Genetic diversity and population structure of Tibetan sheep breeds determined by whole genome resequencing.

Tibetan sheep is one of primitive Chinese sheep breeds, which achieved the divergence about 2500 years ago in Qinghai plateau region. According to different geographic conditions, especially altitudes, Tibetan sheep evolved into different breeds. In this study, we performed whole genome resequencing of 5 representative Tibetan sheep breeds. Comparative genomic analysis showed that they can be divided into different clades with a close genetic relationship. However, some genes with common selective regions were enriched for hypoxic adaptability in different breeds living at higher altitude, including GHR, BMP15, and CPLANE1. Furthermore, breed-specific selective regions about physical characteristics, especially wool growth, were found in genes such as BSND, USP24, NCAPG, and LCORL. This study could contribute to our understanding about trait formation and offer a reference for breeding of Tibetan sheep.

Productivity benefits of warming at regional scale could be offset by detrimental impacts on site level hydrology.

Climate change affects the distribution and persistence of wildlife. Broad scale studies have demonstrated that climate change shifts the geographic ranges and phenology of species. These findings are influential for making high level strategies but not practical enough to guide site specific management. In this study, we explored the environment factors affecting the population of Bar-headed Goose in the key breeding site of Qinghai using generalized additive mixed model (GAMM). Our results showed that 1) there were significant increasing trends in climate variables and river flows to the Qinghai Lake; 2) NDVI in the sites decreased significantly despite the regional positive trend induced by the warmer and wetter climate; 3) NDVI at site scale was negatively correlated to lake water level; and 4) the abundance of Bar-headed Goose decreased significantly at all sites. While the abundance was positively related to NDVI at breeding sites, the GAMM revealed an opposite relationship at foraging areas. Our findings demonstrated the multi-facet effects of climate change on population dynamics; and the effect at global/regional scale could be complicated by site level factors.

Resequencing and comparison of whole mitochondrial genome to gain insight into the evolutionary status of the Shennongjia golden snub-nosed monkey (SNJ R. roxellana).

Shennongjia Rhinopithecus roxellana (SNJ R. roxellana) is the smallest geographical population of R. roxellana. The phylogenetic relationships among its genera and species and the biogeographic processes leading to their current distribution are largely unclear. To address these issues, we resequenced and obtained a new, complete mitochondrial genome of SNJ R. roxellana by next-generation sequencing and standard Sanger sequencing. We analyzed the gene composition, constructed a phylogenetic tree, inferred the divergence ages based on complete mitochondrial genome sequences, and analyzed the genetic divergence of 13 functional mtDNA genes. The phylogenetic tree and divergence ages showed that R. avunculus (the Tonkin snub-nosed monkey) was the first to diverge from the Rhinopithecus genus ca. 2.47 million years ago (Ma). Rhinopithecus bieti and Rhinopithecus strykeri formed sister groups, and the second divergence from the Rhinopithecus genus occurred ca. 1.90 Ma. R. roxellana and R. brelichi diverged from the Rhinopithecus genus third, ca. 1.57 Ma. SNJ R. roxellana was the last to diverge within R. roxellana species in 0.08 Ma, and the most recent common ancestor of R. roxellana is 0.10 Ma. The analyses on gene composition showed SNJ R. roxellana was the newest geographic population of R. roxellana. The work will help to develop a more accurate protection policy for SNJ R. roxellana and facilitate further research on selection and adaptation of R. roxellana.

Gravel bars can be critical for biodiversity conservation: a case study on scaly-sided Merganser in South china.

Gravel bars are characteristic components of river landscapes and are increasingly recognized as key sites for many waterbirds, though detailed studies on the ecological function of gravel bars for waterbirds are rare. In this study, we surveyed the endangered Scaly-sided Merganser Mergus squamatus along a 40 km river section of Yuan River, in Central China, for three consecutive winters. We derived the landscape metrics of river gravel bars from geo-rectified fine resolution (0.6 m) aerial image data. We then built habitat suitability models (Generalized Linear Models-GLMs) to study the effects of landscape metrics and human disturbance on Scaly-sided Merganser presence probability. We found that 1) the Scaly-sided Merganser tended to congregate at river segments with more gravel patches; 2) the Scaly-sided Merganser preferred areas with larger and more contiguous gravel patches; and 3) the number of houses along the river bank (a proxy for anthropogenic disturbance) had significantly negative impacts on the occurrence of the Scaly-sided Merganser. Our results suggest that gravel bars are vital to the Scaly-sided Merganser as shelters from disturbance, as well as sites for feeding and roosting. Therefore, maintaining the exposure of gravel bars in regulated rivers during the low water period in winter might be the key for the conservation of the endangered species. These findings have important implications for understanding behavioral evolution and distribution of the species and for delineating between habitats of different quality for conservation and management.

Using species distribution model to estimate the wintering population size of the endangered scaly-sided merganser in China.

Scaly-sided Merganser is a globally endangered species restricted to eastern Asia. Estimating its population is difficult and considerable gap exists between populations at its breeding grounds and wintering sites. In this study, we built a species distribution model (SDM) using Maxent with presence-only data to predict the potential wintering habitat for Scaly-sided Merganser in China. Area under the receiver operating characteristic curve (AUC) method suggests high predictive power of the model (training and testing AUC were 0.97 and 0.96 respectively). The most significant environmental variables included annual mean temperature, mean temperature of coldest quarter, minimum temperature of coldest month and precipitation of driest quarter. Suitable conditions for Scaly-sided Merganser are predicted in the middle and lower reaches of the Yangtze River, especially in Jiangxi, Hunan and Hubei Provinces. The predicted suitable habitat embraces 6,984 km of river. Based on survey results from three consecutive winters (2010-2012) and previous studies, we estimated that the entire wintering population of Scaly-sided Merganser in China to be 3,561 ± 478 individuals, which is consistent with estimate in its breeding ground.

Optimized spatial priorities for biodiversity conservation in China: a systematic conservation planning perspective.

By addressing several key features overlooked in previous studies, i.e. human disturbance, integration of ecosystem- and species-level conservation features, and principles of complementarity and representativeness, we present the first national-scale systematic conservation planning for China to determine the optimized spatial priorities for biodiversity conservation. We compiled a spatial database on the distributions of ecosystem- and species-level conservation features, and modeled a human disturbance index (HDI) by aggregating information using several socioeconomic proxies. We ran Marxan with two scenarios (HDI-ignored and HDI-considered) to investigate the effects of human disturbance, and explored the geographic patterns of the optimized spatial conservation priorities. Compared to when HDI was ignored, the HDI-considered scenario resulted in (1) a marked reduction (∼9%) in the total HDI score and a slight increase (∼7%) in the total area of the portfolio of priority units, (2) a significant increase (∼43%) in the total irreplaceable area and (3) more irreplaceable units being identified in almost all environmental zones and highly-disturbed provinces. Thus the inclusion of human disturbance is essential for cost-effective priority-setting. Attention should be targeted to the areas that are characterized as moderately-disturbed, <2,000 m in altitude, and/or intermediately- to extremely-rugged in terrain to identify potentially important regions for implementing cost-effective conservation. We delineated 23 primary large-scale priority areas that are significant for conserving China's biodiversity, but those isolated priority units in disturbed regions are in more urgent need of conservation actions so as to prevent immediate and severe biodiversity loss. This study presents a spatially optimized national-scale portfolio of conservation priorities--effectively representing the overall biodiversity of China while minimizing conflicts with economic development. Our results offer critical insights for current conservation and strategic land-use planning in China. The approach is transferable and easy to implement by end-users, and applicable for national- and local-scale systematic conservation prioritization practices.