Tiger Subspecies Research Articles

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.

Predicting the Impact of Climate Change on the Selection of Reintroduction Sites for the South China Tiger (Panthera tigris amoyensis) in China.

The South China tiger (Panthera tigris amoyensis) is a tiger subspecies unique to China and one of the top ten endangered species in the world. It used to play an important role in the overall function of the ecosystem. This study rationally screened out key prey species of the South China tiger-the Chinese serow, Chinese goral, tufted deer, water deer, Chinese muntjac, red muntjac, sambar deer, and wild boar. Candidate sites for the rewilding and reintroduction of the South China tiger were derived by exploring changes in suitable habitats for the prey using the MaxEnt model. The results show that: (1) by 2070, except for the high-suitability areas of water deer and Chinese muntjac, the areas of suitable habitats for the other six prey species would all have decreased significantly; (2) the location of the high-suitability area of the South China tiger obtained by superimposing the suitable areas of the eight prey species would be almost stable in 2050 and 2070, but the habitat index of some high- and medium-suitability areas would decrease and turn into low-suitability areas; (3) the core candidate sites were 83,415 km2 in total, of which 25,630 km2 overlapped with existing protected areas, accounting for 30.7% of the core candidate sites, and the remaining 69.3% of the core candidate sites were mostly distributed around the protected areas; (4) the maximum core candidate site area was projected to be 10,000 km2 by 2070, which could support a small population of 23 male tigers and 66 female tigers to survive and reproduce in the wild. This study revealed the core candidate sites for the rewilding of South China tigers and estimated the number of tigers that could be reintroduced to these areas, providing a preliminary research basis for promoting the rewilding of South China tigers in China.

Mitochondrial CO1 gene haplotype diversity of Sumatran Tiger Panthera tigris sumatrae (Pocock, 1929) (Mammalia: Carnivora: Felidae)

Sumatran Tigers Panthera tigris sumatrae inhabit 12 tiger conservation landscapes that stretch across Sumatra Island. Conservation efforts for these species require robust, information-based research, including a genetic approach. This study analyzed the haplotype diversity of P. t. sumatrae based on the mitochondrial CO1 (Cytochrome Oxidase Subunit 1) gene. Specifically, a nucleotide guanine at position 121 was found, distinguishing P. t. sumatrae from other tiger subspecies. Among the 17 sequences of P. t. sumatrae, two haplotypes were detected: 13 individuals were in haplotype 1 (Hap_1), and four individuals were in haplotype 2 (Hap_2). Hap_1 individuals predominantly originated from Riau and North Sumatra, while Hap_2 individuals were primarily from West Sumatra. Haplotype diversity (Hd) (0.382±0.113) and nucleotide diversity (pi) (0.00038±0.00011) confirmed the low genetic diversity. Five seized samples exhibited Hap_2, suggesting they might have originated from Riau and North Sumatra. However, this result cannot be described as current due to the significant changes in P. t. sumatrae habitat. Further genetic studies, such as whole-genome analysis, are needed to detect the origin and variation of P. t. sumatrae across all landscapes.

Is the Javan tiger Panthera tigris sondaica extant? DNA analysis of a recent hair sample

Abstract The Javan tiger Panthera tigris sondaica and the Bali tiger P. tigris balica were categorized as Extinct on the IUCN Red List in both 2003 and 2008, leaving only the Sumatran subspecies P. tigris sumatrae extant in Indonesia. There have, however, been occasional, more recent reports of the Javan tiger but without conclusive evidence. Here, a potential observation in 2019 of a Javan tiger in a community plantation near the village of Cipendeuy in the forest of South Sukabumi, West Java, and a single hair found on a fence nearby, are assessed. The cytochrome b mitochondrial DNA (mtDNA) gene sequence of the putative Javan tiger hair were compared with that of a Javan tiger specimen in Museum Zoologicum Bogoriense, collected in 1930; hair samples of several tiger subspecies and the Javan leopard Panthera pardus melas were used as controls. The results showed that the genetic distances (d) of the putative Javan tiger hair with the Sumatran, Bengal P. tigris tigris and Amur P. tigris altaica tigers and the Javan leopard are 0.074 ± SE 0.009, 0.071 ± SE 0.009, 0.072 ± SE 0.009 and 0.088 ± SE 0.010, respectively, whereas the genetic distance of the putative Javan tiger hair with the Javan tiger museum specimen is 0.040 ± SE 0.006. In addition, phylogenetic trees showed that the putative Javan tiger hair sample belongs to the same group as the museum specimen of the Javan tiger, but is differentiated from other tiger subspecies and the Javan leopard. Whether the Javan tiger still occurs in the wild needs to be confirmed with further genetic and field studies.

Emerging patterns of genetic diversity in the critically endangered Malayan tiger (Panthera tigris jacksoni)

Southeast Asia experiences some of the highest deforestation in the world. Loss of tropical forest typically leads to widespread habitat fragmentation, with detrimental effects on dispersal ability and gene flow—particularly for large carnivores. We conducted mtDNA and microsatellite analysis to assess—for the first time—contemporary patterns of genetic diversity in the Malayan tiger. We collected 295 suspected carnivore samples in Peninsular Malaysia, from which we identified 26 as originating from tiger using 16 polymorphic microsatellite loci, comprising 22 individual tigers. Despite limitations of the study, our findings suggest tiger subpopulations in the north of the peninsula maintain some genetic connectivity and migration between two putative geographic subpopulations in the Main Range and Greater Taman Negara, with negligible population segregation due to dispersal barriers such as road infrastructure. We identified consistently lower levels of genetic diversity in tigers in the Greater Taman Negara region compared to tigers in the Main Range and small but emerging differences in nuclear and mitochondrial genetic diversity. Our mtDNA haplotype and nuclear DNA analyses suggest the levels of genetic diversity in Malayan tigers may be amongst some of the lowest of the surviving tiger subspecies, though the study is limited both in scale and genomic loci. Our findings are consistent with an expected lag between the rapid decline of tigers in Peninsular Malaysia by over 95% in the last 70 years and observed differences in their levels of genetic diversity.

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.

‘I know the tiger by his paw’: A non-invasive footprint identification technique for monitoring individual Amur tigers (Panthera tigris altaica) in snow

Apex predator populations are in decline around the world. Many exist at low density and are elusive, making the acquisition of reliable data on their numbers and distribution a considerable challenge. The Amur tiger (Panthera tigris altaica) is the largest of the five extant sub-species of tiger. The single most significant, contiguous population, an estimated 550 animals, exists in the Russian Far East, with smaller populations on the far eastern Sino-Russian border. For the last few decades, active efforts on the part of Chinese authorities have encouraged the recolonization of these populations back to their former ranges in Northeast China. Reliable data on Amur tiger numbers and distribution are required to assess population recovery at the landscape scale. Footprints, ubiquitous in the snow over range areas, could inform on these baseline data. This paper describes a statistically robust, cost-effective and non-invasive footprint identification technique (FIT) to identify individual tigers from footprints in snow. It is based on a rigorous data collection and data-processing protocol, combined with a cross-validated discriminant analysis method. A Ward's clustering technique provides a visual output of individual classification. The analytical tools are packaged in a user-friendly analytical interface. Between December 2011 and December 2012, we collected a series of 605 footprint images from 44 captive individual Amur tigers for a reference database from which to derive a classification algorithm. The 23 females and 21 males ranged in age from 3 to 13 years (female mean age 7.95 +/− 0.18; male mean age 8.08 +/− 0.19). 128 measurements (areas, lengths and angles) were taken from each print and analyzed with the FIT add-in to JMP software. The derived classification algorithm was then applied to 21 footprint trails collected from an unknown number of free-ranging Amur tigers during 2012 and 2015/2016. The algorithm predicted 7 Amur tigers at the site surveyed in 2012, and 4 tigers surveyed at two sites in 2015/16. We demonstrate that the footprint identification technique translates traditional tracking methodologies into a statistically robust and objective analytical tool that can be deployed by both scientists and local communities to monitor the recovery of big cat populations.

Developmental stage variation in the gut microbiome of South China tigers.

South China tigers (Panthera tigris amoyensis, SC) are the most threatened tiger subspecies in the world. All the living SCs are captive in zoos or reserves and depend on artificial feeding. The composition of the gut microbiome plays an important role in sustaining the health of the host. A comprehensive understanding of the composition and development of the microbial community of SC is helpful to improve the feeding of captive SC. In this study, we collected 47 fecal samples, 37 of which were from SC of three developmental stages, 5 from adult Amur tigers (Am), and 5 from adult Bengal tigers (Bg), which were all housed in the same zoo. We investigated the diversity, richness, and composition of the bacterial microbiomes and we found that the gut microbiome of SC is strongly affected by host aging. The composition of the gut microbiome of juvenile SC experienced dramatic changes from 5 months old to 1 year old, and it showed much less difference when compared to the samples of 1 year old and the subadult. No significant differences were observed between the samples of subadult and the adult groups. The predominant phylum of 5-month-old SC is Fusobacteriota (33.99%) when the juvenile tigers were older than 5 months, and Firmicutes, but not Fusobacteriota, became the predominant phylum of bacteria in their gut. The gut microbiome of SC, Am, and Bg is possibly affected by their genetic variation; however, the core microbiome of these three subspecies is the same. Our data suggest that the gut microbiome of SC undergoes a developmental progression: a developmental phase (cub), a transitional phase (subadult), and a stable phase (adult). These results expand our understanding of the role of age in the development of the gut microbiome of SC.

Phenotypic plasticity determines differences between the skulls of tigers from mainland Asia.

Tiger subspecific taxonomy is controversial because of morphological and genetic variation found between now fragmented populations, yet the extent to which phenotypic plasticity or genetic variation affects phenotypes of putative tiger subspecies has not been explicitly addressed. In order to assess the role of phenotypic plasticity in determining skull variation, we compared skull morphology among continental tigers from zoos and the wild. In turn, we examine continental tiger skulls from across their wild range, to evaluate how the different environmental conditions experienced by individuals in the wild can influence morphological variation. Fifty-seven measurements from 172 specimens were used to analyse size and shape differences among wild and captive continental tiger skulls. Captive specimens have broader skulls, and shorter rostral depths and mandible heights than wild specimens. In addition, sagittal crest size is larger in wild Amur tigers compared with those from captivity, and it is larger in wild Amur tigers compared with other wild continental tigers. The degree of phenotypic plasticity shown by the sagittal crest, skull width and rostral height suggests that the distinctive shape of Amur tiger skulls compared with that of other continental tigers is mostly a phenotypically plastic response to differences in their environments.

New Evidence of Tiger Subspecies Differentiation and Environmental Adaptation: Comparison of the Whole Genomes of the Amur Tiger and the South China Tiger.

Simple SummaryTigers are top predators and umbrella protectors, vital to the stability of ecosystems. The South China tiger has been declared extinct in the wild and only exists in captivity. The Chinese government is actively promoting the reintroduction of the South China tiger into the wild. The future of the wild population of the Amur tiger in China is not optimistic, and the recovery of the population is an essential task for the conservation of the Amur tiger. The recovery of the population is not only a macroscopic problem but also a significant study of molecular ecology. We used high-throughput sequencing technology to study the differences in adaptive selection between Amur tigers and South China tigers. Significant genetic differences were found between the Amur tiger and the South China tiger based on a principal component analysis and phylogenetic tree. We identified functional genes and regulatory pathways related to reproduction, disease, predation, and metabolism and characterized functional genes related to survival in the wild, such as smell, vision, muscle, and predatory ability. The data also provide new evidence for the adaptation of Amur tigers to cold environments. PRKG1 is involved in temperature regulation in a cold climate. FOXO1 and TPM4 regulate body temperature to keep it constant. The research also provides a molecular basis for future tiger conservation.Panthera tigris is a top predator that maintains the integrity of forest ecosystems and is an integral part of biodiversity. No more than 400 Amur tigers (P. t. altaica) are left in the wild, whereas the South China tiger (P. t. amoyensis) is thought to be extinct in the wild, and molecular biology has been widely used in conservation and management. In this study, the genetic information of Amur tigers and South China tigers was studied by whole-genome sequencing (WGS). A total of 647 Gb of high-quality clean data was obtained. There were 6.3 million high-quality single-nucleotide polymorphisms (SNPs), among which most (66.3%) were located in intergenic regions, with an average of 31.72% located in coding sequences. There were 1.73 million insertion-deletions (InDels), among which there were 2438 InDels (0.10%) in the coding region, and 270 thousand copy number variations (CNVs). Significant genetic differences were found between the Amur tiger and the South China tiger based on a principal component analysis and phylogenetic tree. The linkage disequilibrium analysis showed that the linkage disequilibrium attenuation distance of the South China tiger and the Amur tiger was almost the same, whereas the r2 of the South China tiger was 0.6, and the r2 of the Amur tiger was 0.4. We identified functional genes and regulatory pathways related to reproduction, disease, predation, and metabolism and characterized functional genes related to survival in the wild, such as smell, vision, muscle, and predatory ability. The data also provide new evidence for the adaptation of Amur tigers to cold environments. PRKG1 is involved in temperature regulation in a cold climate. FOXO1 and TPM4 regulate body temperature to keep it constant. Our results can provide genetic support for precise interspecies conservation and management planning in the future.

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.

Phylogeography of Panthera tigris in the mangrove forest of the Sundarbans

Tigers Panthera tigris in the Sundarbans represent the only population adapted to living in mangrove forest habitat. Several studies, based on limited morphological and genetic data, have described the population as being differentiated from the Bengal tiger subspecies P. tigris tigris. The phylogenetic ancestry of the Sundarbans population has also remained poorly understood. We generated 1263 bp of mtDNA sequences across 4 mtDNA genes for 33 tiger samples from the Bangladesh Sundarbans and compared these with 33 mtDNA haplotypes known from all subspecies of extant tigers. We detected 3 haplotypes within the Sundarbans tigers, of which one is unique to this population and the remaining 2 are shared with tiger populations inhabiting central Indian landscapes. Phylogenetic analyses using maximum likelihood and Bayesian inferences supported the Sundarbans tigers as being paraphyletic, indicating a close phylogenetic relationship with other populations of Bengal tigers, from which the Sundarbans population diverged around 26000 yr ago. Our phylogenetic analyses, together with evidence of ecological adaptation to the unique mangrove habitat, indicate that the Sundarbans population should be recognised as a separate management unit. We recommend that conservation management must focus on sustaining this representative tiger population adapted to mangrove habitat while at the same time recognising that trans-boundary conservation efforts through reintroduction or exchange of individuals, to enhance genetic diversity, might be needed in the future as a last resort for population recovery.

Hematological and Biochemical Reference Values in Healthy Captive Tigers (Panthera tigris).

Simple SummaryThe tiger (Panthera tigris) is the largest of the wild cats and is a pivotal member of many ecosystems and cultures. Despite a long history of concern for wild tigers, both their range and total number have collapsed: fewer than 3500 animals now live in the wild. Furthermore, an increased demand for tiger parts and consequent poaching as well as hunting of their prey has decimated populations across Asia, both in and out of reserves. All subspecies of tigers are globally endangered. Given the precarious situation of these wild felid, the health of each individual animal is of utmost importance so thorough health monitoring, including laboratory blood testing and physical evaluation, is vital. In human and veterinary medicine, hematological parameters and blood chemistry analysis are used in the diagnostic process, to establish disease processes and to monitor the progression of disease. Additionally, blood testing in wild animals provides baseline values for future studies and may help to support conservation strategies. It is extremely difficult to obtain biological samples from free-living Panthera tigris, therefore the values obtained from captive tigers provide very useful data. This study reports hematological and serum biochemical data in captive tigers. These results will be useful in the evaluation of physiological and pathological variations in wild and captive tiger populations. Tigers are a conservation-dependent species and require close protection because they are in high demand in the illegal trade. Development of a strong conservation ethic is urgently required for their survival. Pooling of knowledge about this species is essential if it is to be saved.The tiger (Panthera tigris) is an endangered species. The health of individuals is important and any data on hematological and biochemical blood values can provide valuable information; when combined with physical assessment. This data assists in both the diagnosis of disease and some conservation strategies. The behavior of wild tigers makes it is extremely difficult to obtain biological samples from free-living subjects, therefore, data collected from captive tigers is highly valuable. The aim of this study was to provide additional information for the values of hematological and serum biochemical parameters in healthy captive tigers. Blood samples were collected from 22 clinically healthy tigers (Panthera tigris). The following parameters were analyzed: glucose, urea, creatinine, alanine aminotransferase (ALT), alkaline phosphatase (ALP), total protein (TP) and red blood cells (RBCs), hemoglobin (Hb), hematocrit (Hct) and red cell indices; such as mean cell volume (MCV), mean cell Hb (MCH), mean cell Hb concentration (MCHC), platelet (PLT) and white blood cells (WBCs). The mean hematological values in our tiger population were not significantly different when compared with the same parameters in the previously studied tiger population. The mean values of RBCs and PLT were statistically significantly higher and the mean values of Hb, PCV, MCV, MCH, MCHC, and WBC were lower than the mean values obtained in previous studies on the Amur tiger. Further investigation of captive and free-living tigers is needed to identify the normal ranges for parameters in this endangered species.

Using Keeper Questionnaires to Capture Zoo-Housed Tiger (Panthera tigris) Personality: Considerations for Animal Management

Individual personalities affect animal experiences of zoo environments, impact on an animal’s coping ability and have potential implications for welfare. Keeper assessments have been identified as a quick and reliable way of capturing data on personality in a range of species and have practical application in improving animal welfare on an individual level. Despite widespread recognition of the importance of animal personality within a zoo environment, there is a paucity of research into tiger personality and the potential impact of this on tiger experiences within zoos. This research investigated the personality of 34 tigers (19 Amur and 15 Sumatran) across 14 facilities in the UK using keeper ratings and identified changes keepers made in animal husbandry to support tiger welfare. Reliability across keepers (n = 49) was established for nine adjectives and a principal component analysis identified three personality components: ‘anxious’, ‘quiet’ and ‘sociable’. When subspecies were combined, there was no relationship between tiger scores on the personality components and age or sex of tigers (p > 0.05). Subspecies of tiger was not related to scores on the ‘quiet’ or ‘sociable’ components (p > 0.05). Sumatran tigers scored more highly than Amur tigers on the ‘anxious’ component (mean ± SD, Sumatran: 3.0 ± 1.7, Amur: 1.8 ± 0.6, p < 0.05). Analysis within subspecies found that male Amur tigers were more sociable than females (mean ± SD, males: 5.5 ± 0.707; females: 4.15 ± 0.55). Amur tiger age was also negatively correlated with scores on the sociable personality component (R = −0.742, p < 0.05). No significant differences were seen in Sumatran tigers. Keepers reported a number of changes to husbandry routines based on their perceptions of their tigers’ personality/needs. However, there was no significant relationship between these changes and tiger personality scores (p > 0.05). Despite significant evolutionary differences between Amur and Sumatran tigers, there are no subspecies specific guidelines for zoo tigers. This research has highlighted the potential for these two subspecies to display personality differences and we advocate further research into this area. Specifically, we highlight a need to validate the relationship between tiger personality, management protocols and behavioural and physiological metrics of welfare. This will enable a fuller understanding of the impact of personality on zoo tiger experiences and will enable identification of evidence-based best practice guidelines.

Priority areas identified through spatial habitat suitability index and network analysis: Wild boar populations as proxies for tigers in and around the Hupingshan and Houhe National Nature Reserves

The decline and fragmentation of habitats areas are two main factors that lead to the reduction of biodiversity in landscape ecosystems. As a kind of large carnivores, South China tiger (Panthera tigris amoyensis) is one of the most endangered tiger subspecies and considered to be extinct in the wild. The Chinese government has intended to release a certain number of tigers into two of their historically habitats areas, Hupingshan–Houhe national nature reserves (NNR) in central–south China that provides suitable habitats for P. tigris. Because wild boar (Sus scrofa) is a prey of P. tigris, spatially characterizing the populations of the prey and its habitats is critical for the success of habituating the tigers to the areas. Although there has been effort made to protect the habitats of wild boar, there have been no report that deal with investigation and analysis of the habitat suitability and potential for wild boar, especially in terms of landscape connectivity. Here we present the novel integration of the habitat suitability index (HSI) and graph–based network to identify the priority areas for wild boar dispersal in and around the NNR. In addition, a novel method to identify the proper connectivity distance to avoid excessive connectivity when the field data are essentially non-existent. Results showed that in summer and winter, the potential habitat areas were 6848–10,245 and 5984–10,152 km2, respectively. The total area of the priority patches was 1590 km2, approximately occupying 16% of the suitable habitat area. Our study indicated that the novel integration of the HSI and network analysis led to an effective approach to spatially characterize priority patches to support decision-making for landscape planning. The results shown here also have implications for future efforts for habituating large carnivores into their historical habitat regions.

Short notes on a second tiger (Panthera tigris) from Late Pleistocene Borneo

ABSTRACT The tiger (Panthera tigris) has an archaic past on the Malay Archipelago. Despite such, the tiger is poorly recorded on Borneo, with just a single partial metacarpal being previously reported. This study presents the first mandibular remains and just the second fossil tiger from Borneo. The specimen is dated to MIS 2. It is morphologically most like southern subspecies of tiger but much larger than any extant form. The fossil record of the Bornean tiger indicates the region maintained a population of tigers throughout at least MIS 2 to some portion of MIS 1. A mixture of ecological and anthropological factors is likely the cause of the disappearance of the Bornean tiger.

Genome-Wide Evolutionary Analysis of Natural History and Adaptation in the World’s Tigers

No other species attracts more international resources, public attention, and protracted controversies over its intraspecific taxonomy than the tiger (Panthera tigris) [1, 2]. Today, fewer than 4,000 free-ranging tigers survive, covering only 7% of their historical range, and debates persist over whether they comprise six, five, or two subspecies [3-6]. The lack of consensus over the number of tiger subspecies has partially hindered the global effort to recover the species from the brink of extinction, as both captive breeding and landscape intervention of wild populations increasingly require an explicit delineation of the conservation management units [7]. The recent coalescence to a late Pleistocene bottleneck (circa 110 kya) [5, 8, 9] poses challenges for detecting tiger subspecific morphological traits, suggesting that elucidating intraspecific evolution in the tiger requires analyses at the genomic scale. Here, we present whole-genome sequencing analyses from 32 voucher specimens that resolve six statistically robust monophyletic clades corresponding to extant subspecies, including the recently recognized Malayan tiger (P.tigris jacksoni). The intersubspecies gene flow is very low, corroborating the recognizedphylogeographic units. We identified multiple genomic regions that are candidates for identifying the adaptive divergence of subspecies. The body-size-related gene ADH7 appears to have been strongly selected in the Sumatran tiger, perhaps in association with adaptation to the tropical Sunda Islands. The identified genomic signatures provide a solid basis for recognizing appropriate conservation management units in the tiger and can benefit global conservation strategic planning for this charismatic megafauna icon.

Assessing factors influencing a possible South China tiger reintroduction: a survey of international conservation professionals

SUMMARYTigers are among the most at-risk large carnivores and the South China tiger is the most threatened tiger subspecies. Reintroduction programmes are one strategy to re-establishing extirpated populations. China is committed to restoring wild South China tigers, but uncertainty remains about factors constraining these efforts. The aim of this study was to query conservation and reintroduction professionals about their attitudes and concerns and to provide guidance regarding a possible tiger reintroduction effort in South Central China. We carried out a global survey of 287 scholars and practitioners involved with wildlife reintroduction and conservation. We received responses from 68 (23.7%) respondents. More than 70% supported a potential South China tiger reintroduction effort, but many expressed concerns over planning and implementation, adherence to International Union for Conservation of Nature reintroduction guidelines and elimination of underlying threats. Respondents generally believed that China has the capacity to carry out such a programme, but may not have the experience or socio-political environment to address the issues facing human populations; 62% of respondents suggested a plausible release site should be greater than 2000 km2. To our knowledge, this is the first survey related to a potential large carnivore reintroduction programme in Asia; it has implications for future reintroduction and recovery programmes in Asia and globally.

The development and application of a multiplex short tandem repeat (STR) system for identifying subspecies, individuals and sex in tigers.

Poaching and trans-boundary trafficking of tigers and body parts are threatening the world's last remaining wild tigers. Development of an efficient molecular genetic assay for tracing the origins of confiscated specimens will assist in law enforcement and wildlife forensics for this iconic flagship species. We developed a multiplex genotyping system "tigrisPlex" to simultaneously assess 22 short tandem repeat (STR, or microsatellite) loci and a gender-identifying SRY gene, all amplified in 4 reactions using as little as 1 ng of template DNA. With DNA samples used for between-run calibration, the system generates STR genotypes that are directly compatible with voucher tiger subspecies genetic profiles, hence making it possible to identify subspecies via bi-parentally inherited markers. We applied "tigrisPlex" to 12 confiscated specimens from Russia and identified 6 individuals (3 females and 3 males), each represented by duplicated samples and all designated as Amur tigers (Panthera tigris altaica) with high confidence. This STR multiplex system can serve as an effective and versatile approach for genetic profiling of both wild and captive tigers as well as confiscated tiger products, fulfilling various conservation needs for identifying the origins of tiger samples.

Planning tiger recovery: Understanding intraspecific variation for effective conservation.

Although significantly more money is spent on the conservation of tigers than on any other threatened species, today only 3200 to 3600 tigers roam the forests of Asia, occupying only 7% of their historical range. Despite the global significance of and interest in tiger conservation, global approaches to plan tiger recovery are partly impeded by the lack of a consensus on the number of tiger subspecies or management units, because a comprehensive analysis of tiger variation is lacking. We analyzed variation among all nine putative tiger subspecies, using extensive data sets of several traits [morphological (craniodental and pelage), ecological, molecular]. Our analyses revealed little variation and large overlaps in each trait among putative subspecies, and molecular data showed extremely low diversity because of a severe Late Pleistocene population decline. Our results support recognition of only two subspecies: the Sunda tiger, Panthera tigris sondaica, and the continental tiger, Panthera tigris tigris, which consists of two (northern and southern) management units. Conservation management programs, such as captive breeding, reintroduction initiatives, or trans-boundary projects, rely on a durable, consistent characterization of subspecies as taxonomic units, defined by robust multiple lines of scientific evidence rather than single traits or ad hoc descriptions of one or few specimens. Our multiple-trait data set supports a fundamental rethinking of the conventional tiger taxonomy paradigm, which will have profound implications for the management of in situ and ex situ tiger populations and boost conservation efforts by facilitating a pragmatic approach to tiger conservation management worldwide.