Biology subjects

Shi, C.-M.

Publications and source records attributed to Shi, C.-M..

5 recordsLinked to original sources

bioRxiv2023

Molecular evaluation of Conogethes punctiferalis (Guenee, 1854): Species status and intraspecific divergence

Species are not only the fundamental units of taxonomy but also the basic units of pest management. Insects of Conogethes are important agricultural and forestry pests. However, species boundaries within Conogethes often appear obscure. In the present study, we re-evaluated the species status of Conogethes by applying three species delimitation approaches based on the mitochondrial DNA sequences, with particular emphasis on the yellow peach moth C. punctiferalis (Guenee, 1854). We first optimized species delimitation and inter-species genetic divergence threshold using a DNA barcoding dataset. Our results revealed that several nominal species of Conogethes species harbored deeply diverged mitochondrial lineages which were recognized as independent species by the species delimitation methods. The p-distance between the delimited putative species ranged from 0.0159 to 0.1321 with a mean of 0.0841. Then we refined the species status of C. punctiferalis using the smallest interspecific distance threshold based on a geographically comprehensive population-scale dataset. This procedure narrowed the species concept of C. punctiferalis to a genetically coherent unit. Further investigation of its intraspecific divergence in the geographic context revealed that the refined C. punctiferalis was still widely distributed with the same or highly similar mitochondrial haplotypes occurring across South and East Asia.

zoology↗

bioRxiv2023

Asynchronous phylogeographic and demographic dynamics of rodent community in the low latitude Asia

It is increasing evident that demographic history and phylogeographic consequences of past climate changes were unfolded locally and varied from region to region. Despite the high Murinae rodent species richness and endemism in the low latitude Asia, how the past climatic fluctuations shaped the phylogeographic and demographic history in this area remains unknown. Here we trapped 253 field Murine individuals and successfully amplified COI gene sequence for DNA barcoding. The phylogenetic tree showed the Murinae diversification included ten species belong to Rattini and Murini tribes. The divergence dating suggested that the most common ancestor (TMRCA) of each rodent species was estimated in Early or Middle Pleistocene. Bayesian skyline plot (BSP) exhibited the onset of population growth of seven Murinae rodents occurred at penultimate or last glaciation, and while R. losea and R. norvegicus keep effective population size constant through their elapsed time. Additionally, the six rodent species range of refugia area in the LGM projected by ecological niche models (ENMs) exhibited expander than the suitable area on present, meanwhile the remaining four rodent species showed contracted refugia regions. Hence, our results suggested that the rodent community displayed the asynchronous demographic and phylogeographic dynamics in the low latitude Asia.

molecular biology↗

bioRxiv2021

Phylogeography of the desert scorpion Mesobuthus mongolicus illuminates a route out of Central Asia and Junggar Basin as a corridor for faunal exchange between Central and East Asia

A comprehensive understanding of the ecological, evolutionary and genetic consequences of climate changes requires integration of information from different geographic regions and ecosystems. However, a clear knowledge gap exists in arid biota of Asian drylands, where climate change and biological evolution demonstrate high regional specificity. We report here our phylogeographic study on the desert scorpion Mesobuthus mongolicus, attempting to narrow the gap. Range wide samples for one mitochondrial gene and three nuclear loci were subjected to phylogenetic inferences, molecular dating, Bayesian phylogeographic and demographic reconstructions, and population genetic analyses. Ecological niche modeling was employed to generate models of potential distribution range at present and during the last glacial maximum (LGM). Our results revealed that M. mongolicus represents a single coherent lineage that diverged with its most closely related lineage from Central Asia about 1.36 Ma and underwent radiation ever since. Bayesian phylogeographic reconstruction suggested the ancestral population of M. mongolicus dispersed gradually eastward through the Junngar Basin to the Gobi region during the late Pleistocene, strengthening the view that the Junggar Basin has constituted an important corridor for faunal exchange between Central Asian and East Asia. We found that the desert scorpion underwent demographic expansion while experiencing range contraction during the LGM. Development of sandy deserts in northwest China incurred by Eurasian aridification might have opened up substantial empty niches that sustained population expansion during the LGM. Our results suggested that organisms ecological adaptations have acted as an important determinant for their phylogeographic and demographic responses to past climate changes.

evolutionary biology↗

bioRxiv2019

Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski’s scorpion (Scorpiones: Buthidae) in arid Asian inland

Reliable delimitation of venomous scorpions is not only consequential to toxicological studies but also instructive to conservation and exploration of these important medical resources. In the present study, we delimited species boundary for the the Przewalski’s scorpion from arid northwest China through a combined approach employing phylogenetic analysis, ecological niche modeling and morphological comparison. Our results indicate that the the Przewalski’s scorpion represent an independent taxonomic unit and should be recognized as full species rank, Mesobuthus przewalsii stat. n.. This species and the Chinese scorpion M. martensii represent the eastern members of the M. caucasicus species group which manifests a trans-Central Asia distribution across the Tianshan Mountains range. We also discussed the likely geographic barrier and climatic boundary that demarcate distributional range of the the Przewalski’s scorpion.Competing Interest StatementThe authors have declared no competing interest.View Full Text

zoology↗

bioRxiv2018

AIM-SNPtag: a computationally efficient approach for developing ancestry-informative SNP panels

Inferring an individuals ancestry or group membership using a small set of highly informative genetic markers is very useful in forensic and medical genetics. However, given the huge amount of SNP data available from a diverse of populations, it is challenging to develop informative panels by exhaustively searching for all possible SNP combination. In this study, we formulate it as an algorithm problem of selecting an optimal set of SNPs that maximizes the inference accuracy while minimizes the set size. Built on this conception, we develop a computational approach that is capable of constructing ancestry informative panels from multi-population genome-wide SNP data efficiently. We evaluate the performance of the method by comparing the panel size and membership inference accuracy of the constructed SNP panels to panels selected through empirical procedures in former studies. For the membership inference of population groups including Asian, European, African, East Asian and Southeast Asian, a 36-SNP panel developed by our approach has an overall accuracy of 99.07%, and a 21-SNP subset of the panel has an overall accuracy of 95.36%. In comparison, the existing panel requires 74 SNPs to achieve an accuracy of 94.14% on the same set of population groups. We further apply the method to four subpopulations within Europe (Finnish, British, Spain and Italia); a 175-SNP panel can discriminate individuals of those European subpopulations with an accuracy of 99.36%, of which a 68-SNP subset can achieve an accuracy of 95.07%. We expect our method to be a useful tool for constructing ancestry informative markers in forensic genetics.

bioinformatics↗