DNA barcoding revises a misidentification on musk deer

Insight into mtDNA diversity of wild forest musk deer (Moschus berezovskii) in Shanxi Province mountains

Shanxi Province is the northernmost distribution range of Chinese forest musk deer (Moschus berezovskii), with wild populations scattered across Zhongtiao (ZT), Lüliang (LL), and Taiyue (TY) mountain ranges. Using line transect surveys and local guide assistance, coupled with infrared camera data, this study systematically collected fecal samples from wild forest musk deer from five nature reserves across the three mountain ranges. Genetic diversity was analyzed using the mtDNA control region, which yielded 129 effective sequences of 656 bp and 20 distinct haplotypes. Haplotype and nucleotide diversities were 0.916 and 0.01505, respectively, indicating a relatively high overall genetic diversity in the studied populations. Significant genetic differentiation was observed between the Lüliang-Taiyue (LLTY) and ZT mountain range populations, with most of the genetic variation existing within the populations. No significant correlation was detected between the geographical and genetic distances of the samples, which may have resulted from historical agricultural activities in Shanxi impeding gene flow among populations. Therefore, genetic exchange programs are recommended to improve the genetic diversity and population fitness of forest musk deer in this region to facilitate their recovery and growth.

mtDNA analysis confirms the endangered Kashmir musk deer extends its range to Nepal

Musk deer Moschus spp. are endemic to the high mountain forests of central Asia. The taxonomic status of musk deer in the central and western Himalayas is poorly understood. We investigated the phylogenetic relationship of musk deer from the central and western Himalayas based on mitochondrial genomic data of Cytochrome b (380 bps) and D-loop (1000 bps). Our results distinguished two divergent lineages using higher bootstrap support (bs) values from the Maximum likelihood and Bayesian posterior probabilities (bpp). Both the Manang and Kaski lineages from central Nepal are confirmed as Himalayan musk deer Moschus leucogaster and represent a species complex widespread throughout the central and eastern Himalayan region. The musk deer Mustang lineage was confirmed as Kashmir musk deer Moschus cupreus and has wide distribution in the western Himalayas (from central Nepal to Afghanistan). Our analysis validates that Kashmir musk deer is a genetically distinct species and it clarifies that Himalayan musk deer and Kashmir musk deer are confirmed instead of Alpine musk deer Moschus chrysogaster which has been previously described from the southern parts of Himalayas of Nepal, India and Pakistan.

Roads to isolation: Similar genomic history patterns in two species of freshwater crabs with contrasting environmental tolerances and range sizes

Freshwater species often show high levels of endemism and risk of extinction owing to their limited dispersal abilities. This is exemplified by the stenotopic freshwater crab, Johora singaporensis which is one of the world's 100 most threatened species, and currently inhabits less than 0.01 km² of five low order hill streams within the highly urbanized island city‐state of Singapore. We compared populations of J. singaporensis with that of the non‐threatened, widespread, abundant, and eurytopic freshwater crab, Parathelphusa maculata, and found surprisingly high congruence between their population genomic histories. Based on 2,617 and 2,470 genome‐wide SNPs mined via the double‐digest restriction‐associated DNA sequencing method for ~90 individuals of J. singaporensis and P. maculata, respectively, the populations are strongly isolated (F_ST = 0.146–0.371), have low genetic diversity for both species (also for COI), and show signatures of recent genetic bottlenecks. The most genetically isolated populations for both species are separated from other populations by one of the oldest roads in Singapore. These results suggest that anthropogenic developments may have impacted stream‐dependent species in a uniform manner, regardless of ubiquity, habitat preference, or dispersal modes of the species. While signs of inbreeding were not detected for the critically endangered species, the genetic distinctiveness and low diversity of the populations call for genetic rescue and connecting corridors between the remaining fragments of the natural habitat.

DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine

Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.

DNA barcoding of the fishes of the genus Alburnoides (Actinopterygii, Cyprinidae) from Caucasus

Spirlins of the genus Alburnoides are widespread fishes, which taxonomy has been rapidly developing in recent years. Mitochondrial cytochrome c oxidase subunit I (COI) was used as DNA barcode marker to create a reference dataset of Caucasian Alburnoides and to test its barcoding efficiency. All four previously known Caucasian species of Alburnoides were confirmed as valid species with high genetic distances to sister species as well confirmed as Caucasian endemics. Alburnoides samiii, previously known from Sefidroud basin (Iran), was discovered in Transcaucasia. The accuracy of species identification of Ponto-Caspian Alburnoides by DNA barcodes was 100%. In addition, one potentially new species within A. gmelini was revealed. Despite the limited ability of COI to infer phylogenetic relationships, study provided evidence that Ponto-Caspian lineage of Alburnoides includes significantly larger number of species from Caspian Sea basin and inland basins of Central Asia.

Species Delimitation in the Genus Moschus (Ruminantia: Moschidae) and Its High-Plateau Origin

The authenticity of controversial species is a significant challenge for systematic biologists. Moschidae is a small family of musk deer in the Artiodactyla, composing only one genus, Moschus. Historically, the number of species in the Moschidae family has been debated. Presently, most musk deer species were restricted in the Tibetan Plateau and surrounding/adjacent areas, which implied that the evolution of Moschus might have been punctuated by the uplift of the Tibetan Plateau. In this study, we aimed to determine the evolutionary history and delimit the species in Moschus by exploring the complete mitochondrial genome (mtDNA) and other mitochondrial gene. Our study demonstrated that six species, M. leucogaster, M. fuscus, M. moschiferus, M. berezovskii, M. chrysogaster and M. anhuiensis, were authentic species in the genus Moschus. Phylogenetic analysis and molecular dating showed that the ancestor of the present Moschidae originates from Tibetan Plateau which suggested that the evolution of Moschus was prompted by the most intense orogenic movement of the Tibetan Plateau during the Pliocene age, and alternating glacial-interglacial geological eras.