Population Genomics Reveals Low Genetic Diversity and Adaptation to Hypoxia in Snub-Nosed Monkeys.

Snub-nosed monkeys (genus Rhinopithecus) are a group of endangered colobines endemic to South Asia. Here, we re-sequenced the whole genomes of 38 snub-nosed monkeys representing four species within this genus. By conducting population genomic analyses, we observed a similar load of deleterious variation in snub-nosed monkeys living in both smaller and larger populations and found that genomic diversity was lower than that reported in other primates. Reconstruction of Rhinopithecus evolutionary history suggested that episodes of climatic variation over the past 2 million years, associated with glacial advances and retreats and population isolation, have shaped snub-nosed monkey demography and evolution. We further identified several hypoxia-related genes under selection in R. bieti (black snub-nosed monkey), a species that exploits habitats higher than any other nonhuman primate. These results provide the first detailed and comprehensive genomic insights into genetic diversity, demography, genetic burden, and adaptation in this radiation of endangered primates.

Implications of genetics and current protected areas for conservation of 5 endangered primates in China.

Most of China's 24-28 primate species are threatened with extinction. Habitat reduction and fragmentation are perhaps the greatest threats. We used published data from a conservation genetics study of 5 endangered primates in China (Rhinopithecus roxellana, R. bieti, R. brelichi, Trachypithecus francoisi, and T. leucocephalus); distribution data on these species; and the distribution, area, and location of protected areas to inform conservation strategies for these primates. All 5 species were separated into subpopulations with unique genetic components. Gene flow appeared to be strongly impeded by agricultural land, meadows used for grazing, highways, and humans dwellings. Most species declined severely or diverged concurrently as human population and crop land cover increased. Nature reserves were not evenly distributed across subpopulations with unique genetic backgrounds. Certain small subpopulations were severely fragmented and had higher extinction risk than others. Primate mobility is limited and their genetic structure is strong and susceptible to substantial loss of diversity due to local extinction. Thus, to maximize preservation of genetic diversity in all these primate species, our results suggest protection is required for all sub-populations. Key priorities for their conservation include maintaining R. roxellana in Shennongjia national reserve, subpopulations S4 and S5 of R. bieti and of R. brelichi in Fanjingshan national reserve, subpopulation CGX of T. francoisi in central Guangxi Province, and all 3 T. leucocephalus sub-populations in central Guangxi Province.

Full-length Numt analysis provides evidence for hybridization between the Asian colobine genera Trachypithecus and Semnopithecus.

The phylogenetic position of the genus Semnopithecusis unresolved because of topological incongruence when inferred using different molecular markers. Although some studies proposed hybridization between the genera Semnopithecus and Trachypithecus to explain the discordance, no conclusive evidence for hybridization has been identified. To address this issue, we used DNA walking and long-range PCR to describe a nuclear mitochondrial DNA (Numt) segment present in Trachypithecus pileatus which extends over more than 15 kb, and represents approximately 92% of the entire mitochondrial genome. We assessed the presence of this Numt in 16 other colobine species, including four species of the genus Trachypithecus, six species of the genus Semnopithecus, and representative species of six other genera belonging to the subfamily Colobinae. We failed to detect a Numt sequence in any of the other colobine species except for T. shortridgei, which is closely related to T. pileatus. The sister relationship of this Numt within the genus Semnopithecus suggests that it was derived from the mt genome of the genus Semnopithecus and invaded the nuclear genome of T. pileatus by unidirectional introgression hybridization. These results offer the most conclusive evidence for the existence of hybridization between Semnopithecus and Trachypithecus.

Differentiated adaptive evolution, episodic relaxation of selective constraints, and pseudogenization of umami and sweet taste genes TAS1Rs in catarrhine primates.

BACKGROUND: Umami and sweet tastes are two important basic taste perceptions that allow animals to recognize diets with nutritious carbohydrates and proteins, respectively. Until recently, analyses of umami and sweet taste were performed on various domestic and wild animals. While most of these studies focused on the pseudogenization of taste genes, which occur mostly in carnivores and species with absolute feeding specialization, omnivores and herbivores were more or less neglected. Catarrhine primates are a group of herbivorous animals (feeding mostly on plants) with significant divergence in dietary preference, especially the specialized folivorous Colobinae. Here, we conducted the most comprehensive investigation to date of selection pressure on sweet and umami taste genes (TAS1Rs) in catarrhine primates to test whether specific adaptive evolution occurred during their diversification, in association with particular plant diets. RESULTS: We documented significant relaxation of selective constraints on sweet taste gene TAS1R2 in the ancestral branch of Colobinae, which might correlate with their unique ingestion and digestion of leaves. Additionally, we identified positive selection acting on Cercopithecidae lineages for the umami taste gene TAS1R1, on the Cercopithecinae and extant Colobinae and Hylobatidae lineages for TAS1R2, and on Macaca lineages for TAS1R3. Our research further identified several site mutations in Cercopithecidae, Colobinae and Pygathrix, which were detected by previous studies altering the sensitivity of receptors. The positively selected sites were located mostly on the extra-cellular region of TAS1Rs. Among these positively selected sites, two vital sites for TAS1R1 and four vital sites for TAS1R2 in extra-cellular region were identified as being responsible for the binding of certain sweet and umami taste molecules through molecular modelling and docking. CONCLUSIONS: Our results suggest that episodic and differentiated adaptive evolution of TAS1Rs pervasively occurred in catarrhine primates, most concentrated upon the extra-cellular region of TAS1Rs.

Insights into genetic variation and demographic history of sharpnose rays: examinations of three species of Telatrygon (Elasmobranchii, Dasyatidae) from the Indo-West Pacific.

Coastal and demersal chondrichthyans (sharks, rays, and skates) are expected to exhibit high levels of genetic differentiation in areas of complex geomorphology. Population genetic studies investigating the extent to which demographic history shapes the genetic structure of these fishes are rare. Here, we combined mitochondrial DNA (Cytb and ND2) and 8 nuclear microsatellite loci from 244 individuals to examine the population genetic structure and demographic history of the 3 Indo-West Pacific species of sharpnose rays (Telatrygon zugei, Telatrygon biasa, and Trygon crozieri). High levels of genetic variation both within and between species were identified. Phylogenetic analysis partitioned haplotypes into 2 lineages supporting divergence of T. zugei from T. crozieri and T. biasa during the Pleistocene. Furthermore, microsatellite-based clustering analyses identified 4 genetic groups (i.e. T. zugei from Japan, T. zugei from coastal China, T. biasa from Gulf of Thailand, and T. crozieri from the Andaman Sea). Measurements of genetic differentiation also support these 4 groups. Additionally, Pleistocene demographic expansions were examined in all genetic groups. The climate oscillations and current hydrologic cycles in the Indo-West Pacific appear to coincide with the hypothesis regarding speciation and the observed demographic history trends of the sharpnose rays. Considering the species group has, until recently, been thought to be one species, these results are critical for defining management units and guiding conservation efforts to preserve stingray biodiversity.

Insights into the Evolution of Neoteny from the Genome of the Asian Icefish Protosalanx chinensis.

Salangids, known as Asian icefishes, represent a peculiar radiation within the bony fish order Protacanthopterygii where adult fish retain larval characteristics such as transparent and miniaturized bodies and a cartilaginous endoskeleton into adulthood. Here, we report a de novo genome of Protosalanx chinensis, the most widely distributed salangid lineage. The P. chinensis genome assembly is more contiguous and complete than a previous assembly. We estimate that P. chinensis, salmons, trouts, and pikes diverged from a common ancestor 185 million years ago. A juxtaposition with other fish genomes revealed loss of the genes encoding ectodysplasin-A receptor (EDAR), SCPP1, and four Hox proteins and likely lack of canonical fibroblast growth factor 5 (FGF5) function. We also report genomic variations of P. chinensis possibly reflecting the immune system repertoire of a species with a larval phenotype in sexually mature individuals. The new Asian icefish reference genome provides a solid foundation for future studies.

Per- and polyfluoroalkyl substances (PFASs) in the blood of two colobine monkey species from China: Occurrence and exposure pathways.

Per-/polyfluoroalkyl substances (PFASs), which are widely used in industrial and commercial products, have been identified as global and ubiquitous pollutants. Despite this, limited data are available regarding the impacts of PFAS exposure and intake in non-human primates. Here, we report for the first time on the occurrence of PFASs in the blood and dietary sources of two rare and endangered primate species, namely, the golden snub-nosed monkey (Rhinopithecus roxellana) and Francois' leaf monkey (Trachypithecus francoisi). Results showed that perfluorooctanoate (PFOA) and perfluorononanoate (PFNA) were dominant and found at the highest proportions in the blood of both species at the four study sites. The ∑PFAS levels in blood samples from captive golden snub-nosed monkeys in Tongling Zoo (mean: 2.51 ng/mL) and Shanghai Wild Zoo (3.52 ng/mL) near urbanized areas were one order of magnitude higher than the levels in wild monkeys from Shennongjia Nature Reserve (0.27 ng/mL). Furthermore, significant age positive relationships for perfluorodecanoic acid (PFDA), perfluorooctane sulfonate (PFOS), and 6:2 chlorinated polyfluorinated ether sulfonates (6:2 Cl-PFESA) were observed in both golden snub-nosed monkeys at Shanghai Wild Zoo and Francois' leaf monkeys at Wuzhou Breeding Center. In addition, PFAS levels in frequently consumed food and drinking water were analyzed for Francois' leaf monkeys. Results showed that tree leaves accounted for the highest percentage of total daily intake of PFASs, especially PFOA, thus highlighting tree leaf consumption as a primary PFAS exposure route for this species. Overall, however, dietary exposure to PFASs was of relatively low risk to Francois' leaf monkey health.

Complete mitochondrial genome of the Macaca mulatta brevicaudus.

The complete mitochondrial sequence of the Macaca mulatta brevicaudus has been determined by mapping the raw data to previously published mitochondrial assemblies of the corresponding species. The total sequence length is 16,561 bp, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one D-loop control region. The base composition of the mtDNA genome is 31.77% A, 25.14% T, 30.33% C, and 12.76% G, with an AT content of 56.90%. The arrangement of genes in M. m. brevicaudus is identical to that of M. mulatta. All genes are encoded on the heavy strand with the exception of ND6 and eight tRNA genes. The mitochondrial genome of M. m. brevicaudus presented here will contribute to a better understanding of the population genetics, help to protect its genetic diversity and resolve phylogenetic relationships within the family.

Complete mitochondrial genome of the crested black macaque (Macaca nigra).

The complete mitochondrial sequence of the crested black macaque (Macaca nigra) has been determined by mapping the raw data to previously published mitochondrial assemblies of the corresponding species. The total sequence length is 16,564 bp and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 D-loop control region. The base composition of mtDNA genome is 31.76% A, 25.27% T, 30.17% C, and 12.80% G, with an AT content of 57.03%. The arrangement of genes in M. nigra is identical to that of M. mulatta. All genes are encoded on the heavy strand with the exception of ND6 and eight tRNA genes. The mitochondrial genome of M. nigra presented here will contribute to a better understanding of the population genetics, help to protect its genetic diversity and resolve phylogenetic relationships within the family.

Complete mitochondrial genome of the capped langur (Trachypithecus pileatus).

The complete mitochondrial sequence of the capped langur (Trachypithecus pileatus) has been determined using long amplification polymerase chain reaction (LA-PCR). The total sequence length is 16,526 bp and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 D-loop locus. The base composition of H-strand is 31.9% A, 29.1% T, 26.2% C and 12.8% G, with an AT content of 55.3%. The arrangement of genes in T. pileatus is identical to that of other primate species. All genes are encoded on the heavy strand with the exception of ND6 and eight tRNA genes. The mitochondrial genome of T. pileatus presented here will contribute to a better understanding of the species' population genetics, helping to protect its genetic diversity and resolve phylogenetic relationships within the family.

Species identification refined by molecular scatology in a community of sympatric carnivores in Xinjiang, China.

Many ecological studies and conservation management plans employ noninvasive scat sampling based on the assumption that species' scats can be correctly identified in the field. However, in habitats with sympatric similarly sized carnivores, misidentification of scats is frequent and can lead to bias in research results. To address the scat identification dilemma, molecular scatology techniques have been developed to extract DNA from the donor cells present on the outer lining of the scat samples. A total of 100 samples were collected in the winter of 2009 and 2011 in Taxkorgan region of Xinjiang, China. DNA was extracted successfully from 88% of samples and genetic species identification showed that more than half the scats identified in the field as snow leopard (Panthera uncia) actually belonged to fox (Vulpes vulpes). Correlation between scat characteristics and species were investigated, showing that diameter and dry weight of the scat were significantly different between the species. However it was not possible to define a precise range of values for each species because of extensive overlap between the morphological values. This preliminary study confirms that identification of snow leopard feces in the field is misleading. Research that relies upon scat samples to assess distribution or diet of the snow leopard should therefore employ molecular scatology techniques. These methods are financially accessible and employ relatively simple laboratory procedures that can give an indisputable response to species identification from scats.

Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history.

Colobines are a unique group of Old World monkeys that principally eat leaves and seeds rather than fruits and insects. We report the sequencing at 146× coverage, de novo assembly and analyses of the genome of a male golden snub-nosed monkey (Rhinopithecus roxellana) and resequencing at 30× coverage of three related species (Rhinopithecus bieti, Rhinopithecus brelichi and Rhinopithecus strykeri). Comparative analyses showed that Asian colobines have an enhanced ability to derive energy from fatty acids and to degrade xenobiotics. We found evidence for functional evolution in the colobine RNASE1 gene, encoding a key secretory RNase that digests the high concentrations of bacterial RNA derived from symbiotic microflora. Demographic reconstructions indicated that the profile of ancient effective population sizes for R. roxellana more closely resembles that of giant panda rather than its congeners. These findings offer new insights into the dietary adaptations and evolutionary history of colobine primates.

Mitochondrial genome of the Guizhou snub-nosed monkey (Rhinopithecus brelichi).

The Guizhou snub-nosed monkey (Rhinopithecus brelichi) is an endangered species which is endemic to a small region in the fanjing mountain national nature reserve in Guizhou province, China. In this study, we determined the complete mitochondrial genome of R. brelichi. The results showed that the total length of the mitogenome was 16,548 bp and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region. Overall base composition of the complete mitochondrial DNA was 32.35% A, 29.28% T, 25.54% C and 12.83% G. All the genes in R. brelichi were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand.

Mitochondrial genome of Plateau zokor Myospalax baileyi.

Plateau zokors Myospalax baileyi are subterranean rodents and endemic to the cold and hypoxic (2800-4300 m above sea level) climate of the farm, prairie, alpine prairie, and meadow habitats across the Tibetan plateau. The complete mitochondrial (mt) genome of M. baileyi has been determined. Our results showed that the total length of the mitogenome was 16,351 bp, and had a gene content of 13 protein coding, 22 tRNAs and 2 rRNAs. Except for the seven tRNA and Nd6 genes, all other mt genes are encoded on the heavy strand. The overall base composition of the heavy strand is 33.65% A, 29.65% T, 24.42% C, and 12.28% G, with an AT content of 63.3%.