression patterns between rusty-necklaced partridge (Alectoris magna) and chukar partridge (Alectoris chukar) in China.

The rusty-necklaced partridge (Alectoris magna) and the chukar partridge (Alectoris chukar) are the most common gamebirds in northern China. Previous comparisons of mitochondrial DNA (mtDNA) have revealed an introgression phenomenon between 2 species of partridge in the Liupan Mountain region of China. mtDNA is maternally inherited, making it difficult to determine the origin of parental genes. We assessed the genetic variation and gene flow between these 2 species of partridges using 8 microsatellite loci as neutral diagnostic markers in 171 samples from the hybrid zone. Our data revealed an extensive divergence of genetic structure between populations of rusty-necklaced partridges and chukar partridges. In this study, we found that 19 samples had been previously morphologically identified as rusty-necklaced partridge were genetically identified as hybrids through Bayesian analysis using STRUCTURE analysis. These hybrids exhibited a mosaic of alleles that were derived from both parental lineages. However, chukar partridges did not present the genotype of the rusty-necklaced partridge. Thus, our findings demonstrate that the hybridization between the 2 species was the result of asymmetrical introgression, with gene flow occurring only from the chukar partridge to the rusty-necklaced partridge. In addition, we also note the high linkage disequilibrium in populations of the rusty-necklaced partridge. These results indicate that although unidirectional introgression did not reduce genetic diversity of the Alectoris partridges, it affected the balance of gene flow between populations. The data from microsatellite DNA prompted our concern about the genetic integrity of the rusty-necklaced partridge.