Noninvasive genetic analyses for estimating population size and genetic diversity of the remaining Far Eastern leopard (Panthera pardus orientalis) population

Can genetic rescue help save Arabia's last big cat?

Genetic diversity underpins evolutionary potential that is essential for the long-term viability of wildlife populations. Captive populations harbor genetic diversity potentially lost in the wild, which could be valuable for release programs and genetic rescue. The Critically Endangered Arabian leopard (Panthera pardus nimr) has disappeared from most of its former range across the Arabian Peninsula, with fewer than 120 individuals left in the wild, and an additional 64 leopards in captivity. We (i) examine genetic diversity in the wild and captive populations to identify global patterns of genetic diversity and structure; (ii) estimate the size of the remaining leopard population across the Dhofar mountains of Oman using spatially explicit capture-recapture models on DNA and camera trap data, and (iii) explore the impact of genetic rescue using three complementary computer modeling approaches. We estimated a population size of 51 (95% CI 32-79) in the Dhofar mountains and found that 8 out of 25 microsatellite alleles present in eight loci in captive leopards were undetected in the wild. This includes two alleles present only in captive founders known to have been wild-sourced from Yemen, which suggests that this captive population represents an important source for genetic rescue. We then assessed the benefits of reintroducing novel genetic diversity into the wild population as well as the risks of elevating the genetic load through the release of captive-bred individuals. Simulations indicate that genetic rescue can improve the long-term viability of the wild population by reducing its genetic load and realized load. The model also suggests that the genetic load has been partly purged in the captive population, potentially making it a valuable source population for genetic rescue. However, the greater loss of its genetic diversity could exacerbate genomic erosion of the wild population during a rescue program, and these risks and benefits should be carefully evaluated. An important next step in the recovery of the Arabian leopard is to empirically validate these conclusions, implement and monitor a genomics-informed management plan, and optimize a strategy for genetic rescue as a tool to recover Arabia's last big cat.

Diversity of selected toll-like receptor genes in cheetahs (Acinonyx jubatus) and African leopards (Panthera pardus pardus)

The anthropogenic impact on wildlife is ever increasing. With shrinking habitats, wild populations are being pushed to co-exist in proximity to humans leading to an increased threat of infectious diseases. Therefore, understanding the immune system of a species is key to assess its resilience in a changing environment. The innate immune system (IIS) is the body's first line of defense against pathogens. High variability in IIS genes, like toll-like receptor (TLR) genes, appears to be associated with resistance to infectious diseases. However, few studies have investigated diversity in TLR genes in vulnerable species for conservation. Large predators are threatened globally including leopards and cheetahs, both listed as 'vulnerable' by IUCN. To examine IIS diversity in these sympatric species, we used next-generation-sequencing to compare selected TLR genes in African leopards and cheetahs. Despite differences, both species show some TLR haplotype similarity. Historic cheetahs from all subspecies exhibit greater genetic diversity than modern Southern African cheetahs. The diversity in investigated TLR genes is lower in modern Southern African cheetahs than in African leopards. Compared to historic cheetah data and other subspecies, a more recent population decline might explain the observed genetic impoverishment of TLR genes in modern Southern African cheetahs. However, this may not yet impact the health of this cheetah subspecies.

Efficient and cost-effective non-invasive population monitoring as a method to assess the genetic diversity of the last remaining population of Amur leopard (Panthera pardus orientalis) in the Russia Far East

Small populations of the endangered species are more vulnerable to extinction and hence require periodic genetic monitoring to establish and revisit the conservation strategies. The Amur leopard is critically endangered with about 100 individuals in the wild. In this study, we developed a simple and cost-effective noninvasive genetic monitoring protocol for Amur leopards. Also, we investigated the impact of fecal sample's age, storage, and collection season on microsatellite genotyping success and data quality. We identified 89 leopard scats out of the 342 fecal samples collected from Land of the Leopard between 2014-2019. Microsatellite genotyping using 12 markers optimized in 3 multiplex PCR reactions reveals presence of at least 24 leopard individuals (18 males and 6 females). There was a significant difference in the success rate of genotyping depending on the time from feces deposition to collection (p = 0.014, Fisher's exact test), with better genotyping success for samples having <2 weeks of environmental exposure. Amur leopard genetic diversity was found low (Ho- 0.33, HE- 0.35, and NA- 2.57) with no visible population substructure and recent bottleneck signature. Although a historical bottleneck footprint was observed. Mitochondrial DNA diversity was also found low with two haplotypes differing by a point mutation reported in 1,769 bp of investigated sequence covering parts of cytochrome b gene (846 bp), NADH-5 gene (611 bp) and control region (312 bp). We recommend periodic genetic monitoring of wild Amur leopards following the proposed methodology to achieve cost effectiveness and efficiency.

African and Asian leopards are highly differentiated at the genomic level

Leopards are the only big cats still widely distributed across the continents of Africa and Asia. They occur in a wide range of habitats and are often found in close proximity to humans. But despite their ubiquity, leopard phylogeography and population history have not yet been studied with genomic tools. Here, we present population-genomic data from 26 modern and historical samples encompassing the vast geographical distribution of this species. We find that Asian leopards are broadly monophyletic with respect to African leopards across almost their entire nuclear genomes. This profound genetic pattern persists despite the animals' high potential mobility, and despite evidence of transfer of African alleles into Middle Eastern and Central Asian leopard populations within the last 100,000 years. Our results further suggest that Asian leopards originated from a single out-of-Africa dispersal event 500-600 thousand years ago and are characterized by higher population structuring, stronger isolation by distance, and lower heterozygosity than African leopards. Taxonomic categories do not take into account the variability in depth of divergence among subspecies. The deep divergence between the African subspecies and Asian populations contrasts with the much shallower divergence among putative Asian subspecies. Reconciling genomic variation and taxonomy is likely to be a growing challenge in the genomics era.

Spatial ecology of the stone marten in an Alpine area: combining camera-trapping and genetic surveys

A species’ potential distribution can be modelled adequately only if no factor other than habitat availability affects its occurrences. Space use by stone marten Martes foina is likely to be affected by interspecific competition with the strictly related pine marten Martes martes, the latter being able to outcompete the first species in forested habitats. Hence, to point out the environmental factors which determine the distribution and density of the stone marten, a relatively understudied mesocarnivore, we applied two non-invasive survey methods, camera-trapping and faecal-DNA based genetic analysis, in an Alpine area where the pine marten was deemed to be absent (Val Grande National Park N Italy). Camera trapping was conducted from October 2014 to November 2015, using up to 27 cameras. Marten scats were searched for between July and November 2015 and, to assess density, in spring 2017. Species identification was accomplished by a PCR-RFLP method, while 17 autosomal microsatellites were used for individual identification. The stone marten occurred in all available habitats (83% of trapping sites and 73.2% of scats); nonetheless, habitat suitability, as assessed using MaxEnt, depended on four major land cover variables—rocky grasslands, rocks and debris, beech forests and chestnut forests—, martens selecting forests and avoiding open rocky areas. Sixteen individuals were identified, of which 14 related to each other, possibly forming six different groups. Using capwire estimators, density was assessed as 0.95 (0.7–1.3) ind/km2. In the study area, the widespread stone marten selected forested areas, attaining density values like those reported for the pine marten in northern Europe and suggesting that patterns of habitat selection may depend on the relative abundance of the two competing martens.

Phylogenetic study of extirpated Korean leopard using mitochondrial DNA from an old skin specimen in South Korea

The leopard, Panthera pardus, is a threatened species in its range throughout the world. Although, historically, the Korean Peninsula had a high population density of leopards, they were extirpated from South Korea by 1970, leaving almost no genetic specimens. Traditionally, Korean leopards are classified as Panthera pardus orientalis; however, their classification is based only on locality and morphology. Therefore, there is a need for genetic studies to identify the phylogenetic status of Korean leopards at the subspecies level. Presently, no extant wild specimen is available from South Korea; therefore, we extracted genetic material from the old skin of a leopard captured in Jirisan, South Korea in the 1930s and conducted the first phylogenetic study of the South Korean leopard. A total of 726 bp of mitochondrial DNA, including segments of the NADH5 and control region, were amplified by PCR. A phylogenetic analysis of the fragment, along with sequences of nine leopard subspecies from GenBank revealed that the extinct South Korean leopard belonged to the Asian leopard group and in the same clade as the Amur leopard (Panthera pardus orientalis). Thus, the leopard that inhabited South Korea in the past was of the same subspecies as the Amur leopard population currently inhabiting the transboundary region of Russia, China, and North Korea. These results emphasize the importance of conserving the endangered wild Amur leopard population (estimated to be about 60–80 individuals) in Russia and China, for future restoration of leopards in the Korean Peninsula.

The curse of observer experience: Error in noninvasive genetic sampling

Noninvasive genetic sampling (NGS) is commonly used to study elusive or rare species where direct observation or capture is difficult. Little attention has been paid to the potential effects of observer bias while collecting noninvasive genetic samples in the field, however. Over a period of 7 years, we examined whether different observers (n = 58) and observer experience influenced detection, amplification rates, and correct species identification of 4,836 gray wolf (Canis lupus) fecal samples collected in Idaho and Yellowstone National Park, USA and southwestern Alberta, Canada (2008-2014). We compared new observers (n = 33) to experienced observers (n = 25) and hypothesized experience level would increase the overall success of using NGS techniques in the wild. In contrast to our hypothesis, we found that new individuals were better than experienced observers at detecting and collecting wolf scats and correctly identifying wolf scats from other sympatric carnivores present in the study areas. While adequate training of new observers is crucial for the successful use of NGS techniques, attention should also be directed to experienced observers. Observer experience could be a curse because of their potential effects on NGS data quality arising from fatigue, boredom or other factors. The ultimate benefit of an observer to a project is a combination of factors (i.e., field savvy, local knowledge), but project investigators should be aware of the potential negative effects of experience on NGS sampling.

Fecal DNA isolation and degradation in clam Cyclina sinensis: noninvasive DNA isolation for conservation and genetic assessment

Background

To avoid destructive sampling for conservation and genetic assessment, we isolated the DNA of clam Cyclina sinensis from their feces. DNA electrophoresis and PCR amplification were used to determine the quality of fecal DNA. And we analyzed the effects of different conditions on the degradation of feces and fecal DNA.

Results

The clear fecal DNA bands were detected by electrophoresis, and PCR amplification using clam fecal DNA as template was effective and reliable, suggesting that clam feces can be used as an ideal material for noninvasive DNA isolation. In addition, by analyzing the effects of different environmental temperatures and soaking times on the degradation of feces and fecal DNA, we found that the optimum temperature was 4 °C. In 15 days, the feces maintained good texture, and the quality of fecal DNA was good. At 28 °C, the feces degraded in 5 days, and the quality of fecal DNA was poor.

Conclusions

The clam feces can be used as an ideal material for noninvasive DNA isolation. Moreover, the quality of fecal DNA is negatively correlated with environmental temperature and soaking time.

Assessing subspecies status of leopards (Panthera pardus) of northern Pakistan using mitochondrial DNA

Despite being classified as critically endangered, little work has been done on leopard protection in Pakistan. Once widely present throughout this region, leopards are now sparsely distributed, and possibly extinct from much of their previously recorded habitat. While leopards show morphological and genetic variation across their species range worldwide, resulting in the classification of nine different subspecies, the leopard genetic structure across Pakistan is unknown, with previous studies including only a very limited sampling. To clarify the genetic status of leopards in Pakistan we investigated the sequence variation in the subunit 5 of the mitochondrial gene NADH from 43 tissue samples and compared it with 238 sequences available from online databases. Phylogenetic analysis clearly separates the Pakistani leopards from the African and Arabian clades, confirming that leopards from Pakistan are members of the Asian clade. Furthermore, we identified two separate subspecies haplotypes within our dataset: P. p. fusca (N = 23) and P. p. saxicolor (N = 12).

Dispersal of Amur tiger from spatial distribution and genetics within the eastern Changbai mountain of China

Population dispersal and migration often indicate an expanded habitat and reduced inbreeding probability, and to some extend reflects improvement in the condition of the population. The Amur tiger population in the northern region of the Changbai mountain in China mostly distributes along the Sino-Russian border, next to the population in southwest Primorye in Russia. The successful dispersal westward and transboundary movement are crucial for the persistence of the Amur tiger in this area. This study explored the spatial dispersal of the population, transboundary migration, and the genetic condition of the Amur tiger population within the northern Changbai mountain in China, using occurrence data and fecal samples. Our results from 2003 to 2016 showed that the Amur tiger population in this area was spreading westward at a speed of 12.83 ± 4.41 km every three years. Genetic diversity of the Amur tiger populations in southwest Primorye was slightly different than the population in our study area, and the potential individual migration rate between these two populations was shown to be about 13.04%. Furthermore, the relationships between genetic distances and spatial distances indicated the existence of serious limitations to the dispersal of the Amur tiger in China. This study provided important information about spatial dispersal, transboundary migration, and the genetic diversity of Amur tigers in China, showed the urgent need for Amur tiger habitat restoration, and suggested some important conservation measures, such as corridor construction to eliminate dispersal barriers and joint international conservation to promote trans-boundary movement.

Genetic constraints of population expansion of the Carpathian lynx at the western edge of its native distribution range in Central Europe

Even though populations of many large carnivores are expanding throughout Europe, the Eurasian lynx population in the Western Carpathians seems unable to spread beyond the western boundaries of its current distributional range. Many factors, both extrinsic and intrinsic, can influence the potential for range expansion: landscape fragmentation, natal philopatry, low natural fecundity and high mortality, and low and sex-biased dispersal rates. In this study we used non-invasive genetic sampling to determine population size fluctuation, sub-structuring and social organisation of the peripheral lynx population at the Czech-Slovak border. Even though the population size has been relatively stable over the period studied (2010-2016), the individual inbreeding coefficients of residents at the end of the study were much higher than those of founders at the beginning of the study. While non-resident individuals (predominantly males) occurred regularly in the study population, only resident individuals with well-established home ranges participated in breeding and produced offspring. Almost half the offspring detected in the study (predominantly females) settled in or near the natal area. Subsequent incestuous mating resulted in production of inbred individuals, reduction of effective population size of the population, and sub-structuring of the population through formation of two distinct family lineages. Our study illustrates how social constraints, such as territoriality, breeding of residents and natal philopatry of females, lead to incestuous mating in small-sized populations, especially at the periphery of their distribution. This threat should be taken into account in planning of conservation and population recovery of species with similar social structure.

Seasonal food habits and prey selection of Amur tigers and Amur leopards in Northeast China

We analyzed the scats of Amur tigers and Amur leopards, and examined their annual and seasonal food habits in Northeast China to comprehend their coexistence. Wild boar had the highest annual and seasonal consumption frequencies by the tigers, while both roe deer and sika deer were mostly preyed by the leopards annually. The three species appeared to be the key preys in terms of high proportion of consumed biomass by the two felids. Our data also revealed numerous mid-sized carnivores and small mammals included in the two felids’ food list. We used the relative abundance and biomass density estimation in prey density estimation to calculate the prey preferences of tigers and leopards, and both methods confirmed that Amur tigers strongly preferred wild boar. However, preference estimations of Amur leopards were not consistant, or even opposite to one another from the two methods. The results of the study suggested that prey preference of predators is largely determined by body size of the prey species. Variation in diet composition of the two felids suggests that resource partitioning may contribute to their coexistence.

Assessment of genetic diversity, population structure, and gene flow of tigers (Panthera tigris tigris) across Nepal's Terai Arc Landscape

With fewer than 200 tigers (Panthera tigris tigris) left in Nepal, that are generally confined to five protected areas across the Terai Arc Landscape, genetic studies are needed to provide crucial information on diversity and connectivity for devising an effective country-wide tiger conservation strategy. As part of the Nepal Tiger Genome Project, we studied landscape change, genetic variation, population structure, and gene flow of tigers across the Terai Arc Landscape by conducting Nepal’s first comprehensive and systematic scat-based, non-invasive genetic survey. Of the 770 scat samples collected opportunistically from five protected areas and six presumed corridors, 412 were tiger (57%). Out of ten microsatellite loci, we retain eight markers that were used in identifying 78 individual tigers. We used this dataset to examine population structure, genetic variation, contemporary gene flow, and potential population bottlenecks of tigers in Nepal. We detected three genetic clusters consistent with three demographic sub-populations and found moderate levels of genetic variation (H_e = 0.61, A_R = 3.51) and genetic differentiation (F_ST = 0.14) across the landscape. We detected 3–7 migrants, confirming the potential for dispersal-mediated gene flow across the landscape. We found evidence of a bottleneck signature likely caused by large-scale land-use change documented in the last two centuries in the Terai forest. Securing tiger habitat including functional forest corridors is essential to enhance gene flow across the landscape and ensure long-term tiger survival. This requires cooperation among multiple stakeholders and careful conservation planning to prevent detrimental effects of anthropogenic activities on tigers.

Estimating the Population Size and Genetic Diversity of Amur Tigers in Northeast China

Over the past century, the endangered Amur tiger (Panthera tigris altaica) has experienced a severe contraction in demography and geographic range because of habitat loss, poaching, and prey depletion. In its historical home in Northeast China, there appears to be a single tiger population that includes tigers in Southwest Primorye and Northeast China; however, the current demographic status of this population is uncertain. Information on the abundance, distribution and genetic diversity of this population for assessing the efficacy of conservation interventions are scarce. We used noninvasive genetic detection data from scats, capture-recapture models and an accumulation curve method to estimate the abundance of Amur tigers in Northeast China. We identified 11 individual tigers (6 females and 5 males) using 10 microsatellite loci in three nature reserves between April 2013 and May 2015. These tigers are confined primarily to a Hunchun Nature Reserve along the border with Russia, with an estimated population abundance of 9–11 tigers during the winter of 2014–2015. They showed a low level of genetic diversity. The mean number of alleles per locus was 2.60 and expected and observed heterozygosity were 0.42 and 0.49, respectively. We also documented long-distance dispersal (~270 km) of a male Amur tiger to Huangnihe Nature Reserve from the border, suggesting that the expansion of neighboring Russian populations may eventually help sustain Chinese populations. However, the small and isolated population recorded by this study demonstrate that there is an urgent need for more intensive regional management to create a tiger-permeable landscape and increased genetic connectivity with other populations.

Emerging Technologies to Conserve Biodiversity

Technologies to identify individual animals, follow their movements, identify and locate animal and plant species, and assess the status of their habitats remotely have become better, faster, and cheaper as threats to the survival of species are increasing. New technologies alone do not save species, and new data create new problems. For example, improving technologies alone cannot prevent poaching: solutions require providing appropriate tools to the right people. Habitat loss is another driver: the challenge here is to connect existing sophisticated remote sensing with species occurrence data to predict where species remain. Other challenges include assembling a wider public to crowdsource data, managing the massive quantities of data generated, and developing solutions to rapidly emerging threats.