Lichun Jiang

Bio: Lichun Jiang is an academic researcher from Sichuan University. The author has contributed to research in topics: Pseudois & Population. The author has an hindex of 4, co-authored 5 publications receiving 40 citations.

Molecular phylogeny and phylogeography of genus Pseudois (Bovidae, Cetartiodactyla): New insights into the contrasting phylogeographic structure

Abstract: Blue sheep, Pseudois nayaur, is endemic to the Tibetan Plateau and the surrounding mountains, which are the highest-elevation areas in the world. Classical morphological taxonomy suggests that there are two subspecies in genus Pseudois (Bovidae, Artiodactyla), namely Pseudois nayaur nayaur and Pseudois nayaur szechuanensis. However, the validity and geographic characteristics of these subspecies have never been carefully discussed and analyzed. This may be partially because previous studies have mainly focused on the vague taxonomic status of Pseudois schaeferi (dwarf blue sheep). Thus, there is an urgent need to investigate the evolutionary relationship and taxonomy system of this genus. This study enriches a previous dataset by providing a large number of new samples, based on a total of 225 samples covering almost the entire distribution of blue sheep. Molecular data from cytochrome b and the mitochondrial control region sequences were used to reconstruct the phylogeny of this species. The phylogenetic inferences show that vicariance plays an important role in diversification within this genus. In terms of molecular dating results and biogeographic analyses, the striking biogeographic pattern coincides significantly with major geophysical events. Although the results raise doubt about the present recognized distribution range of blue sheep, they have corroborated the validity of the identified subspecies in genus Pseudois. Meanwhile, these results demonstrate that the two geographically distinct populations, the Helan Mountains and Pamir Plateau populations, have been significantly differentiated from the identified subspecies, a finding that challenges the conventional taxonomy of blue sheep.

Genetic variability of the tokay gecko based on mitochondrial and nuclear DNA

Abstract: With largely allopatric distribution, the black tokay and the red tokay are two distinct morphs of the subspecies Gekko gecko gecko. In consideration of their different morphological characteristics, the taxonomic status of G. g. gecko is disputed. Through detailed morphological comparison, it has been proposed that the black tokay should be elevated to species ranking, but without strong genetic evidence. In order to further investigate the taxonomic status of the tokay gecko (G. gecko), we used one mitochondrial marker (ND2) and three nuclear markers (RAG1, c-mos, and ITS2) to explore the phylogenetic and taxonomic relationship of the tokay gecko. Our results revealed a deep phylogeographical divergence in tokay gecko and at the same time provided us with the evidence of possible introgressive hybridization or/and incomplete lineage sorting between the black tokay and the red tokay. The elevation of the black tokay to species level is also supported by our results. However, due to limited sampling and genetic data, this elevation should be further corroborated by more genetic evidence.

The complete mitochondrial genome sequence of the Chinese Serow, Capricornis milneedwardsii (Cetartiodactyla: Caprinae)

Abstract: The Chinese Serow (Capricornis milneedwardsii) is a native species distributed in China and Southeast Asia, and has been listed as one of the Class II national protected species in China. Here we first determined and annotated its complete mitochondrial genome. The mito-genome of Chinese Serow is 16,444 bp in length, consisting of two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, 13 protein-coding genes, and one control region. The overall base composition is A: 33.5%, T: 26.7%, C: 26.6%, and G: 13.2%, with a much higher A + T content.

Development and characterization of nine polymorphic microsatellite markers for the blue sheep (Pseudois nayaur)

Abstract: Pseudois nayaur is a major component of Caprini and a keystone species in Qinghai-Tibet Plateau ecosystems. Due to the excessive hunting and habitat loss, its numbers are being reduced drastically. We developed and characterized the first set of microsatellite markers in this species to investigate its population genetic diversity and structure. Nine polymorphic loci displayed an average of 5.73 alleles (range between 2 and 14) and the levels of expected heterozygosity ranged from 0.422 to 0.816. Cross-amplification within dwarf blue sheep was successful for the nine loci. The loci characterized here will be useful for detecting fine-scale spatial structuring and resolving the taxonomic status of divergent Pseudois populations.

The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep‐sea environment

Abstract: The deep sea is one of the most extensive ecosystems on earth Organisms living there survive in an extremely harsh environment, and their mitochondrial energy metabolism might be a result of evolution As one of the most important organelles, mitochondria generate energy through energy metabolism and play an important role in almost all biological activities In this study, the mitogenome of a deep-sea sea anemone (Bolocera sp) was sequenced and characterized Like other metazoans, it contained 13 energy pathway protein-coding genes and two ribosomal RNAs However, it also exhibited some unique features: just two transfer RNA genes, two group I introns, two transposon-like noncanonical open reading frames (ORFs), and a control region-like (CR-like) element All of the mitochondrial genes were coded by the same strand (the H-strand) The genetic order and orientation were identical to those of most sequenced actiniarians Phylogenetic analyses showed that this species was closely related to Bolocera tuediae Positive selection analysis showed that three residues (31 L and 42 N in ATP6, 570 S in ND5) of Bolocera sp were positively selected sites By comparing these features with those of shallow sea anemone species, we deduced that these novel gene features may influence the activity of mitochondrial genes This study may provide some clues regarding the adaptation of Bolocera sp to the deep-sea environment

Trehalase Gene as a Molecular Signature of Dietary Diversification in Mammals

Abstract: Diet is a key factor in determining and structuring animal diversity and adaptive radiations. The mammalian fossil record preserves phenotypic evidence of many dietary shifts, whereas genetic changes followed by dietary diversification in mammals remain largely unknown. To test whether living mammals preserve molecular evidence of dietary shifts, we examined the trehalase gene (Treh), which encodes an enzyme capable of digesting trehalose from insect blood, in bats and other mammals with diverse diets. Bats represent the largest dietary radiation among all mammalian orders, with independent origins of frugivory, nectarivory, carnivory, omnivory, and even sanguivory in an otherwise insectivorous clade. We found that Treh has been inactivated in unrelated bat lineages that independently radiated into noninsectivorous niches. Consistently, purifying selection has been markedly relaxed in noninsectivorous bats compared with their insectivorous relatives. Enzymatic assays of intestinal trehalase in bats suggest that trehalase activity tends to be lost or markedly reduced in noninsectivorous bats compared with their insectivorous relatives. Furthermore, our survey of Treh in 119 mammal species, which represent a deeper evolutionary timeframe, additionally identified a number of other independent losses of Treh in noninsectivorous species, recapitulating the evolutionary pattern that we found in bats. These results document a molecular record of dietary diversification in mammals, and suggest that such molecular signatures of dietary shifts would help us understand both historical and modern changes of animal diets.

Comparative Genomics Reveals the Genetic Mechanisms of Musk Secretion and Adaptive Immunity in Chinese Forest Musk Deer.

Abstract: The Chinese forest musk deer (Moschus berezovskii; FMD) is an artiodactyl mammal and is both economically valuable and highly endangered To investigate the genetic mechanisms of musk secretion and adaptive immunity in FMD, we compared its genome to nine other artiodactyl genomes Comparative genomics demonstrated that eight positively selected genes (PSGs) in FMD were annotated in three KEGG pathways that were related to metabolic and synthetic activity of musk, similar to previous transcriptome studies Functional enrichment analysis indicated that many PSGs were involved in the regulation of immune system processes, implying important reorganization of the immune system in FMD FMD-specific missense mutations were found in two PSGs (MHC class II antigen DRA and ADA) that were classified as deleterious by PolyPhen-2, possibly contributing to immune adaptation to infectious diseases Functional assessment showed that the FMD-specific mutation enhanced the ADA activity, which was likely to strengthen the immune defense against pathogenic invasion Single nucleotide polymorphism-based inference showed the recent demographic trajectory for FMD Our data and findings provide valuable genomic resources not only for studying the genetic mechanisms of musk secretion and adaptive immunity, but also for facilitating more effective management of the captive breeding programs for this endangered species