Genetic diversity, population genetic structure and demographic history of Przewalski’s gazelle (Procapra przewalskii): implications for conservation

Maintenance of Genetic Diversity Despite Population Fluctuations in the Lesser Prairie-Chicken (Tympanuchus pallidicinctus)

Assessments of genetic diversity, structure, history, and effective population size (N e) are critical for the conservation of imperiled populations. The lesser prairie-chicken (Tympanuchus pallidicinctus) has experienced declines due to habitat loss, degradation, and fragmentation in addition to substantial population fluctuations with unknown effects on genetic diversity. Our objectives were to: (i) compare genetic diversity across three temporally discrete sampling periods (2002, 2007-2010, and 2013-2014) that are characterized by low or high population abundance; (ii) examine genetic diversity at lek and lek cluster spatial scales; (ii) identify potential bottlenecks and characterize genetic structure and relatedness; and (iii) estimate the regional N e. We analyzed 194 samples across the shinnery oak prairie region of eastern New Mexico and western Texas using 13 microsatellite loci. Mean heterozygosity, allelic richness, and inbreeding coefficient were not significantly different between discrete sampling periods, suggesting that this population has maintained its genetic diversity across the sampled population fluctuations. We did not detect genetic structure using multiple Bayesian clustering approaches. Furthermore, there was no support for recent genetic bottlenecks, and we estimated that the N e ranged from 229.5 (p crit = 0.05, 95% CIs = 121.2-1023.1) to 349.1 (p crit = 0.02, 95% CIs = 176.4-2895.2) during our final sampling period (2013-2014). Although we provide evidence for gene flow within this region, continued habitat loss and fragmentation that leads to population declines and isolation could increase the risk of genetic consequences. Continued monitoring of genetic diversity and increasing available habitat that supports robust populations of lesser prairie-chickens may improve the likelihood of the species' persistence.

Exploring the population interaction of Przewalski's gazelle (Procapra przewalskii) based on the variations in gut microbiota across diverse geographic populations

The differences in gut microbiota among different populations, to a certain extent, reflect the degree of interaction between individuals within populations. To assess the interaction levels among several small populations of Przewalski's gazelle (Procapra przewalskii) (n = 105, from seven different regions) based on differences in gut microbiota, we used the closely related Tibetan gazelle (P. picticaudata) (n = 52, from seven different regions) as a control. We then compared the gut microbial communities between different populations of the two species using high-throughput sequencing of the 16S rRNA gene. The results showed that within a 100 km geographical distance, the intergroup differences in relative abundance of dominant bacteria, α-diversity, β-diversity, and functional metabolism abundance were higher or significantly higher in Przewalski's gazelle (narrowly distributed species) compared to the Tibetan gazelle (widely distributed species). Additionally, the proportion of shared OTUs between groups in Przewalski's gazelle was significantly lower than in Tibetan gazelle (p < 0.05). Additionally, neutral community model results also showed lower dispersal limitation in the Tibetan gazelle compared to Przewalski's gazelle. Therefore, based on the above results, we comprehensively speculate that the spatial interaction degree of Przewalski's gazelle in different habitat patches is relatively low. This study, starting from the perspective of gut microbiota, adopts a non-genetic perspective or method to assess whether there is, or to what extent there is, close interaction between species populations.

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.

Demographic and genetic structure of a severely fragmented population of the endangered hog deer (Axis porcinus) in the Indo-Burma biodiversity hotspot

The population of the globally endangered hog deer (Axis porcinus) has declined severely across its geographic range. Intensive monitoring of its demographic and genetic status is necessary. We examined the demographic and genetic structure of a small hog deer population in Keibul Lamjao National Park (KLNP), located on the western fringe of the Indo-Burma biodiversity hotspot for conservation planning. The distribution pattern of hog deer in the Park was derived based on the presence/absence of faecal pellets in 1 km × 1 km grids. We used double-observer distance sampling method to derive the hog deer abundance and population structure and compared with previous data to derive the population trend. We determined the genetic diversity of the population through microsatellite screening and bottleneck detection. The overall pellet density was 0.34 ± 0.02 pellets km^-2 restricted to only 22.34 ± 0.20 km² area of the park. The estimated density of the deer in the park was 1.82–4.32 individuals km^-2. The population showed a declining trend from 2006–08 (p < 0.05, R² = 0.916) with 8% annum^-1 and an increasing trend from 2003–2018 (p < 0.05, R² = 0.9304) with 10% annum^-1. The adult male-to-female ratio and fawn-to-doe ratio were 36.2 ± 1.9 males per 100 females and 16.5 ± 0.4 fawns per 100 females, respectively. The molecular examination suggested that the mean number of alleles at 23 loci was 2.70 ± 0.18, the observed heterozygosity (Ho) ranged from 0.26 to 0.63 (mean 0.42 ± 0.02), the expected heterozygosity (He) ranged from 0.23 to 0.73 (χ = 0.51 ± 0.03), and the polymorphic information content (PIC) ranged from 0.2 to 0.67 (χ = 0.43 ± 0.03) indicating a moderate level of genetic diversity. Although no bottleneck in the population was observed, the loss of genetic diversity may affect the evolutionary potential of the species at the site by limiting the selection flexibility. Conservation planning coupled with scientific management regime will help in the long term persistence of the population in the region.

Conservation Genetic Assessment of Savannah Elephants (Loxodonta africana) in the Greater Kruger Biosphere, South Africa

Savannah elephant populations have been severely reduced and fragmented throughout its remaining range. In general, however, there is limited information regarding their genetic status, which is essential knowledge for conservation. We investigated patterns of genetic variation in savannah elephants from the Greater Kruger Biosphere, with a focus on those in previously unstudied nature reserves adjacent to Kruger National Park, using dung samples from 294 individuals and 18 microsatellites. The results of genetic structure analyses using several different methods of ordination and Bayesian clustering strongly suggest that elephants throughout the Greater Kruger National Park (GKNP) constitute a single population. No evidence of a recent genetic bottleneck was detected using three moment-based approaches and two coalescent likelihood methods. The apparent absence of a recent genetic bottleneck associated with the known early 1900s demographic bottleneck may result from a combination of rapid post-bottleneck population growth, immigration and long generation time. Point estimates of contemporary effective population size (Ne) for the GKNP were ~ 500-700, that is, at the low end of the range of Ne values that have been proposed for maintaining evolutionary potential and the current ratio of Ne to census population size (Nc) may be quite low (<0.1). This study illustrates the difficulties in assessing the impacts on Ne in populations that have suffered demographic crashes but have recovered rapidly and received gene flow, particularly in species with long generation times in which genetic time lags are longer. This work provides a starting point and baseline information for genetic monitoring of the GKNP elephants.

Conservation genetics and genomics of threatened vertebrates in China

Conservation genetics and genomics are two independent disciplines that focus on using new techniques in genetics and genomics to solve problems in conservation biology. During the past two decades, conservation genetics and genomics have experienced rapid progress. Here, we summarize the research advances in the conservation genetics and genomics of threatened vertebrates (e.g., carnivorans, primates, ungulates, cetaceans, avians, amphibians and reptiles) in China. First, we introduce the concepts of conservation genetics and genomics and their development. Second, we review the recent advances in conservation genetics research, including noninvasive genetics and landscape genetics. Third, we summarize the progress in conservation genomics research, which mainly focuses on resolving genetic problems relevant to conservation such as genetic diversity, genetic structure, demographic history, and genomic evolution and adaptation. Finally, we discuss the future directions of conservation genetics and genomics.

Effects of the Qinghai-Tibet Railway on the Landscape Genetics of the Endangered Przewalski's Gazelle (Procapra przewalskii)

The Przewalski’s gazelle (Procapra przewalskii) is one of the most endangered ungulates in the world, with fewer than 2,000 individuals surviving in nine habitat fragments on the Qinghai-Tibet Plateau and isolated by human settlements and infrastructure. In particular, the Qinghai-Tibet railway, which crosses the largest part of the gazelle’s distribution, remains a major concern because of its potential to intensify landscape genetic differentiation. Here, using mtDNA sequencing and microsatellite genotyping to analyze 275 Przewalski’s gazelle samples collected throughout the range, we observed low level of genetic diversity (mtDNA π = 0.0033) and strong phylogeographic structure. Overall, the nine patches of gazelles can be further clustered into five populations, with a strong division between the eastern vs. western side of Qinghai Lake. Our study provides the first evidence of the genetic divergence between the Haergai North and Haergai South gazelle populations, corresponding to the recent construction of a wired enclosure along the Qinghai-Tibet railway less than ten years ago, an equivalent of five generations. Well-designed wildlife corridors across the railway along with long-term monitoring of the anthropogenic effects are therefore recommended to alleviate further habitat fragmentation and loss of genetic diversity in Przewalski’s gazelle.

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

The Tibetan antelope (chiru, Pantholops hodgsoni) is one of the most endangered mammals native to the Qinghai-Tibetan Plateau. The population size has rapidly declined over the last century due to illegal hunting and habitat damage. In the past 10 years, the population has reportedly been expanding due to conservation efforts. Several lines of evidence suggest that the Tibetan antelope has undergone a demographic bottleneck. However, the consequences of the bottleneck on genetic diversity and the post-bottleneck genetic recovery remain unknown. In this study, we investigate the genetic variation of 15 microsatellite loci from two Tibetan antelope populations sampled in 2003 (Pop2003) and 2013 (Pop2013). A higher level of genetic diversity (NA, 13.286; He, 0.840; PIC, 0.813; I, 2.114) was detected in Pop2013, compared to Pop2003 (NA, 12.929; He, 0.818; PIC, 0.789; I, 2.033). We observe that despite passing through the bottleneck, the Tibetan antelope retains high levels of genetic diversity. Furthermore, our results show significant or near significant increases in genetic diversity (He, PIC and I) in Pop2013 compared with Pop2003, which suggests that protection efforts did not arrive too late for the Tibetan antelope.

An evaluation of hair-snaring devices for small-bodied carnivores in southwest China

Human population growth is a major threat to the biodiversity of mammals in China. Rapid development of infrastructure, pollution, and poor enforcement of environmental laws in China have altered the landscape and accelerated the extinction rates of mammals. To maintain biodiversity and conserve the mammals of China, it is essential to develop monitoring protocols for species of concern that are efficient, cost-effective, and current. It is now common practice for ecologists to survey mammals of interest using noninvasive sampling methods. These sampling techniques are affordable, require no handling of the target animals, and generally yield large samples. In China, such sampling methods have rarely been used and evaluated. For this study, we recorded the behavior of masked palm civets ( Paguma larvata ) and Siberian weasels ( Mustela sibirica ) to determine their relative preference for using different hair-snaring devices and evaluated the effectiveness of each device at collecting hair. Our goal was to determine which genetic sampling method(s) should be used to study masked palm civets and Siberian weasels in the future in Southwest China. In March–June of 2014, we monitored 13 hair-snare stations throughout the Main Valley of Laohegou Nature Reserve, Sichuan Province, China. Genetic analysis revealed that we collected 373 hair samples from civets and 47 hair samples from weasels over 104 and 26 sessions, respectively. Both civets and weasels seemed to prefer lure sticks to ground cubbies; however, the latter were more effective at collecting civet hair. Although glue sheets from lure sticks collected large samples of guard hair (&gt; 10), no device in its current design was consistently effective at collecting weasel hair. We suggest researchers in Southwest China use ground cubbies as described in this study to collect hair from masked palm civets and test other cubby designs (e.g., longer gun brushes or smaller in size) for collecting hair from Siberian weasels.

人口增长是中国哺乳动物多样性危机的主要根源之一。在中国，基础建设的快速发展、环境污染，加之环境执法力度不足造成了哺乳动物的栖息地的退化，加速了动物的灭绝速率。为了维持生物多样性水平和保护中国的哺乳动物，有必要针对受关注的物种开发有效、低成本且通用的监测方法。现在，非损伤性取样方法正被生态学家普遍应用于哺乳动物的调查中。这些调查技术在成本上易于接受，不需要接触目标动物，并且通常可以得到大量可靠的样本。在中国，非损伤性取样方法的应用和评估还较少。本研究中，我们在四川省老河沟自然保护区评估了花面狸和黄鼬对毛发陷阱的访问偏好及陷阱收集动物毛发的有效性；目标是选出有效地遗传取样方法用于将来对花面狸和黄鼬的研究。从2014年3月到6月，我们在保护区主要山谷内设置了13个毛发陷阱站，在收集野生动物的毛发同时使用红外相机记录动物访问陷阱站时的行为。我们发现，相比于设置在地面的小室陷阱，花面狸和黄鼬都更喜欢访问直立的木桩陷阱，但是，小室陷阱能够更有效地收集花面狸的毛发。尽管固定有粘性薄片的木桩 陷阱能够少量收集带有直针毛的毛发（&gt;10根）,但是我们评估的毛发陷阱都不能有效地收集黄鼬的 毛发。根据研究，我们建议研究人员在中国西南可以应用固定有枪刷的小室陷阱（如本研究中所评估的）收集花面狸的毛发，而用更长的枪刷，或者更小的小室陷阱，并固定粘性薄片收集黄鼬的毛发。

A spatially explicit model of functional connectivity for the endangered Przewalski's gazelle (Procapra przewalskii) in a patchy landscape

Background

Habitat fragmentation, associated with human population expansion, impedes dispersal, reduces gene flow and aggravates inbreeding in species on the brink of extinction. Both scientific and conservation communities increasingly realize that maintaining and restoring landscape connectivity is of vital importance in biodiversity conservation. Prior to any conservation initiatives, it is helpful to present conservation practitioners with a spatially explicit model of functional connectivity for the target species or landscape.

Methodology/Principal Findings

Using Przewalski’s gazelle (Procapra przewalskii) as a model of endangered ungulate species in highly fragmented landscape, we present a model providing spatially explicit information to inform the long-term preservation of well-connected metapopulations. We employed a Geographic Information System (GIS) and expert-literature method to create a habitat suitability map, to identify potential habitats and to delineate a functional connectivity network (least-cost movement corridors and paths) for the gazelle. Results indicated that there were limited suitable habitats for the gazelle, mainly found to the north and northwest of the Qinghai Lake where four of five potential habitat patches were identified. Fifteen pairs of least-cost corridors and paths were mapped connecting eleven extant populations and two neighboring potential patches. The least-cost paths ranged from 0.2 km to 26.8 km in length (averaging 12.4 km) and were all longer than corresponding Euclidean distances.

Conclusions/Significance

The model outputs were validated and supported by the latest findings in landscape genetics of the species, and may provide impetus for connectivity conservation programs. Dispersal barriers were examined and appropriate mitigation strategies were suggested. This study provides conservation practitioners with thorough and visualized information to reserve the landscape connectivity for Przewalski’s gazelle. In a general sense, we proposed a heuristic framework for species with similar biological and ecological characteristics.

Recent geological events and intrinsic behavior influence the population genetic structure of the chiru and tibetan gazelle on the tibetan plateau

The extent to which a species responds to environmental changes is mediated not only by extrinsic processes such as time and space, but also by species-specific ecology. The Qinghai-Tibetan Plateau uplifted approximately 3000 m and experienced at least four major glaciations during the Pleistocene epoch in the Quaternary Period. Consequently, the area experienced concurrent changes in geomorphological structure and climate. Two species, the Tibetan antelope (Pantholops hodgsonii, chiru) and Tibetan gazelle (Procapra picticaudata), both are endemic on the Qinghai-Tibetan Plateau, where their habitats overlap, but have different migratory behaviors: the chiru is inclined to have female-biased dispersal with a breeding migration during the calving season; in contrast, Tibetan gazelles are year-round residents and never migrate distantly. By using coalescence methods we compared mitochondrial control region DNA sequences and variation at nine microsatellite loci in these two species. Coalescent simulations indicate that the chiru and Tibetan gazelle do not share concordant patterns in their genealogies. The non-migratory Tibetan gazelle, that is more vulnerable to the impact of drastic geographic changes such as the elevation of the plateau, glaciations and so on, appears to have a strong population genetic structure with complicated demographic history. Specifically, the Tibetan gazelle population appears to have experienced isolation and divergence with population fluctuations since the Middle Pleistocene (0.781 Ma). However, it showed continued decline since the Upper Pleistocene (0.126 Ma), which may be attributed to the irreversible impact of increased human activities on the plateau. In contrast, the migratory chiru appears to have simply experienced population expansion. With substantial gene flow among regional populations, this species shows no historical population isolation and divergence. Thus, this study adds to many empirical studies that show historical and contemporary extrinsic and intrinsic processes shape the recent evolutionary history and population genetic structure of species.

Isolation and Characterization of Cross-Amplification Microsatellite Panels for Species of Procapra (Bovidae; Antilopinae)

The three Procapra species, Tibetan gazelle (P. picticaudata), Mongolian gazelle (P. gutturosa) and Przewalski’s gazelle (P. przewalskii) are endemic to Asia. Several intraspecific genetic issues have been studied with species-specific microsatellite loci in these Asian gazelles. However, cross-species microsatellite panels are absent, which inhibits comparative conservation and evolutionary studies of the Procapra. In this study, we isolated 20 cross-species microsatellite loci for Procapra from both related species and the genomic library of P. przewalskii. Fifty-three samples of the three gazelles were used to characterize the markers. Allele numbers ranged from three to 20, with a mean of 7.93 per locus. Observed heterozygosity (H_O) averaged 0.680 and expected heterozygosity (H_E) 0.767. The mean polymorphic information content (PIC) was 0.757 for P. picticaudata, 0.803 for P. gutturosa and 0.590 for P. przewalskii. Nine loci were significantly deviated from Hardy-Weinberg (H-W) equilibrium in the three species. Significant linkage disequilibrium was detected in four pairs of loci in P. przewalskii, five pairs in P. gutturosa and 51 pairs in P. picticaudata. Considering the abundance of published loci and their high success rates of cross-amplification, testing and utilization of loci from related species is efficient for wild species of Bovidae. The cross-species microsatellite loci we developed will facilitate further interspecies genetic studies in Procapra.