Meta-analyses reveal the large-scale spatial patterns of genetic and phylogenetic diversity for Chinese terrestrial vertebrates.

Identifying and protecting hotspots of endemism and species richness is crucial for mitigating the global biodiversity crisis. However, our understanding of spatial diversity patterns is far from complete, which severely limits our ability to conserve biodiversity hotspots. Here, we report a comprehensive analysis of amphibian species diversity in China, one of the most species-rich countries on Earth. Our study combines 20 y of field surveys with new molecular analyses of 521 described species and also identifies 100 potential cryptic species. We identify 10 hotspots of amphibian diversity in China, each with exceptional species richness and endemism and with exceptional phylogenetic diversity and phylogenetic endemism (based on a new time-calibrated, species-level phylogeny for Chinese amphibians). These 10 hotspots encompass 59.6% of China’s described amphibian species, 49.0% of cryptic species, and 55.6% of species endemic to China. Only four of these 10 hotspots correspond to previously recognized biodiversity hotspots. The six new hotspots include the Nanling Mountains and other mountain ranges in South China. Among the 186 species in the six new hotspots, only 9.7% are well covered by protected areas and most (88.2%) are exposed to high human impacts. Five of the six new hotspots are under very high human pressure and are in urgent need of protection. We also find that patterns of richness in cryptic species are significantly related to those in described species but are not identical.

Species richness and composition pattern of amphibians along elevation gradients in eastern Nepal Himalaya are rarely investigated. This is a first ever study in the Himalayan elevation gradient, the world’s highest mountain range and are highly sensitive to the effects of recent global changes. The aim of the present study was to assess amphibian community structure along elevation gradients and identify the potential drivers that regulate community structures. Amphibian assemblages were sampled within 3 months in both 2014 and 2015 (from May to July) using nocturnal time constrained and acoustic aids visual encounter surveys. In total, 79 transects between 78 and 4200 m asl were sampled within 2 years field work. A combination of polynomial regression, generalized linear models, hierarchical partitioning and canonical correspondence analysis were used to determine the effects of elevation and environmental variables on species richness, abundance, and composition of amphibian communities. Species richness and abundance declined linearly with increasing elevation, which did not support the Mid-Domain Model. Among all the environmental variables, elevation, surface area and humidity were the best predictors of species richness, abundance and composition of amphibians. The majority of amphibian species had narrow elevation ranges. There was no significant correlation between species range size and elevation gradients. However, body size significantly increased along elevation gradients, indicating that Bergmann’s rule is valid for amphibians in eastern Nepal Himalaya. This study indicates that eastern Nepal Himalaya is a hotspot in amphibian diversity, and it should be served as a baseline for management and conservation activities.

Codon usage bias patterns have been broadly explored for many viruses. However, the relative importance of mutation pressure and natural selection is still under debate. In the present study, I tried to resolve controversial issues on determining the principal factors of codon usage patterns for DNA and RNA viruses, respectively, by examining over 38000 ORFs. By utilizing variation partitioning technique, the results showed that 27% and 21% of total variation could be attributed to mutational pressure, while 5% and 6% of total variation could be explained by natural selection for DNA and RNA viruses, respectively, in codon usage patterns. Furthermore, the combined effect of mutational pressure and natural selection on influencing codon usage patterns of viruses is substantial (explaining 10% and 8% of total variation of codon usage patterns). With respect to GC variation, GC content is always negatively and significantly correlated with aromaticity. Interestingly, the signs for the significant correlations between GC, gene lengths, and hydrophobicity are completely opposite between DNA and RNA viruses, being positive for DNA viruses while being negative for RNA viruses. At last, GC12 versus G3s plot suggests that natural selection is more important than mutational pressure on influencing the GC content in the first and second codon positions.