Project description:Long-distance migrations of wildlife have been identified as important biological phenomena, but their conservation remains a major challenge. The Mongolian Gobi is one of the last refuges for the Asiatic wild ass (Equus hemionus) and other threatened migratory mammals. Using historic and current distribution ranges, population genetics, and telemetry data we assessed the connectivity of the wild ass population in the context of natural and anthropogenic landscape features and the existing network of protected areas. In the Mongolian Gobi mean biomass production is highly correlated with human and livestock density and seems to predict wild ass occurrence at the upper level. The current wild ass distribution range largely falls into areas below the 250 gC/m(2)/year productivity isoline, suggesting that under the present land use more productive areas have become unavailable for wild asses. Population genetics results identified two subpopulations and delineated a genetic boundary between the Dzungarian and Transaltai Gobi for which the most likely explanation are the mountain ranges separating the two areas. Home ranges and locations of 19 radiomarked wild asses support the assumed restricting effects of more productive habitats and mountain ranges and additionally point towards a barrier effect of fences. Furthermore, telemetry data shows that in the Dzungarian and Transaltai Gobi individual wild ass rarely ventured outside of the protected areas, whereas in the southeast Gobi asses only spend a small fraction of their time within the protected area network. Conserving the continuity of the wild ass population will need a landscape level approach, also including multi-use landscapes outside of protected areas, particularly in the southeast Gobi. In the southwest Gobi, allowing for openings in the border fence to China and managing the border area as an ecological corridor would connect three large protected areas together covering over 70,000 km(2) of wild ass habitat.
Project description:An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from blood samples in two equid species: Somali wild ass and Grevy's zebra. n=12 blood samples
Project description:Taxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genus Equus. To more reliably determine the evolution and phylogeographic history of the endangered Asiatic wild ass, we studied the genetic diversity and inter-relationships of both extinct and extant populations over the last 100,000 years, including samples throughout its previous range from Western Europe to Southwest and East Asia. Using 229 bp of the mitochondrial hypervariable region, an approach which allowed the inclusion of information from extremely poorly preserved ancient samples, we classify all non-African wild asses into eleven clades that show a clear phylogeographic structure revealing their phylogenetic history. This study places the extinct European wild ass, E. hydruntinus, the phylogeny of which has been debated since the end of the 19th century, into its phylogenetic context within the Asiatic wild asses and reveals recent mitochondrial introgression between populations currently regarded as separate species. The phylogeographic organization of clades resulting from these efforts can be used not only to improve future taxonomic determination of a poorly characterized group of equids, but also to identify historic ranges, interbreeding events between various populations, and the impact of ancient climatic changes. In addition, appropriately placing extant relict populations into a broader phylogeographic and genetic context can better inform ongoing conservation strategies for this highly-endangered species.
Project description:Genetic data from extant donkeys (Equus asinus) have revealed two distinct mitochondrial DNA haplogroups, suggestive of two separate domestication events in northeast Africa about 5000 years ago. Without distinct phylogeographic structure in domestic donkey haplogroups and with little information on the genetic makeup of the ancestral African wild ass, however, it has been difficult to identify wild ancestors and geographical origins for the domestic mitochondrial clades. Our analysis of ancient archaeological and historic museum samples provides the first genetic information on the historic Nubian wild ass (Equus africanus africanus), Somali wild ass (Equus africanus somaliensis) and ancient donkey. The results demonstrate that the Nubian wild ass was an ancestor of the first donkey haplogroup. In contrast, the Somali wild ass has considerable mitochondrial divergence from the Nubian wild ass and domestic donkeys. These findings resolve the long-standing issue of the role of the Nubian wild ass in the domestication of the donkey, but raise new questions regarding the second ancestor for the donkey. Our results illustrate the complexity of animal domestication, and have conservation implications for critically endangered Nubian and Somali wild ass.
Project description:Interactions between gut microbiota not only regulate physical health, but also form a vital bridge between the environment and the host, thus helping the host to better adapt to the environment. The improvement of modern molecular sequencing techniques enables in-depth investigations of the gut microbiota of vertebrate herbivores without harming them. By sequencing the 16S rRNA V4-V5 region of the gut microbiota of both the captive and wild kiang in winter and summer, the diversity and function of the microbiota could be compared. The reasons for observed differences were discussed. The results showed that the dominant phyla of the kiang were Bacteroidetes and Firmicutes, and the structure and abundance of the gut microbiota differed significantly between seasons and environments. However, the relatively stable function of the gut microbiota supplies the host with increased adaptability to the environment. The diversity of the intestinal flora of the kiang is relatively low in captivity, which increases their risk to catch diseases to some extent. Therefore, importance should be attached to the impact of captivity on wildlife.
Project description:We report Metagenome from the saline desert soil sample of Little Rann of Kutch, Gujarat State, India. Metagenome consisted of 633,760 sequences with size 141,307,202 bp and 56% G + C content. Metagenome sequence data are available at EBI under EBI Metagenomics database with accession no. ERP005612. Community metagenomics revealed total 1802 species belonged to 43 different phyla with dominating Marinobacter (48.7%) and Halobacterium (4.6%) genus in bacterial and archaeal domain respectively. Remarkably, 18.2% sequences in a poorly characterized group and 4% gene for various stress responses along with versatile presence of commercial enzyme were evident in a functional metagenome analysis.
Project description:The diversity of livestock coat color results from human positive selection and is an indispensable part of breed registration. As an important biodiversity resource, Asiatic wild ass has many special characteristics, including the most visualized feature, its yellowish-brown coat color, and excellent adaptation. To explore the genetic mechanisms of phenotypic characteristics in Asiatic wild ass and its hybrids, we resequenced the whole genome of one Mongolian Kulan (a subspecies of Asiatic wild ass) and 29 Kulan hybrids (Mongolian Kulan ♂×Xinjiang♀), and the ancestor composition indicated the true lineage of the hybrids. XP-EHH (Cross Population Extended Haplotype Homozygosity), θπ-ratio (Nucleotide Diversity Ratio), CLR (Composite Likelihood Ratio) and θπ (Nucleotide Diversity) methods were used to detect the candidate regions of positive selection in Asiatic wild ass and its hybrids. Several immune genes (DEFA1, DEFA5, DEFA7, GIMAP4, GIMAP1, IGLC1, IGLL5, GZMB and HLA) were observed by the CLR and θπ methods. XP-EHH and θπ-ratio revealed that these genes are potentially responsible for coat color (KITLG) and meat quality traits (PDE1B and MYLK2). Furthermore, the heatmap was able to show the clear difference in the haplotype of the KITLG gene between the Kulan hybrids and Asiatic wild ass group and the Guanzhong black donkey group, which is a powerful demonstration of the key role of KITLG in donkey color. Therefore, our study may provide new insights into the genetic basis of coat color, meat quality traits and immunity of Asiatic wild ass and its hybrids.
Project description:Traditional biomarkers for hydrocarbon exposure are not induced by all petroleum substances. The objective of this study was to determine if exposure to a crude oil and different refined oils would generate a common hydrocarbon-specific response in gene expression profiles that could be used as generic biomarkers of hydrocarbon exposure. Juvenile rainbow trout (Oncorhynchus mykiss) were exposed to the water accommodated fraction (WAF) of either kerosene, gas oil, heavy fuel oil, or crude oil for 96 hours. Tissue was collected for RNA extraction and microarray analysis. Exposure to each WAF resulted in a different list of differentially regulated genes, with few genes in common across treatments. Exposure to crude oil WAF changed the expression of genes including CYP1A and GST with known roles in detoxification pathways. These gene expression profiles were compared to others from previous experiments which used a diverse suite of toxicants. Clustering algorithms successfully i dentified gene expression profiles resulting from hydrocarbon exposure. These preliminary analyses highlight the difficulties of using single genes as diagnostic of petroleum hydrocarbon exposures. Further work is needed to determine if multivariate transcriptomic-based biomarkers may be a more effective tool than single gene studies for exposure monitoring of different oils.
Project description:Clostridium botulinum is an important pathogen that causes botulism in humans and animals worldwide. C. botulinum group III strains, which produce a single toxin of type C or D or a chimeric toxin of type C/D or D/C, are responsible for botulism in a wide range of animal species including cattle and birds. We used unbiased high-throughput RNA sequencing (i.e., metatranscriptomics) to identify a strain of group III C. botulinum from a deceased Mongolian wild ass (Equus hemionus). The strain was closely related to some European strains. Genetic analysis of the recovered bacterial sequences showed that the C. botulinum strain identified might represent a type C/D strain of group III. Infection by C. botulinum producing the mosaic toxin of type C/D is the most likely cause of the death of the wild ass.