Showing papers by "Yibo Hu published in 2021"
TL;DR: China is well positioned to become a global leader in biodiversity research in the near future based on the recent rapid progress of biodiversity research, and three future strategies are proposed.
Abstract: Biodiversity science in China has seen rapid growth over recent decades, ranging from baseline biodiversity studies to understanding the processes behind evolution across dynamic regions such as the Qinghai-Tibetan Plateau. We review research, including species catalogues; biodiversity monitoring; the origins, distributions, maintenance and threats to biodiversity; biodiversity-related ecosystem function and services; and species and ecosystems' responses to global change. Next, we identify priority topics and offer suggestions and priorities for future biodiversity research in China. These priorities include (i) the ecology and biogeography of the Qinghai-Tibetan Plateau and surrounding mountains, and that of subtropical and tropical forests across China; (ii) marine and inland aquatic biodiversity; and (iii) effective conservation and management to identify and maintain synergies between biodiversity and socio-economic development to fulfil China's vision for becoming an ecological civilization. In addition, we propose three future strategies: (i) translate advanced biodiversity science into practice for biodiversity conservation; (ii) strengthen capacity building and application of advanced technologies, including high-throughput sequencing, genomics and remote sensing; and (iii) strengthen and expand international collaborations. Based on the recent rapid progress of biodiversity research, China is well positioned to become a global leader in biodiversity research in the near future.
56 citations
TL;DR: It is found that both panda species share more similarities in their gut microbiota structure with each other than each species shares with its carnivorous relatives, indicating that the specialized herbivorous diet rather than host phylogeny is the dominant driver of gut microbiome convergence within Arctoidea.
Abstract: Gut microbiota plays a critical role in host physiology and health The coevolution between the host and its gut microbes facilitates animal adaptation to its specific ecological niche Multiple factors such as host diet and phylogeny modulate the structure and function of gut microbiota However, the relative contribution of each factor in shaping the structure of gut microbiota remains unclear The giant (Ailuropoda melanoleuca) and red (Ailurus styani) pandas belong to different families of order Carnivora They have evolved as obligate bamboo-feeders and can be used as a model system for studying the gut microbiome convergent evolution Here, we compare the structure and function of gut microbiota of the two pandas with their carnivorous relatives using 16S rRNA and metagenome sequencing We found that both panda species share more similarities in their gut microbiota structure with each other than each species shares with its carnivorous relatives This indicates that the specialized herbivorous diet rather than host phylogeny is the dominant driver of gut microbiome convergence within Arctoidea Metagenomic analysis revealed that the symbiotic gut microbiota of both pandas possesses a high level of starch and sucrose metabolism and vitamin B12 biosynthesis These findings suggest a diet-driven convergence of gut microbiomes and provide new insight into host-microbiota coevolution of these endangered species
32 citations
TL;DR: Wang et al. as discussed by the authors performed meta-analyses of genetic diversity in Chinese terrestrial vertebrates based on three genetic markers and investigated their phylogenetic diversity based on a dated phylogenetic tree of 2461 species.
Abstract: Genetic diversity and phylogenetic diversity reflect the evolutionary potential and history of species, respectively. However, the levels and spatial patterns of genetic and phylogenetic diversity of wildlife at the regional scale have largely remained unclear. Here, we performed meta-analyses of genetic diversity in Chinese terrestrial vertebrates based on three genetic markers and investigated their phylogenetic diversity based on a dated phylogenetic tree of 2461 species. We detected strong positive spatial correlations among mitochondrial DNA-based genetic diversity, phylogenetic diversity, and species richness. Moreover, the terrestrial vertebrates harbored higher genetic and phylogenetic diversity in South China and Southwest China than in other regions. Last, climatic factors (precipitation and temperature) had significant positive effects while altitude and human population density had significant negative impacts on levels of mitochondrial DNA-based genetic diversity in most cases. Our findings will help guide national-level genetic diversity conservation plans and a post-2020 biodiversity conservation framework.
31 citations
TL;DR: The upcoming 15th Conference of Parties (COP15) for Convention on Biological Diversity (CBD) serves as an opportunity for China to make ambitious but pragmatic commitments to elevate its wildlife conservation and management activities.
Abstract: Dramatic global changes to the environment have wrought unprecedented reductions in biodiversity, with >28% species assessed by the International Union for Conservation of Nature (IUCN) under the threat of extinction [1]. China, as one of the world’s megadiverse countries, plays a critical role in global biodiversity conservation. The upcoming 15th Conference of Parties (COP15) for Convention on Biological Diversity (CBD) serves as an opportunity for China to make ambitious but pragmatic commitments to elevate its wildlife conservation and management activities. The development of an ‘Ecological Civilization’, which endorses the ancient Taoist idea of Unity of Nature and Man (UNM) to achieve harmony between human beings and nature, has greatly facilitated the mainstreaming of biodiversity conservation in China [2]. Experiences from China will shed light on wildlife conservation worldwide.
18 citations
TL;DR: In this paper, the authors reveal that repeat sequences likely mediated illegitimate recombination to result in chromosome fusions and that 3D chromatin architecture around fusion sites have no significant change, while significant interactions across fusion sites were gradually established after speciation.
Abstract: Muntjac deer have experienced drastic karyotype changes during their speciation, making it an ideal model for studying mechanisms and functional consequences of mammalian chromosome evolution. Here we generated chromosome-level genomes for Hydropotes inermis (2n = 70), Muntiacus reevesi (2n = 46), female and male M. crinifrons (2n = 8/9) and a contig-level genome for M. gongshanensis (2n = 8/9). These high-quality genomes combined with Hi-C data allowed us to reveal the evolution of 3D chromatin architectures during mammalian chromosome evolution. We find that the chromosome fusion events of muntjac species did not alter the A/B compartment structure and topologically associated domains near the fusion sites, but new chromatin interactions were gradually established across the fusion sites. The recently borne neo-Y chromosome of M. crinifrons, which underwent male-specific inversions, has dramatically restructured chromatin compartments, recapitulating the early evolution of canonical mammalian Y chromosomes. We also reveal that a complex structure containing unique centromeric satellite, truncated telomeric and palindrome repeats might have mediated muntjacs’ recurrent chromosome fusions. These results provide insights into the recurrent chromosome tandem fusion in muntjacs, early evolution of mammalian sex chromosomes, and reveal how chromosome rearrangements can reshape the 3D chromatin regulatory conformations during species evolution. Muntjac deer underwent rapid species radiation and dramatic chromosome fusions within a short period of time. Here the authors reveal that repeat sequences likely mediated illegitimate recombination to result in chromosome fusions and that 3D chromatin architecture around fusion sites have no significant change, while significant interactions across fusion sites were gradually established after speciation.
16 citations
TL;DR: In this paper, the authors integrated metabolomic and metagenomic approaches, and in vitro culture experiment, they identified 97 flavonoids in bamboo and most of them have not been identified previously; the utilization of more than 70% flavonoid monomers was attributed to gut microbiota; the variation of flavone in bamboo leaves and shoots shaped the seasonal microbial fluctuation.
Abstract: Background Flavonoids are important plant secondary metabolites (PSMs) that have been widely used for their health-promoting effects. However, little is known about overall flavonoid metabolism and the interactive effects between flavonoids and the gut microbiota. The flavonoid-rich bamboo and the giant panda provide an ideal system to bridge this gap. Results Here, integrating metabolomic and metagenomic approaches, and in vitro culture experiment, we identified 97 flavonoids in bamboo and most of them have not been identified previously; the utilization of more than 70% flavonoid monomers was attributed to gut microbiota; the variation of flavonoid in bamboo leaves and shoots shaped the seasonal microbial fluctuation. The greater the flavonoid content in the diet was, the lower microbial diversity and virulence factor, but the more cellulose-degrading species. Conclusions Our study shows an unprecedented landscape of beneficial PSMs in a non-model mammal and reveals that PSMs remodel the gut microbiota conferring host adaptation to diet transition in an ecological context, providing a novel insight into host-microbe interaction. Video abstract.
11 citations
TL;DR: The genome-wide phylogeny revealed that these parasitic roundworms have not phylogenetically coevolved with their hosts, and seven pairs of interactive proteins had consistent phylogenetic topology, suggesting their coevolution during host–parasite interaction.
Abstract: Antagonistic coevolution between host and parasite drives species evolution. However, most of the studies only focus on parasitism adaptation and do not explore the coevolution mechanisms from the perspective of both host and parasite. Here, through the de novo sequencing and assembly of the genomes of giant panda roundworm, red panda roundworm, and lion roundworm parasitic on tiger, we investigated the genomic mechanisms of coevolution between nonmodel mammals and their parasitic roundworms and those of roundworm parasitism in general. The genome-wide phylogeny revealed that these parasitic roundworms have not phylogenetically coevolved with their hosts. The CTSZ and prolyl 4-hydroxylase subunit beta (P4HB) immunoregulatory proteins played a central role in protein interaction between mammals and parasitic roundworms. The gene tree comparison identified that seven pairs of interactive proteins had consistent phylogenetic topology, suggesting their coevolution during host-parasite interaction. These coevolutionary proteins were particularly relevant to immune response. In addition, we found that the roundworms of both pandas exhibited higher proportions of metallopeptidase genes, and some positively selected genes were highly related to their larvae's fast development. Our findings provide novel insights into the genetic mechanisms of coevolution between nonmodel mammals and parasites and offer the valuable genomic resources for scientific ascariasis prevention in both pandas.
10 citations
1 citations