Subspecies genetic assignments of worldwide captive tigers increase conservation value of captive populations

Tigers (Panthera tigris) are disappearing rapidly from the wild, from over 100,000 in the 1900s to as few as 3000. Javan (P.t. sondaica), Bali (P.t. balica), and Caspian (P.t. virgata) subspecies are extinct, whereas the South China tiger (P.t. amoyensis) persists only in zoos. By contrast, captive tigers are flourishing, with 15,000-20,000 individuals worldwide, outnumbering their wild relatives five to seven times. We assessed subspecies genetic ancestry of 105 captive tigers from 14 countries and regions by using Bayesian analysis and diagnostic genetic markers defined by a prior analysis of 134 voucher tigers of significant genetic distinctiveness. We assigned 49 tigers to one of five subspecies (Bengal P.t. tigris, Sumatran P.t. sumatrae, Indochinese P.t. corbetti, Amur P.t. altaica, and Malayan P.t. jacksoni tigers) and determined 52 had admixed subspecies origins. The tested captive tigers retain appreciable genomic diversity unobserved in their wild counterparts, perhaps a consequence of large population size, century-long introduction of new founders, and managed-breeding strategies to retain genetic variability. Assessment of verified subspecies ancestry offers a powerful tool that, if applied to tigers of uncertain background, may considerably increase the number of purebred tigers suitable for conservation management.     

Phylogeography and genetic ancestry of tigers (Panthera tigris)

Eight traditional subspecies of tiger (Panthera tigris),of which three recently became extinct, are commonly recognized on the basis of geographic isolation and morphological characteristics. To investigate the species' evolutionary history and to establish objective methods for subspecies recognition, voucher specimens of blood, skin, hair, and/or skin biopsies from 134 tigers with verified geographic origins or heritage across the whole distribution range were examined for three molecular markers: (1) 4.0 kb of mitochondrial DNA (mtDNA) sequence; (2) allele variation in the nuclear major histocompatibility complex class II DRB gene; and (3) composite nuclear microsatellite genotypes based on 30 loci. Relatively low genetic variation with mtDNA,DRB,and microsatellite loci was found, but significant population subdivision was nonetheless apparent among five living subspecies. In addition, a distinct partition of the Indochinese subspecies P. t. corbetti in to northern Indochinese and Malayan Peninsula populations was discovered. Population genetic structure would suggest recognition of six taxonomic units or subspecies: (1) Amur tiger P. t. altaica; (2) northern Indochinese tiger P. t. corbetti; (3) South China tiger P. t. amoyensis; (4) Malayan tiger P. t. jacksoni, named for the tiger conservationist Peter Jackson; (5) Sumatran tiger P. t. sumatrae; and (6) Bengal tiger P. t. tigris. The proposed South China tiger lineage is tentative due to limited sampling. The age of the most recent common ancestor for tiger mtDNA was estimated to be 72,000-108,000 y, relatively younger than some other Panthera species. A combination of population expansions, reduced gene flow, and genetic drift following the last genetic diminution, and the recent anthropogenic range contraction, have led to the distinct genetic partitions. These results provide an explicit basis for subspecies recognition and will lead to the improved management and conservation of these recently isolated but distinct geographic populations of tigers.     

Mitochondrial Phylogeography Illuminates the Origin of the Extinct Caspian Tiger and Its Relationship to the Amur Tiger

The Caspian tiger (Panthera tigris virgata) flourished in Central Asian riverine forest systems in a range disjunct from that of other tigers, but was driven to extinction in 1970 prior to a modern molecular evaluation. For over a century naturalists puzzled over the taxonomic validity, placement, and biogeographic origin of this enigmatic animal. Using ancient-DNA (aDNA) methodology, we generated composite mtDNA haplotypes from twenty wild Caspian tigers from throughout their historic range sampled from museum collections. We found that Caspian tigers carry a major mtDNA haplotype differing by only a single nucleotide from the monomorphic haplotype found across all contemporary Amur tigers (P. t. altaica). Phylogeographic analysis with extant tiger subspecies suggests that less than 10,000 years ago the Caspian/Amur tiger ancestor colonized Central Asia via the Gansu Corridor (Silk Road) from eastern China then subsequently traversed Siberia eastward to establish the Amur tiger in the Russian Far East. The conservation implications of these findings are far reaching, as the observed genetic depletion characteristic of modern Amur tigers likely reflects these founder migrations and therefore predates human influence. Also, due to their evolutionary propinquity, living Amur tigers offer an appropriate genetic source should reintroductions to the former range of the Caspian tiger be implemented.     

虎的保护遗传学研究进展

回顾了关于虎的遗传变异、种群结构、系统分类等保护遗传学研究,发现虎在遗传进化上面临的最严重与最需要解决的问题是遗传多样性低,圈养种群存在近交退化。为了有效保护和管理好虎现存的种群,建议划分虎的进化单元与保护管理单元,人工促进同一进化单元虎的基因交流;同时建立虎的基因文库,保护虎的基因资源。     

Why the Indian Subcontinent Holds the Key to Global Tiger Recovery

With only ~3,000 wild individuals surviving restricted to just 7% of their historical range, tigers are now a globally threatened species. Therefore, conservation efforts must prioritize regions that harbor more tigers, as well try to capture most of the remaining genetic variation and habitat diversity. Only such prioritization based on demographic, genetic, and ecological considerations can ensure species recovery and retention of evolutionary flexibility in the face of ongoing global changes. Although scientific understanding of ecological and demographic aspects of extant wild tiger populations has improved recently, little is known about their genetic composition and variability. We sampled 73 individual tigers from 28 reserves spread across a diversity of habitats in the Indian subcontinent to obtain 1,263 bp of mitochondrial DNA and 10 microsatellite loci. Our analyses reveals that Indian tigers retain more than half of the extant genetic diversity in the species. Coalescent simulations attribute this high genetic diversity to a historically large population size of about 58,200 tigers for peninsular India south of the Gangetic plains. Furthermore, our analyses indicate a precipitous, possibly human-induced population crash ~200 years ago in India, which is in concordance with historical records. Our results suggest that only 1.7% (with an upper limit of 13% and a lower limit of 0.2%) of tiger numbers in historical times remain now. In the global conservation context our results suggest that, based on genetic, demographic, and ecological considerations, the Indian subcontinent holds the key to global survival and recovery of wild tigers.     

Tigers of Sundarbans in India: Is the Population a Separate Conservation Unit?

The Sundarbans tiger inhabits a unique mangrove habitat and are morphologically distinct from the recognized tiger subspecies in terms of skull morphometrics and body size. Thus, there is an urgent need to assess their ecological and genetic distinctiveness and determine if Sundarbans tigers should be defined and managed as separate conservation unit. We utilized nine microsatellites and 3 kb from four mitochondrial DNA (mtDNA) genes to estimate genetic variability, population structure, demographic parameters and visualize historic and contemporary connectivity among tiger populations from Sundarbans and mainland India. We also evaluated the traits that determine exchangeability or adaptive differences among tiger populations. Data from both markers suggest that Sundarbans tiger is not a separate tiger subspecies and should be regarded as Bengal tiger (P. t. tigris) subspecies. Maximum likelihood phylogenetic analyses of the mtDNA data revealed reciprocal monophyly. Genetic differentiation was found stronger for mtDNA than nuclear DNA. Microsatellite markers indicated low genetic variation in Sundarbans tigers (He= 0.58) as compared to other mainland populations, such as northern and Peninsular (Hebetween 0.67- 0.70). Molecular data supports migration between mainland and Sundarbans populations until very recent times. We attribute this reduction in gene flow to accelerated fragmentation and habitat alteration in the landscape over the past few centuries. Demographic analyses suggest that Sundarbans tigers have diverged recently from peninsular tiger population within last 2000 years. Sundarbans tigers are the most divergent group of Bengal tigers, and ecologically non-exchangeable with other tiger populations, and thus should be managed as a separate “evolutionarily significant unit” (ESU) following the adaptive evolutionary conservation (AEC) concept.     

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.     

The year of the tiger and the year of tiger genomes!

Tigers are endangered apex predators. They typify endangered species because they are elusive, rare, and face numerous threats across their range. Tigers also symbolize conservation. However, it is very difficult to study tigers because of their stated nature. Also, tiger conservation is a geopolitically sensitive topic, making it difficult to use the studies to propose evidence-based management that allows their recovery, especially in the context of conservation genetics. Zhang et al. (Mol. Ecol. Resour., 2022) have created very valuable and rare resources to aid the community in conserving tigers. First, they present chromosome level genome assemblies of a South China tiger and an Amur tiger. Second, they present whole genome sequences of 16 captive South China tigers. Additionally, by using the assemblies they model the demographic history of these populations, estimate inbreeding and the potential threats they face in captivity. This approach is particularly important because genetic management is now the only remaining option for South China tigers, because they are extinct in the wild. In other words, captive individuals are our only hope for some day restoring the wild populations of South China tigers.     

Chromosome-scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger

The South China tiger (Panthera tigris amoyensis, SCT) is the most critically endangered subspecies of tiger due to functional extinction in the wild. Inbreeding depression is observed among the captive population descended from six wild ancestors, resulting in high juvenile mortality and low reproduction. We assembled and characterized the first SCT genome and an improved Amur tiger (P. t. altaica, AT) genome named AmyTig1.0 and PanTig2.0. The two genomes are the most continuous and comprehensive among any tiger genomes yet reported at the chromosomal level. By using the two genomes and resequencing data of 15 SCT and 13 AT individuals, we investigated the genomic signature of inbreeding depression of the SCT. The results indicated that the effective population size of SCT experienced three phases of decline, ~5.0–1.0 thousand years ago, 100 years ago, and since captive breeding in 1963. We found 43 long runs of homozygosity fragments that were shared by all individuals in the SCT population and covered a total length of 20.63% in the SCT genome. We also detected a large proportion of identical-by-descent segments across the genome in the SCT population, especially on ChrB4. Deleterious nonsynonymous single nucleotide polymorphic sites and loss-of-function mutations were found across genomes with extensive potential influences, despite a proportion of these loads having been purged by inbreeding depression. Our research provides an invaluable resource for the formulation of genetic management policies for the South China tiger such as developing genome-based breeding and genetic rescue strategy.     

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.     

Genetic variation of complete mitochondrial genome sequences of the Sumatran rhinoceros (<Emphasis Type="Italic">Dicerorhinus sumatrensis</Emphasis>)

The Sumatran rhinoceros (Dicerorhinus sumatrensis) is the smallest and one of the most endangered rhinoceros species, with less than 100 individuals estimated to live in the wild. It was originally divided into three subspecies but only two have survived, D. sumatrensis sumatrensis (Sumatran subspecies), and D. s. harrissoni (Bornean). Questions regarding whether populations of the Sumatran rhinoceros should be treated as different management units to preserve genetic diversity have been raised, particularly in light of its severe decline in the wild and low breeding success in captivity. This work aims to characterize genetic differentiation between Sumatran rhinoceros subspecies using complete mitochondrial genomes, in order to unravel their maternal evolutionary history and evaluate their status as separate management units. We identified three major phylogenetic groups with moderate genetic differentiation: two distinct haplogroups comprising individuals from both the Malay Peninsula and Sumatra, and a third group from Borneo. Estimates of divergence time indicate that the most recent common ancestor of the Sumatran rhinoceros occurred approximately 360,000 years ago. The three mitochondrial haplogroups showed a common divergence time about 80,000 years ago corresponding with a major biogeographic event in the Sundaland region. Patterns of mitochondrial genetic differentiation may suggest considering Sumatran rhinoceros subspecies as different conservation units. However, the management of subspecies as part of a metapopulation may appear as the last resource to save this species from extinction, imposing a conservation dilemma.     

Forest corridors maintain historical gene flow in a tiger metapopulation in the highlands of central India

Understanding the patterns of gene flow of an endangered species metapopulation occupying a fragmented habitat is crucial for landscape-level conservation planning and devising effective conservation strategies. Tigers (Panthera tigris) are globally endangered and their populations are highly fragmented and exist in a few isolated metapopulations across their range. We used multi-locus genotypic data from 273 individual tigers (Panthera tigris tigris) from four tiger populations of the Satpura–Maikal landscape of central India to determine whether the corridors in this landscape are functional. This 45 000 km² landscape contains 17% of India''s tiger population and 12% of its tiger habitat. We applied Bayesian and coalescent-based analyses to estimate contemporary and historical gene flow among these populations and to infer their evolutionary history. We found that the tiger metapopulation in central India has high rates of historical and contemporary gene flow. The tests for population history reveal that tigers populated central India about 10 000 years ago. Their population subdivision began about 1000 years ago and accelerated about 200 years ago owing to habitat fragmentation, leading to four spatially separated populations. These four populations have been in migration–drift equilibrium maintained by high gene flow. We found the highest rates of contemporary gene flow in populations that are connected by forest corridors. This information is highly relevant to conservation practitioners and policy makers, because deforestation, road widening and mining are imminent threats to these corridors.     

MHC class I and MHC class II DRB gene variability in wild and captive Bengal tigers (Panthera tigris tigris)

Bengal tigers are highly endangered and knowledge on adaptive genetic variation can be essential for efficient conservation and management. Here we present the first assessment of allelic variation in major histocompatibility complex (MHC) class I and MHC class II DRB genes for wild and captive tigers from India. We amplified, cloned, and sequenced alpha-1 and alpha-2 domain of MHC class I and beta-1 domain of MHC class II DRB genes in 16 tiger specimens of different geographic origin. We detected high variability in peptide-binding sites, presumably resulting from positive selection. Tigers exhibit a low number of MHC DRB alleles, similar to other endangered big cats. Our initial assessment—admittedly with limited geographic coverage and sample size—did not reveal significant differences between captive and wild tigers with regard to MHC variability. In addition, we successfully amplified MHC DRB alleles from scat samples. Our characterization of tiger MHC alleles forms a basis for further in-depth analyses of MHC variability in this illustrative threatened mammal.     

亚洲虎种群恢复的机遇与挑战

虎(Panthera tigris)作为顶级捕食者, 对维持森林生态系统服务和结构完整性有着重要作用, 是研究和保护工作的旗舰物种。历史上, 虎曾广泛分布于亚洲大部分地区, 如今仅分布于南亚、东南亚和东北亚的破碎化栖息地, 各区域种群处于濒危或极度濒危状态。准确了解野生虎的种群状态和生态需求信息对于科学开展保护和恢复工作至关重要。本文通过综述近几十年的研究文献, 总结了野生虎种群现状和主要威胁因素, 评价了已有研究的重点与不足, 为未来亚洲虎种群的研究和保护提出了建议。目前与虎相关的研究主要集中在分布范围最广的孟加拉虎(P. t. tigris)和东北虎(P. t. altaica) 2个亚种, 而最急需关注的其他亚种仍研究不足。经过近十几年的努力和保护投入, 目前野生虎种群数量已从2010年的大约3,200只恢复到现在约4,500只, 但在越南、柬埔寨和老挝3个国家已经灭绝。虎面临的主要威胁包括持续的栖息地破坏和隔离、猎物缺乏、近交衰退、人虎冲突、贸易与盗猎和疾病威胁等。未来的研究和保护工作需要加强种群和栖息地连通性恢复、个体重引入、疾病管控以及加强跨境合作和反盗猎等。     

Spatial variation in the density and vulnerability of preferred prey in the landscape shape patterns of Amur tiger habitat use

Theoretical and empirical research suggests that carnivore distributions are largely determined by prey availability. Availability depends not only on prey density but also on prey accessibility which is affected, in part, by the configuration of landscape attributes that make prey vulnerable to predation. Exactly how spatial variation in these processes shape patterns of carnivore habitat use at the home range scale remains poorly understood. We examined the influence of prey density (negative binomial resource selection function) and vulnerability (kill site resource selection function), mapped separately for each of three species of primary prey, on habitat use patterns within the home range for Amur tigers Panthera tigris altaica in Far East Russia over 20 winters. We developed spatially‐explicit mixed linear regression models to assess these patterns and found that models with parameters for specific primary prey were more robust than models with composite parameters for all primary prey species. This emphasizes the importance of evaluating predation dynamics at a species‐specific level. We also found that Amur tigers used habitat within the home range where red deer Cervus elaphus and wild boar Sus scrofa were dense. These two species were clearly preferred by tigers accounting for 72% (201 of the 278) of the tiger kills detected. The effect of red deer density however, was modulated by the vulnerability of red deer in the landscape. Amur tigers tended to establish their home ranges on habitat where red deer were most vulnerable to predation, but would use habitat where red deer were dense in the peripheral regions of their home ranges. This suggests that tigers may utilize two separate strategies for acquiring prey. As the configuration of resource patches within the home range influences carnivore survival and reproduction, our analysis has implications for tiger conservation that extend beyond our improved understanding of tiger‐prey ecology.     

Connectivity of Tiger (Panthera tigris) Populations in the Human-Influenced Forest Mosaic of Central India

Today, most wild tigers live in small, isolated Protected Areas within human dominated landscapes in the Indian subcontinent. Future survival of tigers depends on increasing local population size, as well as maintaining connectivity between populations. While significant conservation effort has been invested in increasing tiger population size, few initiatives have focused on landscape-level connectivity and on understanding the effect different landscape elements have on maintaining connectivity. We combined individual-based genetic and landscape ecology approaches to address this issue in six protected areas with varying tiger densities and separation in the Central Indian tiger landscape. We non-invasively sampled 55 tigers from different protected areas within this landscape. Maximum-likelihood and Bayesian genetic assignment tests indicate long-range tiger dispersal (on the order of 650 km) between protected areas. Further geo-spatial analyses revealed that tiger connectivity was affected by landscape elements such as human settlements, road density and host-population tiger density, but not by distance between populations. Our results elucidate the importance of landscape and habitat viability outside and between protected areas and provide a quantitative approach to test functionality of tiger corridors. We suggest future management strategies aim to minimize urban expansion between protected areas to maximize tiger connectivity. Achieving this goal in the context of ongoing urbanization and need to sustain current economic growth exerts enormous pressure on the remaining tiger habitats and emerges as a big challenge to conserve wild tigers in the Indian subcontinent.     

Evolutionary Conservation Genomics Reveals Recent Speciation and Local Adaptation in Threatened Takins

Incorrect species delimitation will lead to inappropriate conservation decisions, especially for threatened species. The takin (Budorcas taxicolor) is a large artiodactyl endemic to the Himalayan–Hengduan–Qinling Mountains and is well known for its threatened status and peculiar appearance. However, the speciation, intraspecies taxonomy, evolutionary history, and adaptive evolution of this species still remain unclear, which greatly hampers its scientific conservation. Here, we de novo assembled a high-quality chromosome-level genome of takin and resequenced the genomes of 75 wild takins. Phylogenomics revealed that takin was positioned at the root of Caprinae. Population genomics based on the autosome, X chromosome, and Y chromosome SNPs and mitochondrial genomes consistently revealed the existence of two phylogenetic species and recent speciation in takins: the Himalayan takin (B. taxicolor) and the Chinese takin (B. tibetana), with the support of morphological evidence. Two genetically divergent subspecies were identified in both takin species, rejecting three previously proposed taxonomical viewpoints. Furthermore, their distribution boundaries were determined, suggesting that large rivers play important roles in shaping the genetic partition. Compared with the other subspecies, the Qinling subspecies presented the lowest genomic diversity, higher linkage disequilibrium, inbreeding, and genetic load, thus is in urgent need of genetic management and protection. Moreover, coat color gene (PMEL) variation may be responsible for the adaptive coat color difference between the two species following Gloger’s rule. Our findings provide novel insights into the recent speciation, local adaptation, scientific conservation of takins, and biogeography of the Himalaya–Hengduan biodiversity hotspot.     

Comparative evaluation of tiger reserves in India

Evidence is vital. Understanding what interventions are effective is critical for the conservation of wild tigers and conservation biology in general. We evaluated the effectiveness of tiger reserves within India, a country with more than half of the estimated wild tiger population, with comparative effectiveness research. Other complex environments, medicine and business use these techniques where cause and effects are often non-linear. These techniques also allowed us to evaluate data from the small sample size often seen in conservation interventions. The opinions of three tiger experts were used to generate a list of seven tiger reserves classified as successful and five reserves as failures. We also used expert opinion to identify any key individuals that garnered widespread support for tiger conservation at any of the identified reserves. Using data from the Indian Census, World Database on Protected Areas, and the Socioeconomic Data and Applications Center, we analyzed the human population around the tiger reserves. We found two surprising insights that have received scant attention in the peer-reviewed literature. First, one can achieve tiger conservation success even within a densely populated human landscape where a high percentage of the population is involved in agriculture. Second, the presence of “conservation champions” can dramatically affect the performance of individual reserves and have positive outcomes for tiger conservation.