Showing papers by "Yibo Hu published in 2022"

Conservation priorities for global marine biodiversity across multiple dimensions

Abstract: Abstract Marine biodiversity plays important roles in ocean ecosystem services and has substantial economic value. Species diversity, genetic diversity and phylogenetic diversity, which reflect the number, evolutionary potential and evolutionary history of species in ecosystem functioning, are three important dimensions of biodiversity. Marine-protected areas have been demonstrated as an effective area-based tool for protecting marine biodiversity, but only 2.8% of the ocean has been fully protected. It is urgent to identify global conservation priority areas and percentage of the ocean across multiple dimensions of biodiversity based on Post-2020 Global Biodiversity Framework. Here, we investigate the spatial distribution of marine genetic and phylogenetic diversity using 80 075 mitochondrial DNA barcode sequences from 4316 species and a newly constructed phylogenetic tree of 8166 species. We identify that the Central Indo-Pacific Ocean, Central Pacific Ocean and Western Indian Ocean harbor high levels of biodiversity across three dimensions of biodiversity, which could be designated as conservation priority areas. We also find that strategically protecting ∼22% of the ocean would allow us to reach the target of conserving ∼95% of currently known taxonomic, genetic and phylogenetic diversity. Our study provides insights into the spatial distribution pattern of multiple marine diversities and the findings would help to design comprehensive conservation schemes for global marine biodiversity.

Global patterns of phylogenetic diversity and transmission of bat coronavirus

Abstract: Bats are reservoirs for multiple coronaviruses (CoVs). However, the phylogenetic diversity and transmission of global bat-borne CoVs remain poorly understood. Here, we performed a Bayesian phylogeographic analysis based on 3,594 bat CoV RdRp gene sequences to study the phylogenetic diversity and transmission of bat-borne CoVs and the underlying driving factors. We found that host-switching events occurred more frequently for α-CoVs than for β-CoVs, and the latter was highly constrained by bat phylogeny. Bat species in the families Molossidae, Rhinolophidae, Miniopteridae, and Vespertilionidae had larger contributions to the cross-species transmission of bat CoVs. Regions of eastern and southern Africa, southern South America, Western Europe, and Southeast Asia were more frequently involved in cross-region transmission events of bat CoVs than other regions. Phylogenetic and geographic distances were the most important factors limiting CoV transmission. Bat taxa and global geographic hotspots associated with bat CoV phylogenetic diversity were identified, and bat species richness, mean annual temperature, global agricultural cropland, and human population density were strongly correlated with the phylogenetic diversity of bat CoVs. These findings provide insight into bat CoV evolution and ecological transmission among bat taxa. The identified hotspots of bat CoV evolution and transmission will guide early warnings of bat-borne CoV zoonotic diseases.

Community structure of the solitary giant pandas is maintained by indirect social connections

Abstract: Indirect interactions between individual solitary mammals, such as the giant panda, are often overlooked because of their nature, yet are important for maintaining the necessary sociality in solitary species.Here, we determined the genetic identity of all giant panda individuals in a local population and matched these identities with their associations to determine social network of this solitary animal. Total thirty-five giant panda individuals were found in our field survey, and we constructed genetic and social networks for thirty-three individuals who successfully obtained genetic, age and sex information. The results showed that sex had great impact on both social network and genetic network, and age may have the potential to influence the social network of the giant pandas. Adult males, mostly in the central of the social network, which appeared significantly larger network connections than adult females. Due to the female-biased dispersal pattern of wild giant pandas, male-male pairs showed higher relatedness than female-female ones and multi-generational patrilinear assemblages are expected in the study area.The relatedness of individuals has an influence on the formation of community social structure of giant pandas, and indirect interactions among solitary giant pandas potentially function to reduce competition for resources and inbreeding.

Conservation initiatives in China

Abstract: In this chapter, we summarized the conservation initiatives of red pandas in China, including laws and regulations, public education, nature reserves and important conservation projects. Specifically, we introduced important conservation projects such as the Natural Forest Protection Project, Grain to Green Project, National Wildlife Conservation and Natural Reserve Construction Project and National Park Project. These projects played important roles in red panda conservation in China.

Evolutionary Conservation Genomics Reveals Recent Speciation and Local Adaptation in Threatened Takins

Abstract: Abstract Incorrect species delimitation will lead to inappropriate conservation decisions, especially for threatened species. The takin (Budorcas taxicolor) is a large artiodactyl endemic to the Himalayan–Hengduan–Qinling Mountains and is well known for its threatened status and peculiar appearance. However, the speciation, intraspecies taxonomy, evolutionary history, and adaptive evolution of this species still remain unclear, which greatly hampers its scientific conservation. Here, we de novo assembled a high-quality chromosome-level genome of takin and resequenced the genomes of 75 wild takins. Phylogenomics revealed that takin was positioned at the root of Caprinae. Population genomics based on the autosome, X chromosome, and Y chromosome SNPs and mitochondrial genomes consistently revealed the existence of two phylogenetic species and recent speciation in takins: the Himalayan takin (B. taxicolor) and the Chinese takin (B. tibetana), with the support of morphological evidence. Two genetically divergent subspecies were identified in both takin species, rejecting three previously proposed taxonomical viewpoints. Furthermore, their distribution boundaries were determined, suggesting that large rivers play important roles in shaping the genetic partition. Compared with the other subspecies, the Qinling subspecies presented the lowest genomic diversity, higher linkage disequilibrium, inbreeding, and genetic load, thus is in urgent need of genetic management and protection. Moreover, coat color gene (PMEL) variation may be responsible for the adaptive coat color difference between the two species following Gloger’s rule. Our findings provide novel insights into the recent speciation, local adaptation, scientific conservation of takins, and biogeography of the Himalaya–Hengduan biodiversity hotspot.

Red panda genomics and the evidence for two species

Abstract: This chapter introduces the latest research advances of red panda genomics. Using next-generation sequencing technology, the genome of Chinese red panda has been de novo sequenced and assembled, providing an important genetic resource for red panda study and conservation. Comparative genomics reveals the genetic mechanisms of morphological (pseudo-thumb) and physiological (specialized bamboo diet) convergences between giant and red pandas. Population genomics found that the red pandas could be classified into two phylogenetic species, Himalayan red panda (A. fulgens) and Chinese red panda (A. styani), based on the evidence from whole-genome SNPs, mitochondrial genomes and Y-chromosome SNPs. The Yalu Zangbu River, rather than the Nujiang River, is most likely the boundary of two species. Furthermore, the two species have obviously different evolutionary histories. The southern Tibet-Gaoligong population of Chinese red panda may be the glacial refugia, with the highest genetic diversity and more gene flow output. The Himalayan red panda has much lower genetic diversity, higher linkage disequilibrium and higher genetic load, which could be explained by its continuously decreasing demographic history. These findings have important implications for wild red panda conservation and captive red panda genetic management.