Captive Tigers Research Articles

Gut Microbiome Diversity and Composition in Captive Siberian Tigers (Panthera tigris altaica): The Influence of Diet, Health Status, and Captivity on Microbial Communities

The gut microbiome is essential for the health of carnivorous mammals, including the endangered Siberian tiger (Panthera tigris altaica). However, limited research exists on the gut microbiome of captive Siberian tigers, especially regarding how diet and health status influence microbial diversity. This study addresses this gap by investigating the gut microbiome diversity and composition of six captive-born Siberian tigers housed at the Baekdudaegan National Arboretum in South Korea, using 16S rRNA gene sequencing. The study aimed to examine how diet and health status influence microbial communities, providing baseline data for managing captive tigers. Alpha diversity analysis revealed significant variation in microbial richness and evenness, with Tigers 2 and 6 exhibiting the highest microbial diversity and Tiger 3 the lowest, likely due to its surgical history and limited diet. Beta diversity analysis showed distinct microbial community structures influenced by diet and health. Taxonomic profiling identified Firmicutes and Bacteroidota as the dominant phyla, with Clostridium sensu stricto more prevalent in healthier tigers, while Escherichia-Shigella and Proteobacteria were abundant in tigers with lower diversity, suggesting dysbiosis. Comparisons with other tiger species confirm that diet, health, and captivity significantly shape the gut microbiome. These findings highlight the need for personalized health management in captive environments.

Novel adomavirus associated with proliferative skin lesions affecting the dermal denticles of a sand tiger shark (Carcharias taurus).

A captive sand tiger shark (Carcharias taurus) presented with progressive, hard, raised, miliary skin lesions localized to the lateral trunk and peduncle. Histopathologic evaluation of biopsy samples revealed dysplastic proliferation of odontogenic epithelium with the production of collagenous material. Inclusion bodies and viral particles were not observed with light or transmission electron microscopy, respectively. However, using next generation sequencing with Illumina MiSeq and PCR followed by Sanger sequencing, the complete genome of a novel adomavirus, tentatively named sand tiger shark adomavirus (STAdoV), was obtained from the affected tissue. The genome was circular and 18.5 kilobases with bidirectionally transcribed genes, namely EO1, EO2 & 4, EO3, LO4, LO5, LO6, LO7, LO8, and SET. In situ hybridization using RNAscope® technology and a STAdoV specific probe localized viral DNA to the nuclei of proliferating epithelial cells. Adomaviruses are an emerging viral group with structural and replicative genes sharing a complex evolutionary history with adenoviruses and small circular DNA tumor viruses including papillomaviruses and polyomaviruses. Adomaviruses are described in a number of fish species in association with both necrotizing and proliferative diseases. BLAST analysis of the viral genome revealed greatest nucleotide identity (71.29%) to guitarfish adomavirus (GAdoV), another elasmobranch virus associated with proliferative (epidermal) skin lesions. Lesions in the index animal persisted for approximately 1 year during which time four conspecifics developed similar proliferations. Ultimately, lesions in all sharks regressed spontaneously without recurrence for 2 years.

TigerBase: A DNA registration system to enhance enforcement and compliance testing of captive tiger facilities

The illegal trade in tigers (Panthera tigris) and their derivatives, such as bones, teeth and pelts, is a major threat to the species’ long-term persistence. As wild tiger populations have dwindled, a large proportion of trafficked tiger products now derive from captive breeding facilities found throughout Asia. Moreover, wild tigers have been poached and laundered into captive facilities, then falsely designated as captive-bred. The establishment of a DNA registration system is recognized as a key tool to monitor compliance of captive facilities, support tiger trade investigations and improve prosecution outcomes. Here, we present a standardised wildlife forensic DNA profiling system for captive tigers called TigerBase. TigerBase has been developed in four South-East Asia countries with captive tiger facilities: Malaysia, Vietnam, Thailand and Lao PDR. TigerBase DNA profile data is based on 60 single nucleotide polymorphism (SNP) markers, genotyped using two different TaqMan®-based approaches: OpenArray® chip (capable of genotyping 60 SNPs for 48 samples in a single chip), and singleplex TaqMan® assays (capable of genotyping one SNP for one sample per reaction). Of the 60 SNPs, 53 are autosomal nuclear markers, suitable for individualisation and parentage applications, two are sex-linked markers, suitable for sexing, and five are mtDNA markers, suitable for maternal subspecies identification. We conducted a series of validation experiments to investigate the reliability and limitations of these SNP genotyping platforms. We found that the OpenArray® chip platform is more appropriate for generating reference data given its greater throughput, while the singleplex TaqMan® assays are more appropriate for genotyping lower quality casework samples, given their higher sensitivity and throughput flexibility. Only 19 autosomal nuclear markers were validated as singleplex TaqMan® assays, which generally provides ample power for individualisation analysis (probability of identity among siblings was <6.9 ×10−4), but may lack power for specific parentage questions, such as determining parentage of an offspring when one of the parent’s genotypes is missing. Further, we have developed pipelines to support standardised SNP calling and decrease the chance of genotyping errors through the use of analytical workflows and synthetic positive controls. We expect the implementation of TigerBase will enhance enforcement of tiger trafficking cases and encourage compliance among captive tiger facilities, together contributing to combatting the illegal tiger trade.

Unraveling the genomic diversity and admixture history of captive tigers in the United States

Genomic studies of endangered species have primarily focused on describing diversity patterns and resolving phylogenetic relationships, with the overarching goal of informing conservation efforts. However, few studies have investigated genomic diversity housed in captive populations. For tigers (Panthera tigris), captive individuals vastly outnumber those in the wild, but their diversity remains largely unexplored. Privately owned captive tiger populations have remained an enigma in the conservation community, with some believing that these individuals are severely inbred, while others believe they may be a source of now-extinct diversity. Here, we present a large-scale genetic study of the private (non-zoo) captive tiger population in the United States, also known as "Generic" tigers. We find that the Generic tiger population has an admixture fingerprint comprising all six extant wild tiger subspecies. Of the 138 Generic individuals sequenced for the purpose of this study, no individual had ancestry from only one subspecies. We show that the Generic tiger population has a comparable amount of genetic diversity relative to most wild subspecies, few private variants, and fewer deleterious mutations. We observe inbreeding coefficients similar to wild populations, although there are some individuals within both the Generic and wild populations that are substantially inbred. Additionally, we develop a reference panel for tigers that can be used with imputation to accurately distinguish individuals and assign ancestry with ultralow coverage (0.25×) data. By providing a cost-effective alternative to whole-genome sequencing (WGS), the reference panel provides a resource to assist in tiger conservation efforts for both ex- and in situ populations.

An Analysis of Welfare Standards Within Tiger (Panthera tigris) Facilities in Thailand.

In Thailand, tigers are more numerous in captivity than they are in the wild, with 51 facilities housing approximately 1962 tigers. As charismatic fauna, tigers are popular with tourists, and the majority of facilities offer a variety of entertainment activities with controversial reports towards the animals' welfare. The aim of this research was to investigate tiger welfare in Thai zoos to identify specific welfare issues. We assessed 34 tourism facilities holding tigers in Thailand in 2019 using a 25-point welfare assessment that utilizes the Five Domain model (incorporating all five domains: nutrition, physical environment, health, behavioural interactions and mental state). The mental domain score was derived from the scores of the other four domains. Additional data were collected from each facility, including the number of tigers, any colour variants, types of human interaction and admission cost. Welfare scores for each domain were calculated by totalling the scores per domain and dividing by the number of points allocated to that domain. A multiple regression was used to identify any significant predictors of mental domain score. The results revealed that the provision of a suitable physical environment scored the lowest, while nutrition scored the highest though this was still a low score overall. The multiple regression showed that 45.4% of the variance for the mental domain score was significantly affected by the number of colour variants housed and the types of human interaction available with facilities, with more of both these factors contributing to a more negative score. Our results demonstrate the need for urgent, comprehensive infrastructural, species-appropriate environment and design and animal management improvements to increase animal welfare. Informed institutional change toward the breeding and use of tigers for public interactions is also required. This is the first assessment completed of captive tiger welfare of tiger facilities in Thailand and shows that the welfare concerns encountered are within a high proportion (67%) of Thailand's facilities. This supports the need for the creation and enforcement of effective and clear captive wildlife operational standards to provide a sustained solution for captive tiger welfare and can provide a considered approach to ex-situ tiger management that, in conjunction with in-situ efforts, can improve much needed conservation efforts of this species.

Efficacy of Cyperus spp. Extract Components in Improving Reproductive Performance of Captive Tiger Shrimp (Penaeus monodon)

Efficacy of Cyperus spp. Extract Components in Improving Reproductive Performance of Captive Tiger Shrimp (Penaeus monodon)

Intramural coronary artery and myocardial pathology in captive tigers (Panthera tigris) and African lions (Panthera leo).

There is limited published data regarding cardiovascular disease in nondomestic felid populations. To address this knowledge gap, necropsy cases of tigers and lions with representative myocardial samples submitted to a diagnostic laboratory were histologically assessed with hematoxylin and eosin and Sirius red stains. A total of 32 submissions (15 tigers, 17 lions) were identified in a 4-year period. All tigers and lions had some degree of coronary artery lesions in the left ventricle and/or interventricular septum. Major findings included moderate to marked arteriosclerosis in 8 tigers (53%) and 4 lions (24%) and moderate to marked perivascular fibrosis in 10 tigers (67%) and 9 lions (53%). Moreover, 10 tigers (67%) and 8 lions (47%) had coronary artery lesions with variable degrees of perivascular cardiomyocyte degeneration and/or loss. To our knowledge, this is the first report describing coronary artery pathology in captive tigers and lions.

Welfare Implications for Tigers in Travelling Circuses.

There are very few studies that have focused on species-specific welfare implications for tigers in a travelling circus. The absence of scientific evidence to inform nationwide legislation means that tigers are still commonly used in travelling circuses across the world. A systematic review of relevant published studies was conducted using the bibliographic databases Web of Science and Scopus, supplemented by a narrative search. In total, 42 relevant studies were identified that assessed the welfare of tigers in captivity, including circuses and zoos. Only eight papers assessed the welfare implications for tigers in circuses directly, evidencing the lack of research in this area. Given that circuses provide a sub-optimal environment compared to zoos, implications for tiger welfare were also inferred from zoo research, within the Five Domains framework. Collectively, these papers infer that the travelling nature of a circus often negatively impacts the welfare domains of nutrition, physical environment, health, and mental state. This is due to limitations in enclosure size, as well as in both environmental and behavioural enrichment. There is also often difficulty in sourcing appropriate food and specialised routine veterinary care. The literature is divided concerning behavioural interactions, specifically whether training can improve welfare by offering mental stimulation. However, circus performances are often associated with negative welfare due to noise disruption from spectators. The collective scientific evidence indicates that tigers are not well suited to circus living, due to the inability of a travelling circus to provide for their species-specific psychological, physiological, and behavioural needs.

Insights for the Captive Management of South China Tigers Based on a Large-Scale Genetic Survey.

There is an urgent need to find a way to improve the genetic diversity of captive South China tiger (SCT, Panthera tigris amoyensis), the most critically endangered taxon of living tigers, facing inbreeding depression. The genomes showed that 13 hybrid SCTs from Meihuashan were divided into two groups; one group included three individuals who had a closer relationship with pureblood SCTs than another group. The three individuals shared more that 40% of their genome with pureblood SCTs and might be potential individuals for genetic rescuing in SCTs. A large-scale genetic survey based on 319 pureblood SCTs showed that the mean microsatellite inbreeding coefficient of pureblood SCTs decreased significantly from 0.1789 to 0.0600 (p = 0.000009) and the ratio of heterozygous loci increased significantly from 38.5% to 43.2% (p = 0.02) after one individual of the Chongqing line joined the Suzhou line and began to breed in the mid-1980s, which is a reason why the current SCTs keep a moderate level of microsatellite heterozygosity and nucleotide diversity. However, it is important to establish a back-up population based on the three individuals through introducing one pureblood SCT into the back-up population every year. The back-up population should be an important reserve in case the pureblood SCTs are in danger in the future.

Case study: Visual barriers reduce pacing in captive tigers.

Captive large felines are prone to abnormal repetitive behaviors like pacing, which are associated with welfare issues. Visual contact without the opportunity to engage in appropriate behavior is known to increase pacing. To better understand the relationship between pacing and conspecific visual contact, we investigated this effect by conducting a barrier experiment on a male-female pair of Sumatran tigers (Panthera tigris sumatrae) in Rotterdam Zoo, the Netherlands. The tigers were exposed to four consecutive housing treatments: (i) housed in the same enclosure (baseline), (ii) housed in separate enclosures with visual contact, (iii) housed in separate enclosures without visual contact, and (iv) housed in the same enclosure after the separation. We used focal and scan sampling to measure pacing and recorded the number of visitors. Moreover, we applied scan sampling to measure activity. Overall, our results indicate that the tigers paced significantly more when housed in separate enclosures with conspecific visual contact. Moreover, our results suggest that limiting visual contact between neighboring tigers can mitigate pacing. Implementing these findings in tiger husbandry and enclosure design has the potential to improve animal welfare zoo populations of large felines.

Molecular detection and pathology of cytauxzoonosis in captive royal Bengal tiger

Molecular detection and pathology of cytauxzoonosis in captive royal Bengal tiger

Associations of per‐ and polyfluoroalkyl substance concentrations in the blood of Amur tigers and physiological parameters

AbstractPer‐ and polyfluoroalkyl substances (PFASs) were widely used in industrial production and have posed a certain threat to human and animal health. However, few studies have been made on Amur tigers (Panthera tigris altaica). In this study, we explored the associations between the concentrations of PFASs in the blood of 112 captive Amur tigers and the part physiological parameters to assess the cumulative effect of these chemicals on the health of the Amur tigers. The result showed that perfluorodecanoic acid (PFDA), perfluorohexane sulfonic acid, and 6:2 chlorinated polyfluorinated ether sulfonate (6:2 Cl‐PFESA) have associations with white blood cells (WBCs); perfluorooctanoic acid, perfluoroundecanoic acid, per‐fluorotridecanoate, and 6:2 Cl‐PFESA have a bearing on the changes in red blood cells (RBCs), RBC volume distribution width, hemoglobin, hematocrit, and platelets. In our study, according to the three models, there were significant positive correlations between PFDA and leukocyte parameters (WBCs, neutrophils [NEUs]) and a significant adverse effect between 6:2 Cl‐PFESA and NEU. Therefore, more research concerning PFASs of endangered wildlife species is needed.

Getting to the Meat of It: The Effects of a Captive Diet upon the Skull Morphology of the Lion and Tiger

Zoo animals are crucial for conserving and potentially re-introducing species to the wild, yet it is known that the morphology of captive animals differs from that of wild animals. It is important to know how and why zoo and wild animal morphology differs to better care for captive animals and enhance their survival in reintroductions, and to understand how plasticity may influence morphology, which is supposedly indicative of evolutionary relationships. Using museum collections, we took 56 morphological measurements of skulls and mandibles from 617 captive and wild lions and tigers, reflecting each species’ recent historical range. Linear morphometrics were used to identify differences in size and shape. Skull size does not differ between captive and wild lions and tigers, but skull and mandible shape does. Differences occur in regions associated with biting, indicating that diet has influenced forces acting upon the skull and mandible. The diets of captive big cats used in this study predominantly consisted of whole or partial carcasses, which closely resemble the mechanical properties of wild diets. Thus, we speculate that the additional impacts of killing, manipulating and consuming large prey in the wild have driven differentiation between captive and wild big cats.

Using qualitative behavior assessment to investigate the effect of tourist presence on the welfare in captive tigers (Panthera tigris) in three tourism facilities in Thailand.

Numerous facilities around the world offer tourists interactive experiences with captive tigers. Yet, the animal welfare implications of this practice have not been widely studied. This study aimed to investigate whether qualitative behavioral assessment (QBA) could: (i) provide a valid indicator of tiger's emotional state and (ii) be applied to assess whether unfamiliar human presence with hand-raised captive tigers had an impact on the emotional state of those tigers. To investigate this, QBA was applied to video clips of hand-raised captive tigers from three sites (two offering unfamiliar human interaction, Sites A and C, and one retirement site with no direct interactions, Site B) in Thailand. QBA allows inferences to be made about animal emotion on the basis of descriptions of behavioral expression. Analysis, using a free choice profiling methodology, was provided by observers (N = 38) split between three groups; tiger keepers and vets from the Thai venues (n = 12), UK-based animal behavior MSc and vet students (n = 16), and international tiger keepers (n = 10). Tigers (N = 35) were split between Sites A (n = 7), B (n = 18), and C (n = 10) and filmed at three time points; morning (0800-0930 h); midday, (1130-1230 h); and evening, (1630-1830h) totaling 105 clips. Using generalized procrustes analysis, a consensus profile was calculated for each observer group. Two meaningful dimensions of behavioral expression, explaining 75.0% of the variation, were observed across these groups: Dimension 1 (D1: "active"/"interested"/"agitated" to "relaxed"/"calm"/"chilled-out") and Dimension 2 (D2: "bored"/"stressed"/"frustrated" to "relaxed"/"curious"/"interested"). There was clear agreement between the three observer groups in terms of tiger emotional expression along D1. However, agreement was more variable on D2. The behavioral expression on D1 was not significantly affected by site but was significantly affected by an interaction between age and time of day. Time of day also affected scores on D2, with the Thai observer group also showing an effect of site. During the midday period, when unfamiliar humans were present, all tiger age groups showed more positive behavioral expressions on D1 (lower scores: "relaxed"/"calm"/"chilled-out") and more negative behavioral expressions on D2 (higher scores: "bored"/"stressed"/"frustrated"), which could indicate that the presence of unfamiliar humans was a stressor. However, tigers in the retirement Site C also displayed similar behavioral expressions, which could indicate a deeper welfare issue. With further development, QBA could be used as part of a valid tool for long-term measurement of behavioral expression in captive tigers.

High-throughput DNA metabarcoding for determining the gut microbiome of captive critically endangered Malayan tiger (Pantheratigrisjacksoni) during fasting.

The Malayan tiger (Pantheratigrisjacksoni) is a critically endangered species native to the Malaysian Peninsula. To imitate wild conditions where tigers do not hunt every day, numerous wildlife sanctuaries do not feed their tigers daily. However, the effects of fasting on the gut microbiota of captive Malayan tigers remains unknown. This study aimed to characterise the gut microbiota of captive Malayan tigers by comparing their microbial communities during fasting versus normal feeding conditions. This study was conducted at the Melaka Zoo, Malaysian Peninsula and involved Malayan tigers fasted every Monday. In total, ten faecal samples of Malayan tiger, two of Bengal tiger (outgroup) and four of lion (outgroup) were collected and analysed for metabarcoding targeting the 16S rRNA V3-V4 region. In total, we determined 14 phyla, 87 families, 167 genera and 53 species of gut microbiome across Malayan tiger samples. The potentially harmful bacterial genera found in this study included Fusobacterium, Bacteroides, Clostridium sensu stricto 1, Solobacterium, Echerichiashigella, Ignatzschineria and Negativibacillus. The microbiome in the fasting phase had a higher composition and was more diverse than in the feeding phase. The present findings indicate a balanced ratio in the dominant phyla, reflecting a resetting of the imbalanced gut microbiota due to fasting. These findings can help authorities in how to best maintain and improve the husbandry and health of Malayan tigers in captivity and be used for monitoring in ex-situ veterinary care unit.

The Study on the Behavior of Female White Tigers in Different Captive Conditions at Chiang Mai Night Safari

White tiger is a tiger characterized by its white fur, which is caused by a pigmentation disorder, often found in Bengal tigers with gene abnormalities. White tiger is considered as a vulnerable (IUCN) animal species. Therefore, it is important for conservation. Thus, the objective of this study was to observe the behavior patterns of female white tiger in different captive conditions. Seven female white tigers were used in this study. Three captive conditions were studied: individual captive, dividual captive and captive with other tiger species. The tiger behavior was observed in five groups including daily routine, movement, relaxation, self-grooming and affiliative behaviors. Behavioral observations were performed at 7 hours/day for 90 days. The results showed that the individual captive tigers expressed self-grooming and relaxation higher than dividual captive tigers and white tiger captive with other tigers (P&lt;0.001). Dividual captive showed daily routine and movement higher than individual captive and white tiger captive with the other tiger (P&lt;0.001). White tiger captive tigers with other tiger species showed affiliative behaviors higher than individual captive and dividual captive tigers (P&lt;0.001). This study was able to be used as a guideline for further enhancing behavior and designing display areas that may be suitable for white tigers.

Identification of a Feline Panleukopenia Virus from Captive Giant Pandas (Ailuropoda melanoleuca) and Its Phylogenetic Analysis

The host range of feline panleukopenia virus (FPV) is expanding and is a serious threat to both captive and free-range endangered wildlife. The FPV named FPV-am2020 was isolated from fecal samples from four diarrheal captive giant pandas in 2020, and pathogenicity and phylogenetic analysis were conducted in this study. Three-month-old cats challenged with FPV-am2020 experienced 100% mortality. The complete FPV-am2020 sequence was determined and comprised 5277 base pairs (bp), 36.76% GC content, and two open reading frames. According to the phylogenetic analysis of whole genome sequences and VP2 gene sequences, FPV-am2020 was closely related with MG764511.1 (isolated from captive lions in China, 2015), KX685354.1 (isolated from captive tigers in China, 2016), and KX900570.1 (isolated from captive jaguar in China, 1986). Furthermore, the study identified a G299E mutation in VP2 which was a key residue involved in phenotype changes in FPV. Thus, increased surveillance of FPV mutant isolates must be enacted to protect giant pandas against potential viral threats.

Adult tiger beetles Cicindela gemmata modify their foraging strategy in different hunting contexts.

Predator-prey interaction has long been an interesting item in the research of animal behaviors. Given that live prey can damage their predators, predators must trade foraging efficiency for safety while hunting, but the extent of this trade-off is not yet clear. Tiger beetles display diversity in their diets and hunting strategies, and hence, they become an ideal system to address how self-security affects foraging efficiency. We addressed this question in captive adult tiger beetles Cicindela gemmata. By offering several types of arthropod and plant foods, we confirmed that C.gemmata is carnivorous. We found that C.gemmata hunt by either ambushing or chasing their prey, and that they switch between strategies based on differences in the number of prey, the prey status and encounter rate, and the number of predators. Ambushing success increased with the number of prey but decreased with prey encounter rate. Chasing success decreased as prey body size and encounter rate increased. Foraging Cicindela gemmata often gave up an attack when it was nonfatal. This active giving up of hunting may be a consequence of a trade-off between foraging efficiency and self-security. Therefore, it is an adaptive response to the risk of injury when hunting for larger live prey.

Time series cluster analysis reveals individual assignment of microbiota in captive tiger (Panthera tigris) and wildebeest (Connochaetes taurinus).

Fecal microbiota variability and individuality are well studied in humans and also in farm animals (related to diet- or disease-specific influences), but very little is known for exotic zoo-housed animals. This includes a wide range of species that differ greatly in microbiota composition and variation. For example, herbivorous species show a very similar and constant fecal microbiota over time, whereas carnivorous species appear to be highly variable in fecal microbial diversity and composition. Our objective was to determine whether species-specific and individual-specific clustering patterns were observed in the fecal microbiota of wildebeest (Connochaetes taurinus) and tigers (Panthera tigris). We collected 95 fecal samples of 11 animal individuals that were each sampled over eight consecutive days and analyzed those with Illumina MiSeq sequencing of the V3-V4 region of the 16SrRNA gene. In order to identify species or individual clusters, we applied two different agglomerative hierarchical clustering algorithms - a community detection algorithm and Ward's linkage. Our results showed that both, species-specific and individual-specific clustering is possible, but more reliable results were achieved when applying dynamic time warping which finds the optimal alignment between different time series. Furthermore, the bacterial families that distinguish individuals from each other in both species included daily occurring core bacteria (e.g., Acidaminococcaceae in wildebeests or Clostridiaceae in tigers) as well as individual dependent and more fluctuating bacterial families. Our results suggest that while it is necessary to consider multiple consecutive samples per individual, it is then possible to characterize individual abundance patterns in fecal microbiota in both herbivorous and carnivorous species. This would allow establishing individual microbiota profiles of animals housed in zoos, which is a basic prerequisite to quickly detect deviations and use microbiome analysis as a non-invasive and cost-effective tool in animal welfare.

Population genomic analysis provides evidence of the past success and future potential of South China tiger captive conservation

BackgroundAmong six extant tiger subspecies, the South China tiger (Panthera tigris amoyensis) once was widely distributed but is now the rarest one and extinct in the wild. All living South China tigers are descendants of only two male and four female wild-caught tigers and they survive solely in zoos after 60 years of effective conservation efforts. Inbreeding depression and hybridization with other tiger subspecies were believed to have occurred within the small, captive South China tiger population. It is therefore urgently needed to examine the genomic landscape of existing genetic variation among the South China tigers.ResultsIn this study, we assembled a high-quality chromosome-level genome using long-read sequences and re-sequenced 29 high-depth genomes of the South China tigers. By combining and comparing our data with the other 40 genomes of six tiger subspecies, we identified two significantly differentiated genomic lineages among the South China tigers, which harbored some rare genetic variants introgressed from other tiger subspecies and thus maintained a moderate genetic diversity. We noticed that the South China tiger had higher FROH values for longer runs of homozygosity (ROH > 1 Mb), an indication of recent inbreeding/founder events. We also observed that the South China tiger had the least frequent homozygous genotypes of both high- and moderate-impact deleterious mutations, and lower mutation loads than both Amur and Sumatran tigers. Altogether, our analyses indicated an effective genetic purging of deleterious mutations in homozygous states from the South China tiger, following its population contraction with a controlled increase in inbreeding based on its pedigree records.ConclusionsThe identification of two unique founder/genomic lineages coupled with active genetic purging of deleterious mutations in homozygous states and the genomic resources generated in our study pave the way for a genomics-informed conservation, following the real-time monitoring and rational exchange of reproductive South China tigers among zoos.