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.

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.

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.

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.

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.

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.

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.

The complete mitochondrial genome of Himalayan Snowcock (Tetraogallus himalayensis).

We reported here the first complete sequences of mitogenome of Tetraogallus himalayensis obtained by next generation sequencing methods. The assembled mitogenome is a 16 692 bp circle, comprising of 13 protein-coding genes, two rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and one control region. The resultant phylogenetic tree supported T. himalayensis and T. tibeanus are sister taxon, and Tetraogallus with Alectoris and coturnix formed a monophyletic group.

Refugia persistence of Qinghai-Tibetan plateau by the cold-tolerant bird Tetraogallus tibetanus (Galliformes: Phasianidae).

Most of the temperate species are expected to have moved to lower altitudes during the glacial periods of the Quaternary. Here we tested this hypothesis in a cold-tolerant avian species Tibetan snowcock (Tetraogallus tibetanus) using two segments of mitochondrial gene (a 705bp Cytochrome-b; abbrev. Cyt-b and an 854 bp Control Region; abbrev. CR) and eight microsatellite loci by characterizing population differentiation and gene flow across its range. Combined (Cyt-b + CR) datasets detected several partially lineages with poor support. Microsatellite data, however, identified two distinct lineages congruent with the geographically separated western and central regions of Qinghai-Tibetan Plateau (QTP). The phylogeographic patterns that we observed might be explained by a combination of vicariance events that led to local isolation of T. tibetanus during warm periods and range expansions and population intermixing during cold periods. The results of this study add to our knowledge of population differentiation and connectivity in high altitude mountain ecosystems.

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.

The proximate causes of sexual size dimorphism in Phrynocephalus przewalskii.

Sexual size dimorphism (SSD) is a common phenomenon and is a central topic in evolutionary biology. Recently, the importance of pursuing an ontogenetic perspective of SSD has been emphasized, to elucidate the proximate physiological mechanisms leading to its evolution. However, such research has seldom focused on the critical periods when males and females diverge. Using mark-recapture data, we investigated the development of SSD, sex-specific survivorship, and growth rates in Phrynocephalus przewalskii (Agamidae). We demonstrated that both male and female lizards are reproductively mature at age 10-11 months (including 5 months hibernation). Male-biased SSD in snout-vent length (SVL) was only found in adults and was fully expressed at age 11 months (June of the first full season of activity), just after sexual maturation. However, male-biased SSD in tail length (TL), hind-limb length (LL), and head width (HW) were fully expressed at age 9-10 months, just before sexual maturation. Analysis of age-specific linear growth rates identified sexually dimorphic growth during the fifth growth month (age 10-11 months) as the proximate cause of SSD in SVL. The males experienced higher mortality than females in the first 2 years and only survived better than females after SSD was well developed. This suggests that the critical period of divergence in the sizes of male and female P. przewalskii occurs between 10 and 11 months of age (May to June during the first full season of activity), and that the sexual difference in growth during this period is the proximate cause. However, the sexual difference in survivorship cannot explain the male-biased SSD in SVL. Our results indicate that performance-related characteristics, such as TL, HW, and LL diverged earlier than SVL. The physiological mechanisms underlying the different growth patterns of males and females may reflect different energy allocations associated with their different reproductive statuses.

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.

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.

[A new record of the bird subspecies Black-crested Bulbul (Pycnonotus flaviventris johnsoni) in China].

Several Black-crested Bulbul (Pycnonotus flaviventris) with red throats were observed and photographed in December 2010 and April 2011 in the Youjiang District (N23(o)54', E06(o)36', altitude 179 m) and Jingxi County(N22(o)59', E1 06(o)40', altitude 354 m) of Baise city, northwestern Guangxi, in southern China. These individuals belong to subspecies johnsoni, recorded previously in central and southeastern Thailand as well as the southern Indochina Region. This sighting provides a new record of the subspecies within China, warranting a discussion on the classification and distribution of Pycnonotus flaviventris.

Patterns of diversity, areas of endemism, and multiple glacial refuges for freshwater crabs of the genus Sinopotamon in China (Decapoda: Brachyura: Potamidae).

Previous research has shown that the geographical distribution patterns of freshwater fishes and amphibians have been influenced by past climatic oscillations in China resulting from Pleistocene glacial activity. However, it remains unknown how these past changes have impacted the present-day distribution of Chinese freshwater crabs. This work describes the diversity and endemism of freshwater crabs belonging to Sinopotamon, a highly speciose genus endemic to China, and evaluates its distribution in terms of topography and past climatic fluctuations. Species diversity within Sinopotamon was found to be concentrated in an area from the northeastern edge of the Yunnan-Guizhou Plateau to the Jiangnan Hills, and three areas of endemism were identified. Multiple regression analysis between current climatic variables and Sinopotamon diversity suggested that regional annual precipitation, minimum temperature in the coldest month, and annual temperature range significantly influenced species diversity and may explain the diversity patterns of Sinopotamon. A comparison of ecological niche models (ENMs) between current conditions and the last glacial maximum (LGM) showed that suitable habitat for Sinopotamon in China severely contracted during the LGM. The coincidence of ENMs and the areas of endemism indicated that southeast of the Daba Mountains, and central and southeastern China, are potential Pleistocene refuges for Sinopotamon. The presence of multiple Pleistocene refuges within the range of this genus could further promote inter- and intraspecific differentiations, and may have led to high Sinopotamon species diversity, a high endemism rate and widespread distribution.

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.

[Phylogeny and genetic diversity of Phrynocephalus przewalskii].

Phrynocephalus przewalskii is one kind of lizards inhabiting inclusively in the desert that has controversial viewpoints on its phylogeny. Based on mitochondrial ND2 gene of 119 samples from 12 geographic populations, we analyzed the effects of environmental factors on the variation of genetic diversity, as well as its relationship to P. versicolor. The results showed that these populations clustered into three major lineages, with P. versicolor embedded within one lineage. The twelve populations had great genetic diversity variation, which was tightly linked with local altitude, annual precipitation, and variation of annual precipitation. High latitudes, increased annual precipitation and great variation in annual precipitations may all have resulted in the decrease of genetic diversity. It thus assumed that altitude can change the genetic diversity of different geographic populations of P. przewalskii resulting from the effects of different local annual precipitation.

Bone morphogenetic protein (BMP) signaling regulates mitotic checkpoint protein levels in human breast cancer cells.

Aberrant expression of mitotic checkpoint genes compromises mitotic checkpoint, leads to chromosome instability and tumorigenesis. However, the cell signals that control mitotic checkpoint gene expression have not been reported so far. In the present study we show that, in human breast cancer cells, chemical inhibition of Bone morphogenetic proteins (BMPs), but not Transforming Growth Factor-ß (TGF-ß), abrogates the mitotic arrest induced by nocodazole. Protein expression analysis reveals that inhibition of BMP signaling dramatically down regulates protein levels of mitotic checkpoint components BUB3, Hec1, TTK and MAD2, but inhibition of TGF-ß has relatively minor effect on the expression of these proteins. Activation of BMP signaling specifically up regulates BUB3, and activation of Activin A signaling globally down regulates these proteins level. Furthermore, overexpressing MAD2, TTK, BUB3 or Hec1 significantly rescues the mitotic arrest defect caused by BMP inhibition. Our results demonstrated for the first time that TGF-ß family cytokines are cellular signals regulating mitotic checkpoint and perturbations in intrinsic BMP signaling could lead to suppression of mitotic checkpoint signaling by downregulating key checkpoint proteins. The results suggest a possible mechanism by which dysregulation of TGF-ß signaling causes mitotic checkpoint defects and drives tumorigenesis. The finding also provides a potential and more specific strategy for cancer prevention by targeting BMP and mitotic checkpoint connection.

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.