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

Whole genome resequencing-based analysis of plateau adaptation in Meiren yak (Bos grunniens)

The Meiren yak is an important genetic resource in Gansu Province, China. In this study, we aimed to explore the evolutionary history and population structure of the genetic resource of Meiren yak and to mine the characteristic genes of Meiren yak. We analysed a total of 93 yaks of eight yak breeds based on whole genome resequencing combined with population genomics and used θπ ratio and Fst method to screen the selected sites in the genome region. The results proved that Meiren yak can be used as a potential genetic resource in Gansu Province. The genes in Meiren yak with positive selection in selection signal analysis were subjected to the Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses, which indicated that the genes were related to the adaptability to high altitude and hypoxic environment. By analysing the genetic variation of Meiren yak at the genome-wide level, this study provided a theoretical basis for genetic improvement of Meiren yak and for the development of high-quality yak resources.

Genetic linkage disequilibrium of deleterious mutations in threatened mammals

The impact of negative selection against deleterious mutations in endangered species remains underexplored. Recent studies have measured mutation load by comparing the accumulation of deleterious mutations, however, this method is most effective when comparing within and between populations of phylogenetically closely related species. Here, we introduced new statistics, LDcor, and its standardized form nLDcor, which allows us to detect and compare global linkage disequilibrium of deleterious mutations across species using unphased genotypes. These statistics measure averaged pairwise standardized covariance and standardize mutation differences based on the standard deviation of alleles to reflect selection intensity. We then examined selection strength in the genomes of seven mammals. Tigers exhibited an over-dispersion of deleterious mutations, while gorillas, giant pandas, and golden snub-nosed monkeys displayed negative linkage disequilibrium. Furthermore, the distribution of deleterious mutations in threatened mammals did not reveal consistent trends. Our results indicate that these newly developed statistics could help us understand the genetic burden of threatened species.

Evolutionary insights into Felidae iris color through ancestral state reconstruction

Few studies have explored eye (iris) color evolution beyond humans and domesticated animals. Felids exhibit significant eye color diversity, unlike their brown-eyed relatives, making them an ideal model to study the evolution of eye color in natural populations. Through machine learning analysis of public photographs, five felid eye colors were identified: brown, green, yellow, gray, and blue. The presence or absence of these colors was reconstructed on a phylogeny, as well as their specific quantitative shades. The ancestral felid population likely had brown-eyed and gray-eyed individuals, the latter color being pivotal for the diversification of eye color seen in modern felids. Additionally, yellow eyes are highly associated with and may be necessary for, the evolution of round pupils in felids. These findings enhance the understanding of eye color evolution, and the methods presented in this work are widely applicable and will facilitate future research into the phylogenetic reconstruction of color beyond irises.

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.

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.

Genome sequencing of captive white tigers from Bangladesh

OBJECTIVES

The Bengal tiger Panthera tigris tigris, is an emblematic animal for Bangladesh. Despite being the apex predator in the wild, their number is decreasing due to anthropogenic activities such as hunting, urbanization, expansion of agriculture and deforestation. By contrast, captive tigers are flourishing due to practical conservation efforts. Breeding within the small captive population can produce inbreeding depression and genetic bottlenecks, which may limit the success of conservation efforts. Despite past decades of research, a comprehensive database on genetic variation in the captive and wild Bengal tigers in Bangladesh still needs to be included. Therefore, this research aimed to investigate the White Bengal tiger genome to create a resource for future studies to understand variation underlying important functional traits.

DATA DESCRIPTION

Blood samples from Chattogram Zoo were collected for three white Bengal tigers. Genomic DNA for all collected samples were extracted using a commercial DNA extraction kit. Whole genome sequencing was performed using a DNBseq platform. We generated 77 Gb of whole-genome sequencing (WGS) data for three white Bengal tigers (Average 11X coverage/sample). The data we generated will establish a paradigm for tiger research in Bangladesh by providing a genomic resource for future functional studies on the Bengal white tiger.

The genetic status and rescue measure for a geographically isolated population of Amur tigers

The Amur tiger is currently confronted with challenges of anthropogenic development, leading to its population becoming fragmented into two geographically isolated groups: smaller and larger ones. Small and isolated populations frequently face a greater extinction risk, yet the small tiger population's genetic status and survival potential have not been assessed. Here, a total of 210 samples of suspected Amur tiger feces were collected from this small population, and the genetic background and population survival potentials were assessed by using 14 microsatellite loci. Our results demonstrated that the mean number of alleles in all loci was 3.7 and expected heterozygosity was 0.6, indicating a comparatively lower level of population genetic diversity compared to previously reported studies on other subspecies. The genetic estimates of effective population size (Ne) and the Ne/N ratio were merely 7.6 and 0.152, respectively, representing lower values in comparison to the Amur tiger population in Sikhote-Alin (the larger group). However, multiple methods have indicated the possibility of genetic divergence within our isolated population under study. Meanwhile, the maximum kinship recorded was 0.441, and the mean inbreeding coefficient stood at 0.0868, both of which are higher than those observed in other endangered species, such as the African lion and the grey wolf. Additionally, we have identified a significant risk of future extinction if the lethal equivalents were to reach 6.26, which is higher than that of other large carnivores. Further, our simulation results indicated that an increase in the number of breeding females would enhance the prospects of this population. In summary, our findings provide a critical theoretical basis for further bailout strategies concerning Amur tigers.

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.

Using Computational Simulations to Model Deleterious Variation and Genetic Load in Natural Populations

AbstractDeleterious genetic variation is abundant in wild populations, and understanding the ecological and conservation implications of such variation is an area of active research. Genomic methods are increasingly used to quantify the impacts of deleterious variation in natural populations; however, these approaches remain limited by an inability to accurately predict the selective and dominance effects of mutations. Computational simulations of deleterious variation offer a complementary tool that can help overcome these limitations, although such approaches have yet to be widely employed. In this perspective article, we aim to encourage ecological and conservation genomics researchers to adopt greater use of computational simulations to aid in deepening our understanding of deleterious variation in natural populations. We first provide an overview of the components of a simulation of deleterious variation, describing the key parameters involved in such models. Next, we discuss several approaches for validating simulation models. Finally, we compare and validate several recently proposed deleterious mutation models, demonstrating that models based on estimates of selection parameters from experimental systems are biased toward highly deleterious mutations. We describe a new model that is supported by multiple orthogonal lines of evidence and provide example scripts for implementing this model (https://github.com/ckyriazis/simulations_review).

Extensive Phylogenomic Discordance and the Complex Evolutionary History of the Neotropical Cat Genus Leopardus

Even in the genomics era, the phylogeny of Neotropical small felids comprised in the genus Leopardus remains contentious. We used whole-genome resequencing data to construct a time-calibrated consensus phylogeny of this group, quantify phylogenomic discordance, test for interspecies introgression, and assess patterns of genetic diversity and demographic history. We infer that the Leopardus radiation started in the Early Pliocene as an initial speciation burst, followed by another in its subgenus Oncifelis during the Early Pleistocene. Our findings challenge the long-held notion that ocelot (Leopardus pardalis) and margay (L. wiedii) are sister species and instead indicate that margay is most closely related to the enigmatic Andean cat (L. jacobita), whose whole-genome data are reported here for the first time. In addition, we found that the newly sampled Andean tiger cat (L. tigrinus pardinoides) population from Colombia associates closely with Central American tiger cats (L. tigrinus oncilla). Genealogical discordance was largely attributable to incomplete lineage sorting, yet was augmented by strong gene flow between ocelot and the ancestral branch of Oncifelis, as well as between Geoffroy's cat (L. geoffroyi) and southern tiger cat (L. guttulus). Contrasting demographic trajectories have led to disparate levels of current genomic diversity, with a nearly tenfold difference in heterozygosity between Andean cat and ocelot, spanning the entire range of variability found in extant felids. Our analyses improved our understanding of the speciation history and diversity patterns in this felid radiation, and highlight the benefits to phylogenomic inference of embracing the many heterogeneous signals scattered across the genome.

Ancient DNA reveals genetic admixture in China during tiger evolution

The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.

Evolutionary history of the extinct wolf population from France in the context of global phylogeographic changes throughout the Holocene

Phylogeographic patterns in large mammals result from natural environmental factors and anthropogenic effects, which in some cases include domestication. The grey wolf was once widely distributed across the Holarctic, but experienced phylogeographic shifts and demographic declines during the Holocene. In the 19th-20th centuries, the species became extirpated from large parts of Europe due to direct extermination and habitat loss. We reconstructed the evolutionary history of the extinct Western European wolves based on the mitogenomic composition of 78 samples from France (Neolithic-20th century) in the context of other populations of wolves and dogs worldwide. We found a close genetic similarity of French wolves from ancient, medieval and recent populations, which suggests the long-term continuity of maternal lineages. MtDNA haplotypes of the French wolves showed large diversity and fell into two main haplogroups of modern Holarctic wolves. Our worldwide phylogeographic analysis indicated that haplogroup W1, which includes wolves from Eurasia and North America, originated in Northern Siberia. Haplogroup W2, which includes only European wolves, originated in Europe ~35 kya and its frequency was reduced during the Holocene due to an expansion of haplogroup W1 from the east. Moreover, we found that dog haplogroup D, currently restricted to Europe and the Middle East, was nested within the wolf haplogroup W2. This suggests European origin of haplogroup D, probably as a result of an ancient introgression from European wolves. Our results highlight the dynamic evolutionary history of European wolves during the Holocene, with a partial lineage replacement and introgressive hybridization with local dog populations.

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

BACKGROUND

Among 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.

RESULTS

In 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 F_ROH 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.

CONCLUSIONS

The 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.

Evolution of the germline mutation rate across vertebrates

The germline mutation rate determines the pace of genome evolution and is an evolving parameter itself¹. However, little is known about what determines its evolution, as most studies of mutation rates have focused on single species with different methodologies². Here we quantify germline mutation rates across vertebrates by sequencing and comparing the high-coverage genomes of 151 parent-offspring trios from 68 species of mammals, fishes, birds and reptiles. We show that the per-generation mutation rate varies among species by a factor of 40, with mutation rates being higher for males than for females in mammals and birds, but not in reptiles and fishes. The generation time, age at maturity and species-level fecundity are the key life-history traits affecting this variation among species. Furthermore, species with higher long-term effective population sizes tend to have lower mutation rates per generation, providing support for the drift barrier hypothesis³. The exceptionally high yearly mutation rates of domesticated animals, which have been continually selected on fecundity traits including shorter generation times, further support the importance of generation time in the evolution of mutation rates. Overall, our comparative analysis of pedigree-based mutation rates provides ecological insights on the mutation rate evolution in vertebrates.

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.

The potential and shortcomings of mitochondrial DNA analysis for cheetah conservation management

There are only about 7,100 adolescent and adult cheetahs (Acinonyx jubatus) remaining in the wild. With the majority occurring outside protected areas, their numbers are rapidly declining. Evidence-based conservation measures are essential for the survival of this species. Genetic data is routinely used to inform conservation strategies, e.g., by establishing conservation units (CU). A commonly used marker in conservation genetics is mitochondrial DNA (mtDNA). Here, we investigated the cheetah's phylogeography using a large-scale mtDNA data set to refine subspecies distributions and better assign individuals to CUs. Our dataset mostly consisted of historic samples to cover the cheetah's whole range as the species has been extinct in most of its former distribution. While our genetic data largely agree with geography-based subspecies assignments, several geographic regions show conflicting mtDNA signals. Our analyses support previous findings that evolutionary forces such as incomplete lineage sorting or mitochondrial capture likely confound the mitochondrial phylogeography of this species, especially in East and, to some extent, in Northeast Africa. We caution that subspecies assignments solely based on mtDNA should be treated carefully and argue for an additional standardized nuclear single nucleotide polymorphism (SNP) marker set for subspecies identification and monitoring. However, the detection of the A. j. soemmeringii specific haplogroup by a newly designed Amplification-Refractory Mutation System (ARMS) can already provide support for conservation measures.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10592-022-01483-1.

Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation

The tiger, a poster child for conservation, remains an endangered apex predator. Continued survival and recovery will require a comprehensive understanding of genetic diversity and the use of such information for population management. A high-quality tiger genome assembly will be an important tool for conservation genetics, especially for the Indian tiger, the most abundant subspecies in the wild. Here, we present high-quality near-chromosomal genome assemblies of a female and a male wild Indian tiger (Panthera tigris tigris). Our assemblies had a scaffold N50 of >140 Mb, with 19  scaffolds corresponding to the 19 numbered chromosomes, containing 95% of the genome. Our assemblies also enabled detection of longer stretches of runs of homozygosity compared to previous assemblies, which will help improve estimates of genomic inbreeding. Comprehensive genome annotation identified 26,068 protein-coding genes, including several gene families involved in key morphological features such as the teeth, claws, vision, olfaction, taste, and body stripes. We also identified 301 microRNAs, 365 small nucleolar RNAs, 632 transfer RNAs, and other noncoding RNA elements, several of which are predicted to regulate key biological pathways that likely contribute to the tiger's apex predatory traits. We identify signatures of positive selection in the tiger genome that are consistent with the Panthera lineage. Our high-quality genome will enable use of noninvasive samples for comprehensive assessment of genetic diversity, thus supporting effective conservation and management of wild tiger populations.

Mitochondrial genomes assembled from non-invasive eDNA metagenomic scat samples in the endangered Amur tiger Panthera tigris altaica

The Amur or Siberian tiger Panthera tigris altaica (Temminck, 1844) is currently restricted to a small region of its original geographical range in northwestern Asia and is considered 'endangered' by the IUCN Red List of Threatened Species. This solitary, territorial, and large top predator is in major need of genomic resources to inform conservation management strategies. This study formally tested if complete mitochondrial genomes of P. tigris altaica can be assembled from non-enriched metagenomic libraries generated from scat eDNA samples using the Illumina sequencing platform and open-access bioinformatics pipelines. The mitogenome of P. tigris altaica was assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 322.7x to 17.6x in four different scat eDNA samples. A nearly complete mitochondrial genome (101x) was retrieved from a fifth scat eDNA sample. The complete or nearly complete mitochondrial genomes of P. tigris altaica were AT-rich and composed of 13 protein coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Synteny observed in all assembled mitogenomes was identical to that reported before for P. tigris altaica and other felids. A phylogenomic analysis based on all PCGs demonstrated that the mitochondrial genomes assembled from scat eDNA reliably identify the sequenced samples as belonging to P. tigris and distinguished the same samples from closely and distantly related congeneric species. This study demonstrates that it is viable to retrieve accurate whole and nearly complete mitochondrial genomes of P. tigris altaica (and probably other felids) from scat eDNA samples without library enrichment protocols and using open-access bioinformatics workflows. This new genomic resource represents a new tool to support conservation strategies (bio-prospecting and bio-monitoring) in this iconic cat.

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.

Whole-genome resequencing of Chinese pangolins reveals a population structure and provides insights into their conservation

Poaching and trafficking have a substantial negative impact on the population growth and range expansion of the Chinese pangolin (Manis pentadactyla). However, recently reported activities of Chinese pangolins in several sites of Guangdong province in China indicate a promising sign for the recovery of this threatened species. Here, we re-sequence genomes of 15 individuals and perform comprehensive population genomics analyses with previously published 22 individuals. These Chinese pangolins are found to be divided into three distinct populations. Multiple lines of evidence indicate the existence of a newly discovered population (CPA) comprises entirely of individuals from Guangdong province. The other two populations (CPB and CPC) have previously been documented. The genetic differentiation of the CPA and CPC is extremely large (FST = 0.541), which is larger than many subspecies-level differentiations. Even for the closer CPA and CPB, their differentiation (FST = 0.101) is still comparable with the population-level differentiation of many endangered species. Further analysis reveals that the CPA and CPB populations separate 2.5-4.0 thousand years ago (kya), and on the other hand, CPA and CPC diverge around 25-40 kya. The CPA population harbors more runs of homozygosity (ROHs) than the CPB and CPC populations, indicating that inbreeding is more prevalent in the CPA population. Although the CPC population has less mutational load than CPA and CPB populations, we predict that several Loss of Function (LoF) mutations will be translocated into the CPA or CPB populations by using the CPC as a donor population for genetic rescue. Our findings imply that the conservation of Chinese pangolins is challenging, and implementing genetic rescue among the three groups should be done with extreme caution.

Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus)

We live in a world characterized by biodiversity loss and global environmental change. The extinction of large carnivores can have ramifying effects on ecosystems like an uncontrolled increase in wild herbivores, which in turn can have knock-on impacts on vegetation regeneration and communities. Cheetahs (Acinonyx jubatus) serve important ecosystem functions as apex predators; yet, they are quickly heading towards an uncertain future. Threatened by habitat loss, human-wildlife conflict and illegal trafficking, there are only approximately 7100 individuals remaining in nature. We present the most comprehensive genome-wide analysis of cheetah phylogeography and conservation genomics to date, assembling samples from nearly the entire current and past species' range. We show that their phylogeography is more complex than previously thought, and that East African cheetahs (A. j. raineyi) are genetically distinct from Southern African individuals (A. j. jubatus), warranting their recognition as a distinct subspecies. We found strong genetic differentiation between all classically recognized subspecies, thus refuting earlier findings that cheetahs show only little differentiation. The strongest differentiation was observed between the Asiatic and all the African subspecies. We detected high inbreeding in the Critically Endangered Iranian (A. j. venaticus) and North-western (A. j. hecki) subspecies, and show that overall cheetahs, along with snow leopards, have the lowest genome-wide heterozygosity of all the big cats. This further emphasizes the cheetah's perilous conservation status. Our results provide novel and important information on cheetah phylogeography that can support evidence-based conservation policy decisions to help protect this species. This is especially relevant in light of ongoing and proposed translocations across subspecies boundaries, and the increasing threats of illegal trafficking.

An extinct and deeply divergent tiger lineage from northeastern China recognized through palaeogenomics

Tigers (Panthera tigris) are flagship big cats and attract extensive public attention due to their charismatic features and endangered status. Despite this, little is known about their prehistoric lineages and detailed evolutionary histories. Through palaeogenomic analyses, we identified a Pleistocene tiger from northeastern China, dated to beyond the limits of radiocarbon dating (greater than 43 500 years ago). We used a simulated dataset and different reads processing pipelines to test the validity of our results and confirmed that, in both mitochondrial and nuclear phylogenies, this ancient individual belongs to a previously unknown lineage that diverged prior to modern tiger diversification. Based on the mitochondrial genome, the divergence time of this ancient lineage was estimated to be approximately 268 ka (95% CI: 187-353 ka), doubling the known age of tigers' maternal ancestor to around 125 ka (95% CI: 88-168 ka). Furthermore, by combining our findings with putative mechanisms underlying the discordant mito-nuclear phylogenetic placement for the South China tigers, we proposed a more complex scenario of tiger evolution that would otherwise be missed using data from modern tigers only. Our study provides the first glimpses of the genetic antiquity of tigers and demonstrates the utility of aDNA-based investigation for further understanding tiger evolution.

A decade of GigaScience: A perspective on conservation genetics

Wide interest in species conservation is young. To many it began early in 1903 when Teddy Roosevelt and John Muir set up a camp under the Grizzly Giant in the Mariposa Grove of California's Yosemite Valley. Over three days they decided to broaden the US National Park footprint across the USA. Conservationists were inspired in the coming decades by the writings of wildlife conservation pioneers-Osa Johnson (I Married Adventure), Karen Blixen (Out of Africa) and Rachel Carson (The Silent Spring). Countless crusaders developed a passion for preserving dwindling species in those early days, yet none of these conservation advocates mentioned the word genetics, let alone genomics. The genome sequencing projects that have followed on from these have brought in an enormous amount of data, including whole genome sequences for thousands of non-human species, both individual and population wide. This huge resource has revolutionized conservation genetics, bringing in ways to assess the health of at-risk populations, devise genetic-driven breeding strategies, and other means to attempt to preserve the over 1 million species (and growing) under threat today.

How methodological changes have influenced our understanding of population structure in threatened species: insights from tiger populations across India

Unprecedented advances in sequencing technology in the past decade allow a better understanding of genetic variation and its partitioning in natural populations. Such inference is critical to conservation: to understand species biology and identify isolated populations. We review empirical population genetics studies of Endangered Bengal tigers within India, where 60-70% of wild tigers live. We assess how changes in marker type and sampling strategy have impacted inferences by reviewing past studies, and presenting three novel analyses including a single-nucleotide polymorphism (SNP) panel, genome-wide SNP markers, and a whole-mitochondrial genome network. At a broad spatial scale, less than 100 SNPs revealed the same patterns of population clustering as whole genomes (with the exception of one additional population sampled only in the SNP panel). Mitochondrial DNA indicates a strong structure between the northeast and other regions. Two studies with more populations sampled revealed further substructure within Central India. Overall, the comparison of studies with varied marker types and sample sets allows more rigorous inference of population structure. Yet sampling of some populations is limited across all studies, and these should be the focus of future sampling efforts. We discuss challenges in our understanding of population structure, and how to further address relevant questions in conservation genetics. This article is part of the theme issue 'Celebrating 50 years since Lewontin's apportionment of human diversity'.

Genetic guidelines for translocations: Maintaining intraspecific diversity in the lion (Panthera leo)

Conservation translocations have become an important management tool, particularly for large wildlife species such as the lion (Panthera leo). When planning translocations, the genetic background of populations needs to be taken into account; failure to do so risks disrupting existing patterns of genetic variation, ultimately leading to genetic homogenization, and thereby reducing resilience and adaptability of the species. We urge wildlife managers to include knowledge of the genetic background of source/target populations, as well as species-wide patterns, in any management intervention. We present a hierarchical decision-making tool in which we list 132 lion populations/lion conservation units and provide information on genetic assignment, uncertainty and suitability for translocation for each source/target combination. By including four levels of suitability, from 'first choice' to 'no option', we provide managers with a range of options. To illustrate the extent of international trade of lions, and the potential disruption of natural patterns of intraspecific diversity, we mined the CITES Trade Database for estimated trade quantities of live individuals imported into lion range states during the past 4 decades. We identified 1056 recorded individuals with a potential risk of interbreeding with wild lions, 772 being captive-sourced. Scoring each of the records with our decision-making tool illustrates that only 7% of the translocated individuals were 'first choice' and 73% were 'no option'. We acknowledge that other, nongenetic factors are important in the decision-making process, and hence a pragmatic approach is needed. A framework in which source/target populations are scored based on suitability is not only relevant to lion, but also to other species of wildlife that are frequently translocated. We hope that the presented overview supports managers to include genetics in future management decisions and contributes towards conservation of the lion in its full diversity.

Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers

Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small-isolated and two large-connected populations in India. As expected, the small-isolated population had substantially higher average genomic inbreeding (FROH = 0.57) than the large-connected (FROH = 0.35 and FROH = 0.46) populations. The small-isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small-isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small-isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small-isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.

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.

Population dynamics of caribou shaped by glacial cycles before the last glacial maximum

Pleistocene glacial cycles influenced the diversification of high‐latitude wildlife species through recurrent periods of range contraction, isolation, divergence, and expansion from refugia and subsequent admixture of refugial populations. We investigate population size changes and the introgressive history of caribou (Rangifer tarandus) in western Canada using 33 whole genome sequences coupled with larger‐scale mitochondrial data. We found that a major population expansion of caribou occurred starting around 110,000 years ago (kya), the start of the last glacial period. Additionally, we found effective population sizes of some caribou reaching ~700,000 to 1,000,000 individuals, one of the highest recorded historical effective population sizes for any mammal species thus far. Mitochondrial analyses dated introgression events prior to the LGM dating to 20–30 kya and even more ancient at 60 kya, coinciding with colder periods with extensive ice coverage, further demonstrating the importance of glacial cycles and events prior to the LGM in shaping demographic history. Reconstructing the origins and differential introgressive history has implications for predictions on species responses under climate change. Our results have implications for other whole genome analyses using pairwise sequentially Markovian coalescent (PSMC) analyses, as well as highlighting the need to investigate pre‐LGM demographic patterns to fully reconstruct the origin of species diversity, especially for high‐latitude species.

Sympatric and independently evolving lineages in the Thoropa miliaris - T. taophora species complex (Anura: Cycloramphidae)

Species delimitation can be challenging and affected by subjectivity. Sibling lineages that occur in sympatry constitute good candidates for species delimitation regardless of the adopted species concept. The Thoropa miliaris + T. taophora species complex exhibits high genetic diversity distributed in several lineages that occur sympatrically in the southeastern Atlantic Forest of Brazil. We used 414 loci obtained by anchored hybrid enrichment to characterize genetic variation in the Thoropa miliaris species group (T. saxatilis, T megatympanum, T. miliaris, and T. taophora), combining assignment analyses with traditional and coalescent phylogeny reconstruction. We also investigated evolutionary independence in co-occurring lineages by estimating gene flow, and validated lineages under the multispecies coalescent. We recovered most previously described lineages as unique populations in assignment analyses; exceptions include two lineages within T. miliaris that are further substructured, and the merging of all T. taophora lineages. We found very low probabilities of gene flow between sympatric lineages, suggesting independent evolution. Species tree inferences and species delimitation yielded resolved relationships and indicate that all lineages constitute putative species that diverged during the Pliocene and Pleistocene, later than previously estimated.

Recent Evolutionary History of Tigers Highlights Contrasting Roles of Genetic Drift and Selection

Species conservation can be improved by knowledge of evolutionary and genetic history. Tigers are among the most charismatic of endangered species and garner significant conservation attention. However, their evolutionary history and genomic variation remain poorly known, especially for Indian tigers. With 70% of the world’s wild tigers living in India, such knowledge is critical. We re-sequenced 65 individual tiger genomes representing most extant subspecies with a specific focus on tigers from India. As suggested by earlier studies, we found strong genetic differentiation between the putative tiger subspecies. Despite high total genomic diversity in India, individual tigers host longer runs of homozygosity, potentially suggesting recent inbreeding or founding events, possibly due to small and fragmented protected areas. We suggest the impacts of ongoing connectivity loss on inbreeding and persistence of Indian tigers be closely monitored. Surprisingly, demographic models suggest recent divergence (within the last 20,000 years) between subspecies and strong population bottlenecks. Amur tiger genomes revealed the strongest signals of selection related to metabolic adaptation to cold, whereas Sumatran tigers show evidence of weak selection for genes involved in body size regulation. We recommend detailed investigation of local adaptation in Amur and Sumatran tigers prior to initiating genetic rescue.

Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management

Background

While recent advances in genomics has enabled vast improvements in the quantification of genome-wide diversity and the identification of adaptive and deleterious alleles in model species, wildlife and non-model species have largely not reaped the same benefits. This has been attributed to the resources and infrastructure required to develop essential genomic datasets such as reference genomes. In the absence of a high-quality reference genome, cross-species alignments can provide reliable, cost-effective methods for single nucleotide variant (SNV) discovery. Here, we demonstrated the utility of cross-species genome alignment methods in gaining insights into population structure and functional genomic features in cheetah (Acinonyx jubatas), snow leopard (Panthera uncia) and Sumatran tiger (Panthera tigris sumatrae), relative to the domestic cat (Felis catus).

Results

Alignment of big cats to the domestic cat reference assembly yielded nearly complete sequence coverage of the reference genome. From this, 38,839,061 variants in cheetah, 15,504,143 in snow leopard and 13,414,953 in Sumatran tiger were discovered and annotated. This method was able to delineate population structure but limited in its ability to adequately detect rare variants. Enrichment analysis of fixed and species-specific SNVs revealed insights into adaptive traits, evolutionary history and the pathogenesis of heritable diseases.

Conclusions

The high degree of synteny among felid genomes enabled the successful application of the domestic cat reference in high-quality SNV detection. The datasets presented here provide a useful resource for future studies into population dynamics, evolutionary history and genetic and disease management of big cats. This cross-species method of variant discovery provides genomic context for identifying annotated gene regions essential to understanding adaptive and deleterious variants that can improve conservation outcomes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07899-2.

Taxonomy and Translocations of African Mammals: A Plea for a Cautionary Approach

Ecotourism can fuel an important source of financial income for African countries and can therefore help biodiversity policies in the continent. Translocations can be a powerful tool to spread economic benefits among countries and communities; yet, to be positive for biodiversity conservation, they require a basic knowledge of conservation units through appropriate taxonomic research. This is not always the case, as taxonomy was considered an outdated discipline for almost a century, and some plurality in taxonomic approaches is incorrectly considered as a disadvantage for conservation work. As an example, diversity of the genus Giraffa and its recent taxonomic history illustrate the importance of such knowledge for a sound conservation policy that includes translocations. We argue that a fine-grained conservation perspective that prioritizes all remaining populations along the Nile Basin is needed. Translocations are important tools for giraffe diversity conservation, but more discussion is needed, especially for moving new giraffes to regions where the autochthonous taxa/populations are no longer existent. As the current discussion about the giraffe taxonomy is too focused on the number of giraffe species, we argue that the plurality of taxonomic and conservation approaches might be beneficial, i.e., for defining the number of units requiring separate management using a (majority) consensus across different concepts (e.g., MU—management unit, ESU—evolutionary significant unit, and ECU—elemental conservation unit). The taxonomically sensitive translocation policy/strategy would be important for the preservation of current diversity, while also supporting the ecological restoration of some regions within rewilding. A summary table of the main translocation operations of African mammals that have underlying problems is included. Therefore, we call for increased attention toward the taxonomy of African mammals not only as the basis for sound conservation but also as a further opportunity to enlarge the geographic scope of ecotourism in Africa.

Lifespan decreases with proportion of sons in males but not females of zoo-housed tigers and lemurs

Several studies have shown higher costs of rearing sons than daughters in mammals where males are larger than females. These studies typically focus on females by examining how the offspring sex ratio during a single reproductive event affected mothers' subsequent reproduction or survival probability. Here, we examine relationships between offspring sex ratio during single or multiple reproductive events and several survival metrics in mothers and fathers, using data from zoo-housed tigers (Panthera tigris) and ruffed lemurs (Varecia sp.). Our analyses failed to reveal an overall cost of reproduction or a higher cost of sons to mothers. In male ruffed lemurs, the proportion of sons produced during early life (before 10 years old) was negatively correlated with lifespan later in life. In tigers, males with a higher proportion of sons during their lifetime had shorter lifespans. One likely mechanism is the difference in testosterone levels between males: a high concentration of testosterone can increase the proportion of sons and compromise immune function. Our results suggest studies in wild populations should address the outstanding challenge of understanding consequences of sex allocation for males, and open an opportunity to predict lifespan in an applied conservation context.

Sex-specific actuarial and reproductive senescence in zoo-housed tiger (Panthera tigris): The importance of sub-species for conservation

A fifth of all known species are currently classified as threatened in the wild: the rate of biodiversity loss is rapid, continuous, and mostly due to anthropogenic activities. To slow down this decline, the accurate estimation of demographic parameters for threatened species is critical. With this aim, zoo institutions play an important role, giving access to data on zoo-housed animals, which aids researchers working on species life-history traits and intrinsic factors influencing the fitness of both sexes, such as age. While tigers (Panthera tigris) are particularly threatened in their natural environment, few of their demographic parameters have been determined because of their solitary and elusive nature as well as low population density. Using individual-based information for more than 9200 tigers (from 1938 to 2018) recorded in the International Tiger Studbook 2018, we aimed to determine sub-species and sex-specific variability of survival and reproductive parameters with age. No significant sex-difference in actuarial senescence (i.e., decline of survival probabilities with age) was observed but males tended to have a higher juvenile mortality and a faster senescence than females. Reproductive senescence (i.e., decline of reproductive parameters with age) was more pronounced in females than males. Moreover, we observed sub-species-specific variation in mortality and reproductive patterns, pointing out the necessity to consider them independently for conservation goals. Our findings can provide meaningful improvements to the husbandry of zoo-housed tigers, emphasizing the importance of adult breeding females of 7-9 years-old to control zoo-housed population size, but also providing accurate demographic estimates, crucial to set up effective conservation plans.

Population genomic data in spider mites point to a role for local adaptation in shaping range shifts

Local adaptation is particularly likely in invertebrate pests that typically have short generation times and large population sizes, but there are few studies on pest species investigating local adaptation and separating this process from contemporaneous and historical gene flow. Here, we use a population genomic approach to investigate evolutionary processes in the two most dominant spider mites in China, Tetranychus truncatus Ehara and Tetranychus pueraricola Ehara et Gotoh, which have wide distributions, short generation times, and large population sizes. We generated genome resequencing of 246 spider mites mostly from China, as well as Japan and Canada at a combined total depth of 3,133×. Based on demographic reconstruction, we found that both mite species likely originated from refugia in southwestern China and then spread to other regions, with the dominant T. truncatus spreading ~3,000 years later than T. pueraricola. Estimated changes in population sizes of the pests matched known periods of glaciation and reinforce the recent expansion of the dominant spider mites. T. truncatus showed a greater extent of local adaptation with more genes (76 vs. 17) associated with precipitation, including candidates involved in regulation of homeostasis of water and ions, signal transduction, and motor skills. In both species, many genes (135 in T. truncatus and 95 in T. pueraricola) also showed signatures of selection related to elevation, including G-protein-coupled receptors, cytochrome P450s, and ABC-transporters. Our results point to historical expansion processes and climatic adaptation in these pests which could have contributed to their growing importance, particularly in the case of T. truncatus.

Can Zoos Ever Be Big Enough for Large Wild Animals? A Review Using an Expert Panel Assessment of the Psychological Priorities of the Amur Tiger (Panthera tigris altaica) as a Model Species

Simple Summary

The reduction in space available to wild animals in zoos and aquariums is widely perceived to be detrimental to their welfare by scientists and the general public alike. Evidence suggests that naturally wide-ranging carnivores are more likely to suffer in captivity than those that travel less widely. Using the Amur tiger as a representative for wide-ranging species frequently held in zoos, an expert panel assessment was undertaken to identify psychological priorities in order to see how the negative welfare impacts of reduced ranging opportunities might be most effectively overcome. This assessment highlights that whilst reduced access to space may be central to compromised welfare for many species, there may be more effective strategies in safeguarding welfare than simply making captive habitats marginally bigger. Central to this for Amur tigers is providing appropriate mental stimulation rather than focusing only on behaviours linked to hunting. Various strategies intended to safeguard welfare are discussed for Amur tigers, which can also be considered for other wide-ranging species.

Abstract

The ecology of large, wide-ranging carnivores appears to make them vulnerable to conservation challenges in the wild and welfare challenges in captivity. This poses an ethical dilemma for the zoo community and supports the case that there is a need to reconsider prevailing management paradigms for these species in captivity. Whilst the welfare challenges wide ranging carnivores face have been attributed to reduced ranging opportunities associated with the decreased size of captive habitats, attempts to augment wild carnivore welfare in captivity typically focus on behaviours linked to hunting. Thus far, this has yet to result in the systematic elimination of signs of compromised welfare amongst captive carnivores. Here an assessment is carried out to identify the likely welfare priorities for Amur tigers, which, as one of the widest ranging terrestrial carnivores, serves as an excellent exemplar for species experiencing extreme compression of their ranging opportunities in captivity. These priorities are then used to consider novel strategies to address the welfare challenges associated with existing management paradigms, and in particular, attempt to overcome the issue of restricted space. The insights generated here have wider implications for other species experiencing substantive habitat compression in captivity. It is proposed here that the impact of habitat compression on captive carnivore welfare may not be a consequence of the reduction in habitat size per se, but rather the reduction in cognitive opportunities that likely covary with size, and that this should inform strategies to augment welfare.

Sorting Out the Genetic Background of the Last Surviving South China Tigers

The South China tiger (Panthera tigris amoyensis) is endemic to China and also the most critically endangered subspecies of living tigers. It is considered extinct in the wild and only about 150 individuals survive in captivity to date, whose genetic heritage, however, is ambiguous and controversial. Here, we conducted an explicit genetic assessment of 92 studbook-registered South China tigers from 14 captive facilities using a subspecies-diagnostic system in the context of comparison with other voucher specimens to evaluate the genetic ancestry and level of distinctiveness of the last surviving P. t. amoyensis. Three mtDNA haplotypes were identified from South China tigers sampled in this study, including a unique P. t. amoyensis AMO1 haplotype not found in other subspecies, a COR1 haplotype that is widespread in Indochinese tigers (P. t. corbetti), and an ALT haplotype that is characteristic of Amur tigers (P. t. altaica). Bayesian STRUCTURE analysis and parentage verification confirmed the verified subspecies ancestry (VSA) as the South China tiger in 74 individuals. Genetic introgression from other tigers was detected in 18 tigers, and subsequent exclusion of these and their offspring from the breeding program is recommended. Both STRUCTURE clustering and microsatellite-based phylogenetic analyses demonstrated a close genetic association of the VSA South China tigers to Indochinese tigers, an issue that could only be elucidated by analysis of historical South China tiger specimens with wild origin. Our results also indicated a moderate level of genetic diversity in the captive South China tiger population, suggesting a potential for genetic restoration.

Are shed hair genomes the most effective noninvasive resource for estimating relationships in the wild?

Knowledge of relationships in wild populations is critical for better understanding mating systems and inbreeding scenarios to inform conservation strategies for endangered species. To delineate pedigrees in wild populations, study genetic connectivity, study genotype-phenotype associations, trace individuals, or track wildlife trade, many identified individuals need to be genotyped at thousands of loci, mostly from noninvasive samples. This requires us to (a) identify the most common noninvasive sample available from identified individuals, (b) assess the ability to acquire genome-wide data from such samples, and (c) evaluate the quality of such genome-wide data, and its ability to reconstruct relationships between animals within a population.We followed identified individuals from a wild endangered tiger population and found that shed hair samples were the most common compared to scat samples, opportunistically found carcasses, and opportunistic invasive samples. We extracted DNA from these samples, prepared whole genome sequencing libraries, and sequenced genomes from these.Whole genome sequencing methods resulted in between 25%-98% of the genome sequenced for five such samples. Exploratory population genetic analyses revealed that these data were free of holistic biases and could recover expected population structure and relatedness. Mitochondrial genomes recovered matrilineages in accordance with long-term monitoring data. Even with just five samples, we were able to uncover the matrilineage for three individuals with unknown ancestry.In summary, we demonstrated that noninvasive shed hair samples yield adequate quality and quantity of DNA in conjunction with sensitive library preparation methods, and provide reliable data from hundreds of thousands of SNPs across the genome. This makes shed hair an ideal noninvasive resource for studying individual-based genetics of elusive endangered species in the wild.

Tigers of the World: Genomics and Conservation

Of all the big cats, or perhaps of all the endangered wildlife, the tiger may be both the most charismatic and most well-recognized flagship species in the world. The rapidly changing field of molecular genetics, particularly advances in genome sequencing technologies, has provided new tools to reconstruct what characterizes a tiger. Here we review how applications of molecular genomic tools have been used to depict the tiger's ancestral roots, phylogenetic hierarchy, demographic history, morphological diversity, and genetic patterns of diversification on both temporal and geographical scales. Tiger conservation, stabilization, and management are important areas that benefit from use of these genome resources for developing survival strategies for this charismatic megafauna both in situ and ex situ.

A Beautiful Life: High Risk-High Payoff in Genetic Science

This narrative is a personal view of adventures in genetic science and society that have blessed my life and career across five decades. The advances I enjoyed and the lessons I learned derive from educational training, substantial collaboration, and growing up in the genomics age. I parse the stories into six research disciplines my students, fellows, and colleagues have entered and, in some cases, made an important difference. The first is comparative genetics, where evolutionary inference is applied to genome organization, from building gene maps in the 1970s to building whole genome sequences today. The second area tracks the progression of molecular evolutionary advances and applications to resolve the hierarchical relationship among living species in the silence of prehistory. The third endeavor outlines the birth and maturation of genetic studies and application to species conservation. The fourth theme discusses how emerging viruses studied in a genomic sense opened our eyes to host-pathogen interaction and interdependence. The fifth research emphasis outlines the population genetic-based search and discovery of human restriction genes that influence the epidemiological outcome of abrupt outbreaks, notably HIV-AIDS and several cancers. Finally, the last arena explored illustrates how genetic individualization in human and animals has improved forensic evidence in capital crimes. Each discipline has intuitive and technological overlaps, and each has benefitted from the contribution of genetic and genomic principles I learned so long ago from Drosophila. The journey continues.

Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii

Accurate knowledge of geographic ranges and genetic relationships among populations is important when managing a species or population of conservation concern. Along the western coast of Canada, a subspecies of the northern goshawk (Accipiter gentilis laingi) is legally designated as Threatened. The range and distinctness of this form, in comparison with the broadly distributed North American subspecies (Accipiter gentilis atricapillus), is unclear. Given this morphological uncertainty, we analyzed genomic relationships in thousands of single nucleotide polymorphisms identified using genotyping-by-sequencing of high-quality genetic samples. Results revealed a genetically distinct population of northern goshawks on the archipelago of Haida Gwaii and subtle structuring among other North American sampling regions. We then developed genotyping assays for ten loci that are highly differentiated between the two main genetic clusters, allowing inclusion of hundreds of low-quality samples and confirming that the distinct genetic cluster is restricted to Haida Gwaii. As the laingi form was originally described as being based on Haida Gwaii (where the type specimen is from), further morphological analysis may result in this name being restricted to the Haida Gwaii genetic cluster. Regardless of taxonomic treatment, the distinct Haida Gwaii genetic cluster along with the small and declining population size of the Haida Gwaii population suggests a high risk of extinction of an ecologically and genetically distinct form of northern goshawk. Outside of Haida Gwaii, sampling regions along the coast of BC and southeast Alaska (often considered regions inhabited by laingi) show some subtle differentiation from other North American regions. These results will increase the effectiveness of conservation management of northern goshawks in northwestern North America. More broadly, other conservation-related studies of genetic variation may benefit from the two-step approach we employed that first surveys genomic variation using high-quality samples and then genotypes low-quality samples at particularly informative loci.