Microsatellite Loci Analysis Reveals Post-bottleneck Recovery of Genetic Diversity in the Tibetan Antelope

Population Genetic Diversity and Viability of the North China Leopard (Panthera pardus japonensis) in the Eastern Loess Plateau, China

The North China leopard population in the eastern Loess Plateau, China, is highly fragmented and faces an increased risk of extinction due to habitat loss and environmental change. Therefore, timely research on leopard conservation in the Loess Plateau region can provide scientific guidance for its management and population recovery. To investigate the impacts of habitat fragmentation on genetic diversity, we analyzed 129 fecal samples from the eastern foot of the Loess Plateau, China. Using eight pairs of microsatellite loci and mitochondrial ND-5 gene sequences, we genetically identified 41 individual leopards. Analysis of microsatellite data showed an intermediate level of genetic diversity (PIC = 0.60). Based on the ND-5 gene sequence, five haplotypes were identified, with a moderate level of genetic diversity (Hd = 0.23, Pi = 0.00048). Inbreeding analyses documented significant population inbreeding pressure. Using VORTEX, we also explored the future development of the population by analyzing the population viability. The results indicated no extinction risk for the leopard population in the next 100 years under current genetic conditions. However, a loss of 22% genetic diversity is expected. These results emphasize the need to strengthen leopard monitoring, mitigate inbreeding, and restore habitat connectivity to preserve genetic diversity.

Genetic Identity and Diversity of Loggerhead Sea Turtles in the Central Mediterranean Sea

Background: The conservation of loggerhead sea turtles (Caretta caretta) in the central Mediterranean benefits from an in-depth understanding of its population genetic structure and diversity. Methods: This study, therefore, investigates C. caretta in Maltese waters by genetically analysing 63 specimens collected through strandings and in-water sampling, using mitochondrial DNA control region and microsatellites. Additionally, the two nests detected in Malta in 2023 were analysed for the same markers. Results: Mitochondrial data identified 10 haplotypes, with mixed stock analyses tracing 87.5% of the specimens to Mediterranean origins, primarily from Libyan rookeries, with contributions from Lebanon, Israel and Turkey. Three Atlantic haplotypes were identified in six specimens, with CC-A17.1 linking central Mediterranean foraging individuals to rookeries in Cape Verde. Five of these six Atlantic haplotype records were from recently sampled individuals (2022-2023), possibly indicating a recent eastward expansion of Atlantic haplotypes into the Mediterranean. Bayesian clustering (K = 2) of microsatellite data using haplotypes as priori revealed similar proportions for clusters across most specimens, except for three specimens with Atlantic haplotypes CC-A1.1 and CC-A1.3, which exhibited distinct patterns. The two nests examined here displayed Mediterranean haplotypes, with nuclear DNA matching the predominant Mediterranean profiles found in foraging individuals, suggesting that local clutches originated from Mediterranean parents. Conclusions: Increasing nesting activity on Maltese beaches and this archipelago's geographical position highlight the need for ongoing genetic monitoring to track changes in genetic diversity and develop conservation strategies that support the effective protection of this species and its habitats.

A high-quality chromosome-level reference genome assembly of Tibetan antelope (Pantholops hodgsonii)

Tibetan antelope (Pantholops hodgsonii), a wild ruminant endemic to the Qinghai-Tibetan Plateau (QTP) in China, has evolved a series of genetic and physiological adaptation strategies to thrive in the harsh plateau environments. However, limited research on the genome of this species exists. Here, we established a high-quality chromosome-level reference genome assembly of the Tibetan antelope using PacBio HiFi, DNBSEQ, and Hi-C sequencing data. The assembly, totaling 3.13 GB, consists of 31 chromosomes (29 + X + partial Y), with a Scaffold N50 length of 92.23 Mb. The quality value (QV) and Benchmarking Universal Single-Copy Ortholog (BUSCO) score were 70.14 and 98.20%, respectively, indicating that our genome sequence is of high quality and completeness. Our genome not only contribute to the genetic conservation of Tibetan antelope but also provides a valuable resource for genetic, ecological, and evolutionary research within the sub-family Caprinae.

Large‐scale genetic surveys for main extant population of wild giant panda ( Ailuropoda melanoleuca ) reveals an urgent need of human management

There are only six isolated living giant panda populations, and a comprehensive understanding of their genetic health status is crucial for the conservation of this vulnerable species. Liangshan Mountains is one of the main distribution areas of living giant pandas and is outside the newly established Giant panda national park. In this study, 971 giant panda fecal samples were collected in the heartland of Liangshan Mountains (Mabian Dafengding Nature Reserve: MB; Meigu Dafengding Nature Reserve: MG; and Heizhugou Nature Reserve: HZG). Microsatellite markers and mitochondrial D-loop sequences were used to estimate population size and genetic diversity. We identified 92 individuals (MB: 27, MG: 22, HZG: 43) from the three reserves. Our results showed that: (1) genetic diversity of three giant panda populations was moderate; (2) several loci deviated significantly from the Hardy-Weinberg equilibrium and almost all these deviated loci showed significant heterozygote deficiencies and inbreeding; (3) three giant panda populations have substantial genetic differentiation with the most differentiation between MB and the two other populations; and (4) a large amount of giant panda feces outside the three reserves were found, implying the existence of protection gap. These results indicated that under stochastic events, the giant panda populations in Liangshan Mountains are at risk of genetic decline or extinction and urgent need of human management. This study revealed that high attention should be paid to the protection of these giant panda populations outside the Giant panda national park, to ensure their survival in their distribution areas.

Identifying priority reserves favors the sustainable development of wild ungulates and the construction of Sanjiangyuan National Park

Sanjiangyuan National Park (SNP), the first national park in China, is one of the most important biodiversity conservation areas in the Sanjiangyuan National Nature Reserve (SNNR) and even the world. The threatened ungulates play an irreplaceable role in maintaining the ecosystem diversity and stability in SNNR. Here, based on 1434 occurrence records of six ungulates, the maximum entropy model, with two different strategies, was utilized to determine the priority reserves. The results indicated that the priority reserves in SNNR was mainly located in and around SNP, which were mainly distributed in the middle east, middle west, and southwest of SNNR. Six ungulates shared preference for altitude ranging 4000-5000 m, the average annual temperature below -3.0°C, and average annual precipitation ranging 200-400 mm on meadow, steppe, and unused land. The proportion of high and medium suitable areas for ungulates in SNP was higher than that in SNNR. As the SNP is not contiguously spaced in space, and some core wildlife habitats are not included, it is suggested to optimize the functional areas and adjust the boundary range on the basis of the pilot scope of SNP, so as to enhance the integrity and connectivity of each functional area.

Resistance-Based Connectivity Model to Construct Corridors of the Przewalski’s Gazelle (Procapra Przewalskii) in Fragmented Landscape

Habitat connectivity is indispensable for the survival of species that occupy a small habitat area and have isolated habitat patches from each other. At present, the development of human economy squeezes the living space of wildlife and interferes and hinders the dispersal of species. The Przewalski’s gazelle (Procapra przewalskii) is one of the most endangered ungulates, which has experienced a significant reduction in population and severe habitat shrinkage. Although the population of this species has recovered to a certain extent, human infrastructure severely hinders the gene flow between several patches of this species. Therefore, we used the maximum entropy (MaxEnt) model to simulate the habitat suitability of the Przewalski’s gazelle. In addition, we combined habitat suitability and ecological characteristics of the species to obtain eight habitat patches. Finally, we used the least-cost path (LCP) and circuit theory based on the resistance model to simulate the landscape network of this species. The results showed that habitat patches and connectivity in the east of the Qinghai Lake were crucial to the communication between populations of the Przewalski gazelle, and our study provided important reference for the distribution of important habitats and the construction of corridor between patches. Our study aimed to provide habitat networks and maintain landscape connectivity for achieving the fundamental goal of protecting and revitalizing populations of the Przewalski’s gazelle.

Microsatellite Genotyping Corroborated Loss of Genetic Diversity in Clarias batrachus as a Result of Lack of Regulatory Reforms in Aquaculture

In India, over the past 50 years, aquaculture practices of species such as those used for Clarias batrachus were developed without adequate regulatory oversight. In these situations, it is important to consider the influence that genetic factors can have on such vulnerable aquaculture species. Population genetic structure can be evaluated through the use of neutral molecular markers, and this can aid in predicting the risk of the demise of populations and for framing management strategies to conserve remaining populations. The study presented here reports on the genetic status of C. batrachus populations through the analysis of data collected using 22 microsatellite markers from seven natural and one hatchery population. The mean values for observed heterozygosity across loci within populations ranged from 0.242 to 0.485. Measures of genetic differentiation were low overall, with mean values for F_ST of 0.270, F_IS of 0.113 and F_IT of 0.353. An AMOVA analysis revealed that percentages of variation among and within populations were 27.16 and 6.86, respectively, and Bayesian clustering analyses showed a population subdivision consisting of five clusters with admixture of haplotypes from other populations leading to genetic bottleneck. We also examined how hatchery management factors leading to excessive exchanges of fish between river systems through could impact the structure of the C. batrachus populations. Overall, this study shows how the systematic use of molecular markers can facilitate the development of management policies for these populations and for the development of a comprehensive set of rules for hatcheries and aquaculture practices, including avoidance of excessive homozygosity by avoiding repeated use of feral broodstock and their interrogation.

Population genetics reveals high connectivity of giant panda populations across human disturbance features in key nature reserve

The giant panda is an example of a species that has faced extensive historical habitat fragmentation, and anthropogenic disturbance and is assumed to be isolated in numerous subpopulations with limited gene flow between them. To investigate the population size, health, and connectivity of pandas in a key habitat area, we noninvasively collected a total of 539 fresh wild giant panda fecal samples for DNA extraction within Wolong Nature Reserve, Sichuan, China. Seven validated tetra-microsatellite markers were used to analyze each sample, and a total of 142 unique genotypes were identified. Nonspatial and spatial capture-recapture models estimated the population size of the reserve at 164 and 137 individuals (95% confidence intervals 153-175 and 115-163), respectively. Relatively high levels of genetic variation and low levels of inbreeding were estimated, indicating adequate genetic diversity. Surprisingly, no significant genetic boundaries were found within the population despite the national road G350 that bisects the reserve, which is also bordered with patches of development and agricultural land. We attribute this to high rates of migration, with four giant panda road-crossing events confirmed within a year based on repeated captures of individuals. This likely means that giant panda populations within mountain ranges are better connected than previously thought. Increased development and tourism traffic in the area and throughout the current panda distribution pose a threat of increasing population isolation, however. Maintaining and restoring adequate habitat corridors for dispersal is thus a vital step for preserving the levels of gene flow seen in our analysis and the continued conservation of the giant panda meta-population in both Wolong and throughout their current range.

The roles of calving migration and climate change in the formation of the weak genetic structure in the Tibetan antelope (Pantholops hodgsonii)

Geographical barriers and distance can reduce gene exchange among animals, resulting in genetic divergence of geographically isolated populations. The Tibetan antelope (Pantholops hodgsonii) has a geographical range of approximately 1600 km across the Qinghai-Tibet Plateau, which comprises a series of tall mountains and big rivers. However, previous studies indicate that there is little genetic differentiation among their geographically delineated populations. To better understand the genetic structure of P. hodgsonii populations, we collected 145 samples from the 3 major calving regions, taking into consideration their various calving grounds and migration routes. We used a combination of mitochondrial sequences (Cyt b, ATPase, D-loop and COX I) to investigate the genetic structure and the evolutionary divergence of the populations. Significant, albeit weak, genetic differentiation was detected among the 3 geographical populations. Analysis of the genetic divergence process revealed that the animals gradually entered a period of rapid genetic differentiation approximately 60 000 years ago. The calving migration of P. hodgsonii cannot be the main cause of their weak genetic structure because this cannot fully homogenize the genetic pool. Instead, the geological and climatic events as well as the coupling vegetation succession process during this period have been suggested to greatly contribute to the genetic structure and the expansion of genetic diversity.