Boshi Wang

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.

The effect of landscape features on population genetic structure in Yunnan snub-nosed monkeys (Rhinopithecus bieti) implies an anthropogenic genetic discontinuity.

The Tibetan Plateau is one of the top 10 biodiversity hotspots in the world and acts as a modern harbour for many rare species because of its relatively pristine state. In this article, we report a landscape genetic study on the Yunnan snub‐nosed monkey (Rhinopithecus bieti), a primate endemic to the Tibetan Plateau. DNA was extracted from blood, tissue and fecal samples of 135 wild individuals representing 11 out of 15 extant monkey groups. Ten microsatellite loci were used to characterize patterns of genetic diversity. The most striking feature of the population structure is the presence of five subpopulations with distinct genetic backgrounds and unique spatial regions. The population structure of R. bieti appears to be shaped by anthropogenic landscape features as gene flow between subpopulations is strongly impeded by arable land, highways and human habitation. A partial Mantel test showed that 36.23% (r = 0.51, P = 0.01) of the genetic distance was explained by habitat gaps after controlling for the effect of geographical distance. Only 4.92% of the genetic distance was explained by geographical distance in the partial Mantel test, and no significant correlation was found. Estimation of population structure history indicates that environmental change during the last glacial maximum and human impacts since the Holocene, or a combination of both, have shaped the observed population structure of R. bieti. Increasing human activity on the Plateau, especially that resulting in habitat fragmentation, is becoming an important factor in shaping the genetic structure and evolutionary potential of species inhabiting this key ecosystem.

Relatively recent evolution of pelage coloration in Colobinae: phylogeny and phylogeography of three closely related langur species.

To understand the evolutionary processes leading to the diversity of Asian colobines, we report here on a phylogenetic, phylogeographical and population genetic analysis of three closely related langurs, Trachypithecus francoisi, T. poliocephalus and T. leucocephalus, which are all characterized by different pelage coloration predominantly on the head and shoulders. Therefore, we sequenced a 395 bp long fragment of the mitochondrial control region from 178 T. francoisi, 54 T. leucocephalus and 19 T. poliocephalus individuals, representing all extant populations of these three species. We found 29 haplotypes in T. francoisi, 12 haplotypes in T. leucocephalus and three haplotypes in T. poliocephalus. T. leucocephalus and T. poliocephalus form monophyletic clades, which are both nested within T. francoisi, and diverged from T. francoisi recently, 0.46-0.27 (T. leucocephalus) and 0.50-0.25 million years ago (T. poliocephalus). Thus, T. francoisi appears as a polyphyletic group, while T. leucocephalus and T. poliocephalus are most likely independent descendents of T. francoisi that are both physically separated from T. francoisi populations by rivers, open sea or larger habitat gaps. Since T. francoisi populations show no variability in pelage coloration, pelage coloration in T. leucocephalus and T. poliocephalus is most likely the result of new genetic mutations after the split from T. francoisi and not of the fixation of different characters derived from an ancestral polymorphism. This case study highlights that morphological changes for example in pelage coloration can occur in isolated populations in relatively short time periods and it provides a solid basis for studies in related species. Nevertheless, to fully understand the evolutionary history of these three langur species, nuclear loci should be investigated as well.

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.

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. Am. J. Primatol. 77:901–910, 2015.

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

Most of Chinas 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.

Development of 34 SNP markers developed from the genome resequencing dataset in golden snub-nosed monkey (Rhinopithecus roxellana) using high resolution melting (HRM)

As single nucleotide polymorphisms (SNPs), known as the third-generation molecular markers, are extensively used in genetic studies. The rapid development of high-throughput sequencing technologies has enabled the development of a large number of SNP markers to be cost-effective and rapid. Based on the genome resequencing dataset of Rhinopithecus roxellana, we characterized 34 polymorphic SNP markers using a high resolution melting diversity assay. The observed heterozygosity varied from 0.323 to 0.725, while the expected heterozygosity ranged from 0.352 to 0.638. In addition, the MAF varied from 0.206 to 0.5000, while HWE values varied from 0.060 to 0.725. To the best of our knowledge, this is the largest set of SNP markers developed for R. roxellana by far, and could be useful in further geographic populations, analysis of evolutionary relationships and conservation genetics of this species.

Complete mitochondrial genome of the capped langur (Trachypithecus pileatus)

Abstract 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.

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.