Sympatric Asian felid phylogeography reveals a major Indochinese-Sundaic divergence

Scrutinising an inscrutable bark-nesting ant: Exploring cryptic diversity in the Rhopalomastix javana (Hymenoptera: Formicidae) complex using DNA barcodes, genome-wide MIG-seq and geometric morphometrics

Overlooking cryptic species diversity has grave implications on assessments of climate change impacts on biodiversity, ecosystems and organismal populations. Discriminating between cryptic species has long been challenging even for seasoned taxonomists, as interspecies morphological differences are often indiscernible by visual observation. Multi-disciplinary methods involving genetic analyses in conjunction with quantitative morphological data, should therefore be used to investigate boundaries between cryptic species. We adopted an integrated approach combining analyses of mitochondrial COI barcodes, a genome-wide dataset obtained via multiplexed inter-simple sequence repeats (ISSRs) genotyping by sequencing (MIG-seq), and geometric morphometrics to investigate species divergences in the inscrutable Rhopalomastix javana species complex. Objective clustering of COI suggested five putative molecular species units divergent from each other by thresholds within 4.2-10.6% uncorrected pairwise distance. Phylogenetic analyses based on concatenated MIG-seq data also recovered and strongly supported the monophyly of five major lineages in agreement with COI clusters. Co-ancestry analyses based on MIG-seq data using fineRADstructure resolved variable patterns of admixture linked to geography, and potential genetic drift within some putative species. Geometric morphometric analyses of specimen images further detected statistically significant differences in at least one of three anatomical aspects (Head, Meso, Profile) between all pairs of putative species. Head shape (full-face view) was determined to be the most informative character for species diagnosis, with relatively high classification accuracy. Thin-plate spline deformation grids highlighted areas of high variation between species in each shape for deeper taxonomic scrutiny. The presence of species from multiple distinct lineages existing in near-sympatry firmly demonstrates that R. javana comprises more than one closely-related species, but exact species boundaries are difficult to ascertain. Differences in elevation and its associated abiotic effects on ant adaptations and reproductive phenology may contribute to restricting gene flow and maintaining species boundaries between sympatric populations of the R. javana complex. We further assess the advantages and limitations of geometric morphometrics as a taxonomic tool. Despite its drawbacks, our combined approach has helped draw important insights on cryptic diversity in R. javana, and also identified gaps of knowledge that await address. Results from this study will inform and prime future in-depth taxonomic investigation on the R. javana complex, including formal descriptions and establishment of the five putative species.

Pangolin Genomes Offer Key Insights and Resources for the World's Most Trafficked Wild Mammals

Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and purported medicinal properties. Despite their conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3,238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight extant pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera and highlighted the existence of an undescribed species closely related to Southeast Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of Southeast Asian pangolins, provide new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental versus island populations and species lineages, suggesting that conservation planning should consider intraspecific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet realized in pangolins, we recommend that populations be genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors for pangolins, including tracing their illegal trade. These comprise the completion of whole-genomes for pangolins through the hybrid assembly of the first reference genome for the giant pangolin (Smutsia gigantea) and new draft genomes (∼43x-77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.

Whole genome analysis of clouded leopard species reveals an ancient divergence and distinct demographic histories

Similar to other apex predator species, populations of mainland (Neofelis nebulosa) and Sunda (Neofelis diardi) clouded leopards are declining. Understanding their patterns of genetic variation can provide critical insights on past genetic erosion and a baseline for understanding their long-term conservation needs. As a step toward this goal, we present draft genome assemblies for the two clouded leopard species to quantify their phylogenetic divergence, genome-wide diversity, and historical population trends. We estimate that the two species diverged 5.1 Mya, much earlier than previous estimates of 1.41 Mya and 2.86 Mya, suggesting they separated when Sundaland was becoming increasingly isolated from mainland Southeast Asia. The Sunda clouded leopard displays a distinct and reduced effective population size trajectory, consistent with a lower genome-wide heterozygosity and SNP density, relative to the mainland clouded leopard. Our results provide new insights into the evolutionary history and genetic health of this unique lineage of felids.

A chromosome-level genome assembly reveals genomic characteristics of the American mink (Neogale vison)

Availability of a contiguous chromosome-level genome assembly is the foundational step to develop genome-based studies in American mink (Neogale vison). The main objective of this study was to provide a high quality chromosome-level genome assembly for American mink. An initial draft of the genome assembly was generated using 2,884,047 PacBio long reads. Integration of Hi-C data into the initial draft led to an assembly with 183 scaffolds and scaffold N50 of 220 Mb. This gap-free genome assembly of American mink (ASM_NN_V1) had a length of 2.68 Gb in which about 98.6% of the whole genome was covered by 15 chromosomes. In total, 25,377 genes were predicted across the American mink genome using the NCBI Eukaryotic Genome Annotation Pipeline. In addition, gene orthology, demographic history, synteny blocks, and phylogenetic relationships were studied in connection with the genomes of other related Carnivora. Furthermore, population-based statistics of 100 sequenced mink were presented using the newly assembled genome. Remarkable improvements were observed in genome contiguity, the number of scaffolds, and annotation compared to the first draft of mink genome assembly (NNQGG.v01). This high-quality genome assembly will support the development of efficient breeding strategies as well as conservation programs for American mink.

Genomic evidence for the Chinese mountain cat as a wildcat conspecific (Felis silvestris bieti) and its introgression to domestic cats

The Qinghai-Tibet Plateau endemic Chinese mountain cat has a controversial taxonomic status, whether it is a true species or a wildcat (Felis silvestris) subspecies and whether it has contributed to cat (F. s. catus) domestication in East Asia. Here, we sampled F. silvestris lineages across China and sequenced 51 nuclear genomes, 55 mitogenomes, and multilocus regions from 270 modern or museum specimens. Genome-wide analyses classified the Chinese mountain cat as a wildcat conspecific F. s. bieti, which was not involved in cat domestication of China, thus supporting a single domestication origin arising from the African wildcat (F. s. lybica). A complex hybridization scenario including ancient introgression from the Asiatic wildcat (F. s. ornata) to F. s. bieti, and contemporary gene flow between F. s. bieti and sympatric domestic cats that are likely recent Plateau arrivals, raises the prospect of disrupted wildcat genetic integrity, an issue with profound conservation implications.

Small cats in big trouble? Diet, activity, and habitat use of jungle cats and leopard cats in threatened dry deciduous forests, Cambodia

Dry deciduous dipterocarp forests (DDF) cover about 15%-20% of Southeast Asia and are the most threatened forest type in the region. The jungle cat (Felis chaus) is a DDF specialist that occurs only in small isolated populations in Southeast Asia. Despite being one of the rarest felids in the region, almost nothing is known about its ecology. We investigated the ecology of jungle cats and their resource partitioning with the more common leopard cats (Prionailurus bengalensis) in a DDF-dominated landscape in Srepok Wildlife Sanctuary, Cambodia. We used camera-trap data collected from 2009 to 2019 and DNA-confirmed scats to determine the temporal, dietary and spatial overlap between jungle cats and leopard cats. The diet of jungle cats was relatively diverse and consisted of murids (56% biomass consumed), sciurids (15%), hares (Lepus peguensis; 12%), birds (8%), and reptiles (8%), whereas leopard cats had a narrower niche breadth and a diet dominated by smaller prey, primarily murids (73%). Nonetheless, dietary overlap was high because both felid species consumed predominantly small rodents. Both species were primarily nocturnal and had high temporal overlap. Two-species occupancy modelling suggested jungle cats were restricted to DDF and had low occupancy, whereas leopard cats had higher occupancy and were habitat generalists. Our study confirmed that jungle cats are DDF specialists that likely persist in low numbers due to the harsh conditions of the dry season in this habitat, including annual fires and substantial decreases in small vertebrate prey. The lower occupancy and more diverse diet of jungle cats, together with the broader habitat use of leopard cats, likely facilitated the coexistence of these species. The low occupancy of jungle cats in DDF suggests that protection of large areas of DDF will be required for the long-term conservation of this rare felid in Southeast Asia.

Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 21 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.

Closely related species show species-specific environmental responses and different spatial conservation needs: Prionailurus cats in the Indian subcontinent

Phylogenetically closely related species are often assumed to have similar responses to environmental conditions, but species-specific responses have also been described. These two scenarios may have different conservation implications. We tested these two hypotheses for Prionailurus cats (P. rubiginosus, P. bengalensis, P. viverrinus) in the Indian subcontinent and show its implications on species current protected area coverage and climatic suitability trends through time. We fitted ecological niche models with current environmental conditions and calculated niche overlap. In addition, we developed a model for the Jungle Cat Felis chaus to compare species responses and niche overlap estimates within Prionailurus with those for a related sympatric small cat species. Then we estimated the proportion of current suitable environment covered by protected area and projected climatic models from past (last interglacial) to future (2070; RCP4.5 and RCP8.5) conditions to show implications on population management and conservation. The hypothesis of a similar response and niche overlap among closely related species is not supported. Protected area coverage was lowest for P. viverrinus (mean = 0.071, SD = 0.012) and highest for P. bengalensis (mean = 0.088, SD = 0.006). In addition, the proportion of the subcontinent with suitable climate varied through time and was species-specific. For P. bengalensis, climatic suitability shrunk since at least the mid-Holocene, a trend that can be intensified by human-induced climate warming. Concerning P. viverrinus, most predictions show stable future climatic suitability, but a few indicated potential loss. Climatic suitability for P. rubiginous was predicted to remain stable but the species exhibited a negative association with intensive agriculture. Similar responses to environmental change by phylogenetically closely related species should not be assumed and have implications on protected area coverage and natural trends of species climatic suitability over time. This should be taken into account during conservation and management actions.

Diet, prey selection, and activity of Asian golden cats and leopard cats in northern Laos

The Asian golden cat (Catopuma temminckii) occurs in small, declining, and highly fragmented populations throughout Southeast Asia, whereas the smaller leopard cat (Prionailurus bengalensis) is common and widespread. In contrast to leopard cats, little is known about the ecology of Asian golden cats, and resource partitioning between these species has not been studied. We used DNA-confirmed scats, camera-trap data, and prey surveys, to determine the diet, prey selection, and activity, of Asian golden cats and leopard cats in a protected area in northern Laos. The two felids had different diets: Asian golden cats consumed mostly ungulates (35% biomass consumed), murid rodents (23%), and carnivores (15%), whereas leopard cats consumed mostly murid rodents (79%). Asian golden cats were not random in their consumption of ungulates, because muntjac (Muntiacus spp.) were selectively consumed over larger ungulates, indicating muntjac were preyed upon rather than scavenged. Dietary overlap between the two felid species was moderate (R0 = 0.60), and the dietary niche breadth of Asian golden cats (B = 8.44) was nearly twice as high as that of leopard cats (4.54). The mean (± SD) scat diameter was greater for Asian golden cats (2.1 ± 0.3 cm) than leopard cats (1.8 ± 0.2 cm), although diameters of leopard cat scats were considerably larger than previously assumed for this species. The felid species differed in their activity patterns, because Asian golden cats were diurnal, whereas leopard cats were nocturnal, although they did not differ in their use of elevation, suggesting there was no habitat segregation. Overall, leopard cats appeared to coexist with Asian golden cats, a potential predator and competitor, by exhibiting dietary and temporal partitioning. Our results showed that muntjac were important prey of Asian golden cats, suggesting the management of muntjac might be important for conserving populations of Asian golden cats.

Investigation of hemotropic Mycoplasma spp. genotypes in client-owned cats in Thailand

The genetic information for three feline hemoplasmas is limited in Southeast Asia. According to the limited genetic data, this study modified a nested-PCR method targeting the 16S rRNA gene by designing a novel primary forward degenerate primer. Two hundred and thirty-one archived DNA extracts from the blood of client-owned cats with a variety of diseases were used. The modified nested PCR detected feline hemoplasma DNA in 64 of 231 (27.7 %) samples. Sanger DNA sequencing, BLAST, and phylogenetic analyses revealed nine nucleotide sequences of Mycoplasma haemofelis (Mhf) (3.9 %, 9/231), fifty-three nucleotide sequences of Candidatus Mycoplasma haemominutum (CMhm) (22.94 %, 53/231) and two nucleotide sequences of Candidatus Mycoplasma turicensis (CMtc) (0.86 %, 2/231). The phylogenetic analysis demonstrated separate genotypes of 30 DNA sequences of Thai CMhm. In addition, this analysis elucidated distinct genotypes of CMhm in Thai fishing cats (Prionailurus viverrinus). The domestic cat and Thai fishing cat groups were the two major groups separating Thai CMhm genotypes based on the 16S rRNA. One CMhm sequence in Thai fishing cats was also present in domestic cat CMhm genotypes. This result suggests that transmission of CMhm between domestic cats and Thai fishing cats has likely occurred. One Mhf sequence had low genetic identity (82 % similarity). The phylogenetic analysis confirmed that this sequence was still very closely related to Mhf reference sequences. This Mhf-like genotype could be a candidate novel Mhf genotype. This new genetic information for feline hemotropic Mycoplasma provides valuable information for future feline-related clinical studies.

Neofunctionalization of the UCP1 mediated the non-shivering thermogenesis in the evolution of small-sized placental mammals

The acquisition of UCP1-mediated non-shivering thermogenesis (NST) was an important event during the evolution of mammals. Here, we assessed the thermogenic neofunctionalization that occurred in the mammalian UCP1, by performing detailed comparative evolutionary genomics analyses (including phylogenetic and selection analyses) of the UCP family members across all major vertebrate classes. Heterogeneously distributed positive selection signatures were found in several UCPs, being preferably located in the mitochondrial matrix domains. Additionally, comparisons with non-mammalian orthologs showed increased evolutionary rates of the mammalian UCP1, not observable in the phylogenetically related UCP2 and UCP3 paralogs. Also, parallel signatures of episodic positive selection (ω > 1) were found in the ancestral branches of both Glires (rodents and lagomorphs) and Afroinsectivores (afrosoricids and macroscelids), underlining the importance of the UCP1 thermogenic activity in these mammalian groups. Finally, we hypothesize that the independent positive selection events that occurred in these two lineages resulted in two UCP1-mediated NST approaches, namely the cold acute response in the Glires and the reproduction success enhancement in the Afroinsectivores.

Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of postspeciation gene flow that can produce a mosaic of phylogenetic signals that interact with recombinational variation. Here, we tested the validity of this assumption with a phylogenomic analysis of 27 species of the cat family, assessing local effects of recombination rate on species tree inference and divergence time estimation across their genomes. We found that the prevailing phylogenetic signal within the autosomes is not always representative of the most probable speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within regions of low recombination, and notably enriched within large X chromosome recombination cold spots that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ∼40%. We conclude that existing phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic architecture of phylogenetic signal relative to recombination rate and its interplay with historical hybridization.

Genetic diversity and structure of the binturong Arctictis binturong (Carnivora: Viverridae) – status of the elusive Palawan binturong and implications for conservation

The binturong or bearcat is a forest mesocarnivore ranging from Nepal to Indonesia and the Philippines. Several subspecies of binturongs are recognized but a revision is needed. The binturong from Palawan was described as a species and is now considered a subspecies, but its status has never been checked using molecular approaches. Owing to its restricted range and the pressure on its habitat, the Palawan binturong may be endangered. It is, therefore, of crucial importance to clarify its taxonomic status, particularly for the management of captive populations. We sequenced one nuclear and two mitochondrial markers for binturongs from locations across the species range and from zoos. Our results provide an assessment of the genetic polymorphism and structure within the binturong, resulting in two groups, corresponding to the Indochinese and the Sundaic regions. Within the latter were found the Palawan binturongs on one side, and an individual from Sulu archipelago (a locality not reported before) on the other side. The Palawan binturongs form a monophyletic group, genetically close to Bornean binturongs, which suggests that they may have dispersed from Borneo, and represents a lineage worth preserving, but which is not a separate species nor a separate subspecies.

Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus)

BACKGROUND

The Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information at landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on 249 field-collected dhole faeces from five protected areas of the central Indian landscape in the state of Maharashtra, India.

RESULTS

We tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57-88%), polymorphism (3-9 alleles), heterozygosity (0.23-0.63) and produced a cumulative misidentification rate or PID(unbiased) and PID(sibs) value of 4.7 × 10-10 and 1.5 × 10-4, respectively, indicating a high statistical power in individual discrimination from poor quality samples.

CONCLUSION

Our results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. This genetic approach would be useful in dhole population estimation across its range and will help in assessing population trends and other genetic parameters for this elusive, social carnivore.

Genetic Structure and Phylogeography of the Leopard Cat (Prionailurus bengalensis) Inferred from Mitochondrial Genomes

The Leopard cat Prionailurus bengalensis is a habitat generalist that is widely distributed across Southeast Asia. Based on morphological traits, this species has been subdivided into 12 subspecies. Thus far, there have been few molecular studies investigating intraspecific variation, and those had been limited in geographic scope. For this reason, we aimed to study the genetic structure and evolutionary history of this species across its very large distribution range in Asia. We employed both PCR-based (short mtDNA fragments, 94 samples) and high throughput sequencing based methods (whole mitochondrial genomes, 52 samples) on archival, noninvasively collected and fresh samples to investigate the distribution of intraspecific genetic variation. Our comprehensive sampling coupled with the improved resolution of a mitochondrial genome analyses provided strong support for a deep split between Mainland and Sundaic Leopard cats. Although we identified multiple haplogroups within the species' distribution, we found no matrilineal evidence for the distinction of 12 subspecies. In the context of Leopard cat biogeography, we cautiously recommend a revision of the Prionailurus bengalensis subspecific taxonomy: namely, a reduction to 4 subspecies (2 mainland and 2 Sundaic forms).

Mapping black panthers: Macroecological modeling of melanism in leopards (Panthera pardus)

The geographic distribution and habitat association of most mammalian polymorphic phenotypes are still poorly known, hampering assessments of their adaptive significance. Even in the case of the black panther, an iconic melanistic variant of the leopard (Panthera pardus), no map exists describing its distribution. We constructed a large database of verified records sampled across the species’ range, and used it to map the geographic occurrence of melanism. We then estimated the potential distribution of melanistic and non-melanistic leopards using niche-modeling algorithms. The overall frequency of melanism was ca. 11%, with a significantly non-random spatial distribution. Distinct habitat types presented significantly different frequencies of melanism, which increased in Asian moist forests and approached zero across most open/dry biomes. Niche modeling indicated that the potential distributions of the two phenotypes were distinct, with significant differences in habitat suitability and rejection of niche equivalency between them. We conclude that melanism in leopards is strongly affected by natural selection, likely driven by efficacy of camouflage and/or thermoregulation in different habitats, along with an effect of moisture that goes beyond its influence on vegetation type. Our results support classical hypotheses of adaptive coloration in animals (e.g. Gloger’s rule), and open up new avenues for in-depth evolutionary analyses of melanism in mammals.

Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

BACKGROUND

There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups.

RESULTS

We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status.

CONCLUSIONS

Our study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research.

Two species of Southeast Asian cats in the genus Catopuma with diverging histories: an island endemic forest specialist and a widespread habitat generalist

Background. The bay cat Catopuma badia is endemic to Borneo, whereas its sister species the Asian golden cat Catopuma temminckii is distributed from the Himalayas and southern China through Indochina, Peninsular Malaysia and Sumatra. Based on morphological data, up to five subspecies of the Asian golden cat have been recognized, but a taxonomic assessment, including molecular data and morphological characters, is still lacking. Results. We combined molecular data (whole mitochondrial genomes), morphological data (pelage) and species distribution projections (up to the Late Pleistocene) to infer how environmental changes may have influenced the distribution of these sister species over the past 120 000 years. The molecular analysis was based on sequenced mitogenomes of 3 bay cats and 40 Asian golden cats derived mainly from archival samples. Our molecular data suggested a time of split between the two species approximately 3.16 Ma and revealed very low nucleotide diversity within the Asian golden cat population, which supports recent expansion of the population. Discussion. The low nucleotide diversity suggested a population bottleneck in the Asian golden cat, possibly caused by the eruption of the Toba volcano in Northern Sumatra (approx. 74 kya), followed by a continuous population expansion in the Late Pleistocene/Early Holocene. Species distribution projections, the reconstruction of the demographic history, a genetic isolation-by-distance pattern and a gradual variation of pelage pattern support the hypothesis of a post-Toba population expansion of the Asian golden cat from south China/Indochina to Peninsular Malaysia and Sumatra. Our findings reject the current classification of five subspecies for the Asian golden cat, but instead support either a monotypic species or one comprising two subspecies: (i) the Sunda golden cat, distributed south of the Isthmus of Kra: C. t. temminckii and (ii) Indochinese, Indian, Himalayan and Chinese golden cats, occurring north of the Isthmus: C. t. moormensis.

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

Inter-species hybridization has been recently recognized as potentially common in wild animals, but the extent to which it shapes modern genomes is still poorly understood. Distinguishing historical hybridization events from other processes leading to phylogenetic discordance among different markers requires a well-resolved species tree that considers all modes of inheritance and overcomes systematic problems due to rapid lineage diversification by sampling large genomic character sets. Here, we assessed genome-wide phylogenetic variation across a diverse mammalian family, Felidae (cats). We combined genotypes from a genome-wide SNP array with additional autosomal, X- and Y-linked variants to sample ∼150 kb of nuclear sequence, in addition to complete mitochondrial genomes generated using light-coverage Illumina sequencing. We present the first robust felid time tree that accounts for unique maternal, paternal, and biparental evolutionary histories. Signatures of phylogenetic discordance were abundant in the genomes of modern cats, in many cases indicating hybridization as the most likely cause. Comparison of big cat whole-genome sequences revealed a substantial reduction of X-linked divergence times across several large recombination cold spots, which were highly enriched for signatures of selection-driven post-divergence hybridization between the ancestors of the snow leopard and lion lineages. These results highlight the mosaic origin of modern felid genomes and the influence of sex chromosomes and sex-biased dispersal in post-speciation gene flow. A complete resolution of the tree of life will require comprehensive genomic sampling of biparental and sex-limited genetic variation to identify and control for phylogenetic conflict caused by ancient admixture and sex-biased differences in genomic transmission.

The Centipede Genus Scolopendra in Mainland Southeast Asia: Molecular Phylogenetics, Geometric Morphometrics and External Morphology as Tools for Species Delimitation

Seven Scolopendra species from the Southeast Asian mainland delimited based on standard external morphological characters represent monophyletic groups in phylogenetic trees inferred from concatenated sequences of three gene fragments (cytochrome c oxidase subunit 1, 16S rRNA and 28S rRNA) using Maximum likelihood and Bayesian inference. Geometric morphometric description of shape variation in the cephalic plate, forcipular coxosternite, and tergite of the ultimate leg-bearing segment provides additional criteria for distinguishing species. Colouration patterns in some Scolopendra species show a high degree of fit to phylogenetic trees at the population level. The most densely sampled species, Scolopendra dehaani Brandt, 1840, has three subclades with allopatric distributions in mainland SE Asia. The molecular phylogeny of S. pinguis Pocock, 1891, indicated ontogenetic colour variation among its populations. The taxonomic validation of S. dawydoffi Kronmüller, 2012, S. japonica Koch, 1878, and S. dehaani Brandt, 1840, each a former subspecies of S. subspinipes Leach, 1814 sensu Lewis, 2010, as full species was supported by molecular information and additional morphological data. Species delimitation in these taxonomically challenging animals is facilitated by an integrative approach that draws on both morphology and molecular phylogeny.

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.

Genetic ancestry of the extinct Javan and Bali tigers

The Bali (Panthera tigris balica) and Javan (P. t. sondaica) tigers are recognized as distinct tiger subspecies that went extinct in the 1940s and 1980s, respectively. Yet their genetic ancestry and taxonomic status remain controversial. Following ancient DNA procedures, we generated concatenated 1750bp mtDNA sequences from 23 museum samples including 11 voucher specimens from Java and Bali and compared these to diagnostic mtDNA sequences from 122 specimens of living tiger subspecies and the extinct Caspian tiger. The results revealed a close genetic affinity of the 3 groups from the Sunda Islands (Bali, Javan, and Sumatran tigers P. t. sumatrae). Bali and Javan mtDNA haplotypes differ from Sumatran haplotypes by 1-2 nucleotides, and the 3 island populations define a monophyletic assemblage distinctive and equidistant from other mainland subspecies. Despite this close phylogenetic relationship, no mtDNA haplotype was shared between Sumatran and Javan/Bali tigers, indicating little or no matrilineal gene flow among the islands after they were colonized. The close phylogenetic relationship among Sunda tiger subspecies suggests either recent colonization across the islands, or else a once continuous tiger population that had subsequently isolated into different island subspecies. This supports the hypothesis that the Sumatran tiger is the closest living relative to the extinct Javan and Bali tigers.