Zhijin Liu

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.

Phylogeography and population structure of the Yunnan snub‐nosed monkey (Rhinopithecus bieti) inferred from mitochondrial control region DNA sequence analysis

Rhinopithecus bieti, the Yunnan snub‐nosed monkey, is the nonhuman primate with the highest altitudinal distribution and is also one of the 25 most globally endangered primate species. Currently, R. bieti is found in forests between 3000 and 4500 m above sea level, within a narrow area on the Tibetan Plateau between the Yangtze and Mekong rivers, where it is suffering from loss of habitat and shrinking population size (~1500). To assess the genetic diversity within this species, its population structure and to infer its evolutionary history, we sequenced 401 bp of the hypervariable I (HVI) segment from the mitochondrial DNA control region (CR) for 157 individuals from 11 remnant patches throughout the fragmented distribution area. Fifty‐two variable sites were observed and 30 haplotypes were defined. Compared with other primate species, R. bieti cannot be regarded as a taxon with low genetic diversity. Phylogenetic analysis partitioned haplotypes into two divergent haplogroups (A and B). Haplotypes from the two mitochondrial clades were found to be mixed in some patches although the distribution of haplotypes displayed local homogeneity, implying a strong population structure within R. bieti. Analysis of molecular variance detected significant differences among the different geographical regions, suggesting that R. bieti should be separated into three management units (MUs) for conservation. Based on our results, it can be hypothesized that the genetic history of R. bieti includes an initial, presumably allopatric divergence between clades A and B 1.0–0.7 million years ago (Ma), which might have been caused by the Late Cenozoic uplift of the Tibetan Plateau, secondary contact after this divergence as a result of a population expansion 0.16–0.05 Ma, and population reduction and habitat fragmentation in the very recent past.

Evolutionary History of the Odd-Nosed Monkeys and the Phylogenetic Position of the Newly Described Myanmar Snub-Nosed Monkey Rhinopithecus strykeri

Odd-nosed monkeys represent one of the two major groups of Asian colobines. Our knowledge about this primate group is still limited as it is highlighted by the recent discovery of a new species in Northern Myanmar. Although a common origin of the group is now widely accepted, the phylogenetic relationships among its genera and species, and the biogeographic processes leading to their current distribution are largely unknown. To address these issues, we have analyzed complete mitochondrial genomes and 12 nuclear loci, including one X chromosomal, six Y chromosomal and five autosomal loci, from all ten odd-nosed monkey species. The gene tree topologies and divergence age estimates derived from different markers were highly similar, but differed in placing various species or haplogroups within the genera Rhinopithecus and Pygathrix. Based on our data, Rhinopithecus represent the most basal lineage, and Nasalis and Simias form closely related sister taxa, suggesting a Northern origin of odd-nosed monkeys and a later invasion into Indochina and Sundaland. According to our divergence age estimates, the lineages leading to the genera Rhinopithecus, Pygathrix and Nasalis+Simias originated in the late Miocene, while differentiation events within these genera and also the split between Nasalis and Simias occurred in the Pleistocene. Observed gene tree discordances between mitochondrial and nuclear datasets, and paraphylies in the mitochondrial dataset for some species of the genera Rhinopithecus and Pygathrix suggest secondary gene flow after the taxa initially diverged. Most likely such events were triggered by dramatic changes in geology and climate within the region. Overall, our study provides the most comprehensive view on odd-nosed monkey evolution and emphasizes that data from differentially inherited markers are crucial to better understand evolutionary relationships and to trace secondary gene flow.

Complex population genetic and demographic history of the Salangid, Neosalanx taihuensis , based on cytochrome b sequences

BackgroundThe Salangid icefish Neosalanx taihuensis (Salangidae) is an economically important fish, which is endemic to China, restricted to large freshwater systems (e.g. lakes, large rivers and estuaries) and typically exhibit low vagility. The continuous distribution ranges from the temperate region of the Huai and Yellow River basins to the subtropical region of the Pearl River basin. This wide ranging distribution makes the species an ideal model for the study of palaeoclimatic effects on population genetic structure and phylogeography. Here, we aim to analyze population genetic differentiation within and between river basins and demographic history in order to understand how this species responded to severe climatic oscillations, decline of the sea levels during the Pleistocene ice ages and tectonic activity.ResultsWe obtained the complete mtDNA cytochrome b sequences (1141 bp) of 354 individuals from 13 populations in the Pearl River, the Yangze River and the Huai River basin. Thirty-six haplotypes were detected. Haplotype frequency distributions were strongly skewed, with most haplotypes (n = 24) represented only in single samples each and thus restricted to a single population. The most common haplotype (H36) was found in 49.15% of all individuals. Analysis of molecular variance (AMOVA) revealed a random pattern in the distribution of genetic diversity, which is inconsistent with contemporary hydrological structure. Significant levels of genetic subdivision were detected among populations within basins rather than between the three basins. Demographic analysis revealed that the population size in the Pearl River basin has remained relatively constant whereas the populations in the Yangze River and the Huai River basins expanded about 221 and 190 kyr ago, respectively, with the majority of mutations occurring after the last glacial maximum (LGM).ConclusionThe observed complex genetic pattern of N. taihuensis is coherent with a scenario of multiple unrelated founding events by long-distance colonization and dispersal combined with contiguous population expansion and locally restricted gene flow. We also found that this species was likely severely impacted by past glaciations. More favourable climate and the formation of large suitable habitations together facilitated population expansion after the late Quaternary (especially the LGM). We proposed that all populations should be managed and conserved separately, especially for habitat protection.

Historical geographic dispersal of the golden snub-nosed monkey (Rhinopithecus roxellana) and the influence of climatic oscillations.

Current understanding of historic climate oscillations that have occurred over the past few million years has modified scientific views on evolution. Major climatic events have caused local and global extinction of plants and animals and have impacted the spatial distribution of many species. The endangered golden snub‐nosed monkey (Rhinopithecus roxellana) currently inhabits three isolated regions of China: the Sichuan and Gansu provinces (SG), the Qinling Mountains in Shaanxi province (QL), and the Shennongjia Forestry District in Hubei province (SNJ). However, considerable uncertainty still exists about their historical dispersal routes under the influence of environment change. To date, two dispersal routes have been proposed: (1) the QL and SNJ populations originated from the SG population; and (2) the SG population recolonized from the QL and SNJ populations. We used the mitochondrial DNA complete control region to perform statistical assessments of the relative probability of alternative migration scenarios and the role of environmental change on the geographic dispersal of Rhinopithecus roxellana. Thirty haplotypes were identified from the three geographic regions and a high degree of genetic structure was observed. The most recent common ancestor among the mitochondrial DNA haplotypes was estimated to live around 0.47–1.88 million years ago and five notable haplotype clusters were found. Phylogenetic analysis and historical gene flow estimates suggested that the QL and SNJ populations originated from the SG population, with at least two dispersal events from the SG population occurring during the Pleistocene (1.17±0.70 and 0.53±0.30 Ma). Composite dispersal history of the golden snub‐nosed monkey can be explained by both environmental change inducing global climate change and the influence of the Tibetan Plateau uplift. Such range shifts involved considerable demographic changes, as revealed in the dramatic decreases in population size during the last 25,000 years.

Balancing selection and genetic drift at major histocompatibility complex class II genes in isolated populations of golden snub-nosed monkey (Rhinopithecus roxellana)

BackgroundSmall, isolated populations often experience loss of genetic variation due to random genetic drift. Unlike neutral or nearly neutral markers (such as mitochondrial genes or microsatellites), major histocompatibility complex (MHC) genes in these populations may retain high levels of polymorphism due to balancing selection. The relative roles of balancing selection and genetic drift in either small isolated or bottlenecked populations remain controversial. In this study, we examined the mechanisms maintaining polymorphisms of MHC genes in small isolated populations of the endangered golden snub-nosed monkey (Rhinopithecus roxellana) by comparing genetic variation found in MHC and microsatellite loci. There are few studies of this kind conducted on highly endangered primate species.ResultsTwo MHC genes were sequenced and sixteen microsatellite loci were genotyped from samples representing three isolated populations. We isolated nine DQA1 alleles and sixteen DQB1 alleles and validated expression of the alleles. Lowest genetic variation for both MHC and microsatellites was found in the Shennongjia (SNJ) population. Historical balancing selection was revealed at both the DQA1 and DQB1 loci, as revealed by excess non-synonymous substitutions at antigen binding sites (ABS) and maximum-likelihood-based random-site models. Patterns of microsatellite variation revealed population structure. FST outlier analysis showed that population differentiation at the two MHC loci was similar to the microsatellite loci.ConclusionsMHC genes and microsatellite loci showed the same allelic richness pattern with the lowest genetic variation occurring in SNJ, suggesting that genetic drift played a prominent role in these isolated populations. As MHC genes are subject to selective pressures, the maintenance of genetic variation is of particular interest in small, long-isolated populations. The results of this study may contribute to captive breeding and translocation programs for endangered species.

Dietary specialization drives multiple independent losses and gains in the bitter taste gene repertoire of Laurasiatherian Mammals

BackgroundBitter taste perception is essential for species with selective food intake, enabling them to avoid unpalatable or toxic items. Previous studies noted a marked variation in the number of TAS2R genes among various vertebrate species, but the underlying causes are not well understood. Laurasiatherian mammals have highly diversified dietary niche, showing repeated evolution of specialized feeding preferences in multiple lineages and offering a unique chance to investigate how various feeding niches are associated with copy number variation for bitter taste receptor genes.ResultsHere we investigated the evolutionary trajectories of TAS2Rs and their implications on bitter taste perception in whole-genome assemblies of 41 Laurasiatherian species. The number of intact TAS2Rs copies varied considerably, ranging from 0 to 52. As an extreme example of a narrow dietary niche, the Chinese pangolin possessed the lowest number of intact TAS2Rs (n = 2) among studied terrestrial vertebrates. Marine mammals (cetacea and pinnipedia), which swallow prey whole, presented a reduced copy number of TAS2Rs (n = 0-5). In contrast, independent insectivorous lineages, such as the shrew and insectivorous bats possessed a higher TAS2R diversity (n = 52 and n = 20-32, respectively), exceeding that in herbivores (n = 9-22) and omnivores (n = 18-22).ConclusionsBesides herbivores, insectivores in Laurasiatheria tend to have more functional TAS2Rs in comparison to carnivores and omnivores. Furthermore, animals swallowing food whole (cetacean, pinnipedia and pangolin) have lost most functional TAS2Rs. These findings provide the most comprehensive view of the bitter taste gene repertoire in Laurasiatherian mammals to date, casting new light on the relationship between losses and gains of TAS2Rs and dietary specialization in mammals.

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.