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Pantherine felids (‘big cats’) include the largest living cats, apex predators in their respective ecosystems. They are also the earliest diverging living cat lineage, and thus are important for understanding the evolution of all subsequent felid groups. Although the oldest pantherine fossils occur in Africa, molecular phylogenies point to Asia as their region of origin. This paradox cannot be reconciled using current knowledge, mainly because early big cat fossils are exceedingly rare and fragmentary. Here, we report the discovery of a fossil pantherine from the Tibetan Himalaya, with an age of Late Miocene–Early Pliocene, replacing African records as the oldest pantherine. A ‘total evidence’ phylogenetic analysis of pantherines indicates that the new cat is closely related to the snow leopard and exhibits intermediate characteristics on the evolutionary line to the largest cats. Historical biogeographic models provide robust support for the Asian origin of pantherines. The combined analyses indicate that 75% of the divergence events in the pantherine lineage extended back to the Miocene, up to 7 Myr earlier than previously estimated. The deeper evolutionary origin of big cats revealed by the new fossils and analyses indicate a close association between Tibetan Plateau uplift and diversification of the earliest living cats.

Modern felid species descend from relatively recent (<11 million years ago) divergence and speciation events that produced successful predatory carnivores worldwide but that have confounded taxonomic classifications. A highly resolved molecular phylogeny with divergence dates for all living cat species, derived from autosomal, X-linked, Y-linked, and mitochondrial gene segments (22,789 base pairs) and 16 fossil calibrations define eight principal lineages produced through at least 10 intercontinental migrations facilitated by sea-level fluctuations. A ghost lineage analysis indicates that available felid fossils underestimate (i.e., unrepresented basal branch length) first occurrence by an average of 76%, revealing a low representation of felid lineages in paleontological remains. The phylogenetic performance of distinct gene classes showed that Y-chromosome segments are appreciably more informative than mitochondrial DNA, X-linked, or autosomal genes in resolving the rapid Felidae species radiation.

Tissue vibrations in the larynx produce most sounds that comprise vocal communication in mammals. Larynx morphology is thus predicted to be a key target for selection, particularly in species with highly developed vocal communication systems. Here, we present a novel database of digitally modeled scanned larynges from 55 different mammalian species, representing a wide range of body sizes in the primate and carnivoran orders. Using phylogenetic comparative methods, we demonstrate that the primate larynx has evolved more rapidly than the carnivoran larynx, resulting in a pattern of larger size and increased deviation from expected allometry with body size. These results imply fundamental differences between primates and carnivorans in the balance of selective forces that constrain larynx size and highlight an evolutionary flexibility in primates that may help explain why we have developed complex and diverse uses of the vocal organ for communication.

Nine small felid species, including the introduced domestic cat, inhabit Southeast Asia. We analysed their skull morphology, using 36 selected morphometric measurements of up to 465 specimens. Of the species examined, the fishing cat and the Asian golden cat were the largest, whilst the mainland and Sunda leopard cats were the smallest. However, there was substantial overlap in size amongst these species. Principal Component Analysis and Quadratic Discriminant Analysis revealed that the skulls of fishing cats and flat-headed cats were clearly distinguishable from those of the other species. Additionally, the skulls of male Asian golden cats, female jungle cats, female Sunda leopard cats, and male marbled cats were well differentiated. In contrast, those of female Asian golden cats, male jungle cats, male domestic cats, and female marbled cats showed considerable morphological overlap with other morphospecies. When analysing only sympatric assemblages (i.e., on the continental mainland, Borneo, Sumatra, and Java), each morphospecies was generally well differentiated from the others although conspecific males and females were not clearly differentiated. Notable exceptions were female Asian golden cats and male jungle cats, female mainland leopard cats and female domestic cats, and female marbled cats and male domestic cats on the mainland, and female marbled cats and male domestic cats on Borneo and Sumatra. More detailed research is necessary to understand the impacts of introduced domestic cats on indigenous small wild felids in Southeast Asia through niche overlap and competition.

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.

Studies of biological shape evolution are greatly enhanced when framed in a phylogenetic perspective. Inclusion of fossils amplifies the scope of macroevolutionary research, offers a deep-time perspective on tempo and mode of radiations, and elucidates life-trait changes. We explore the evolution of skull shape in felids (cats) through morphometric analyses of linear variables, phylogenetic comparative methods, and a new cladistic study of saber-toothed cats. A new phylogenetic analysis supports the monophyly of saber-toothed cats (Machairodontinae) exclusive of Felinae and some basal felids, but does not support the monophyly of various saber-toothed tribes and genera. We quantified skull shape variation in 34 extant and 18 extinct species using size-adjusted linear variables. These distinguish taxonomic group membership with high accuracy. Patterns of morphospace occupation are consistent with previous analyses, for example, in showing a size gradient along the primary axis of shape variation and a separation between large and small-medium cats. By combining the new phylogeny with a molecular tree of extant Felinae, we built a chronophylomorphospace (a phylogeny superimposed onto a two-dimensional morphospace through time). The evolutionary history of cats was characterized by two major episodes of morphological divergence, one marking the separation between saber-toothed and modern cats, the other marking the split between large and small-medium cats. Ancestors of large cats in the 'Panthera' lineage tend to occupy, at a much later stage, morphospace regions previously occupied by saber-toothed cats. The latter radiated out into new morphospace regions peripheral to those of extant large cats. The separation between large and small-medium cats was marked by considerable morphologically divergent trajectories early in feline evolution. A chronophylomorphospace has wider applications in reconstructing temporal transitions across two-dimensional trait spaces, can be used in ecophenotypical and functional diversity studies, and may reveal novel patterns of morphospace occupation.

We extend our recently developed Markov chain Monte Carlo algorithm for Bayesian estimation of species divergence times to allow variable evolutionary rates among lineages. The method can use heterogeneous data from multiple gene loci and accommodate multiple fossil calibrations. Uncertainties in fossil calibrations are described using flexible statistical distributions. The prior for divergence times for nodes lacking fossil calibrations is specified by use of a birth-death process with species sampling. The prior for lineage-specific substitution rates is specified using either a model with autocorrelated rates among adjacent lineages (based on a geometric Brownian motion model of rate drift) or a model with independent rates among lineages specified by a log-normal probability distribution. We develop an infinite-sites theory, which predicts that when the amount of sequence data approaches infinity, the width of the posterior credibility interval and the posterior mean of divergence times form a perfect linear relationship, with the slope indicating uncertainties in time estimates that cannot be reduced by sequence data alone. Simulations are used to study the influence of among-lineage rate variation and the number of loci sampled on the uncertainty of divergence time estimates. The analysis suggests that posterior time estimates typically involve considerable uncertainties even with an infinite amount of sequence data, and that the reliability and precision of fossil calibrations are critically important to divergence time estimation. We apply our new algorithms to two empirical data sets and compare the results with those obtained in previous Bayesian and likelihood analyses. The results demonstrate the utility of our new algorithms.

Increased attention towards the Neotropical cats Leopardus guttulus and L. geoffroyi was prompted after genetic studies identified the occurrence of extensive hybridization between them at their geographic contact zone in southern Brazil. This is a region where two biomes intersect, each of which is associated with one of the hybridizing species (Atlantic Forest with L. guttulus and Pampas with L. geoffroyi). In this study, we conducted in-depth analyses of multiple molecular markers aiming to characterize the magnitude and spatial structure of this hybrid zone. We also performed a morphological assessment of these species, aiming to test their phenotypic differentiation at the contact zone, as well as the correlation between morphological features and the admixture status of the individuals. We found strong evidence for extensive and complex hybridization, with at least 40% of the individuals sampled in Rio Grande do Sul state (southernmost Brazil) identified as hybrids resulting from post-F1 generations. Despite such a high level of hybridization, samples collected in this state still comprised two recognizable clusters (genetically and morphologically). Genetically pure individuals were sampled mainly in regions farther from the contact zone, while hybrids concentrated in a central region (exactly at the interface between the two biomes). The morphological data set also revealed a strong spatial structure, which was correlated with the molecular results but displayed an even more marked separation between the clusters. Hybrids often did not present intermediate body sizes and could not be clearly distinguished morphologically from the parental forms. This observation suggests that some selective pressure may be acting on the hybrids, limiting their dispersal away from the hybrid zone and perhaps favoring genomic combinations that maintain adaptive phenotypic features of one or the other parental species.

The ancestor of all modern domestic cats is the wildcat, Felis silvestris lybica, with archaeological evidence indicating it was domesticated as early as 10,000 years ago in South-West Asia. A recent study, however, claims that cat domestication also occurred in China some 5,000 years ago and involved the same wildcat ancestor (F. silvestris). The application of geometric morphometric analyses to ancient small felid bones from China dating between 5,500 to 4,900 BP, instead reveal these and other remains to be that of the leopard cat (Prionailurus bengalensis). These data clearly indicate that the origins of a human-cat 'domestic' relationship in Neolithic China began independently from South-West Asia and involved a different wild felid species altogether. The leopard cat's 'domestic' status, however, appears to have been short-lived--its apparent subsequent replacement shown by the fact that today all domestic cats in China are genetically related to F. silvestris.

Species Survival Plans and European Endangered Species Programmes have been developed for several species of endangered felids in order to build up captive reserve populations and support their conservation in the wild. The Siberian tiger (Panthera tigris altaica), snow leopard (Uncia uncia), cheetah (Acinonyx jubatus) and clouded leopard (Neofelis nebulosa) are managed in such ex situ conservation programmes. Many zoological institutions hand-rear offspring if rearing by the mother fails. Hand-rearing can cause behavioural problems, resulting in decreased copulation and lower breeding success in some species. In this study, studbook data subsets were examined: from 1901 to 2011; and 2000 to 2011. We analysed records from 4273 Siberian tigers, 2045 snow leopards, 3435 cheetahs, and 804 clouded leopards. We assessed the number of offspring produced, litter size, age at first reproduction, longevity, infant mortality and generational rearing of hand-reared versus parent-reared individuals. Hand-reared Siberian tigers (p<0.01; p = 0.0113), snow leopards (p<0.01), male cheetahs (p<0.01) and female clouded leopards (p<0.01) produced fewer offspring than parent-reared individuals. Hand-reared snow leopard breeding pairs had larger litters than parent-reared pairs (p = 0.0404). Hand-reared snow leopard females reproduced later in life (p<0.01). Hand-reared female Siberian tigers lived shorter lives, while hand-reared cheetahs lived longer (p<0.01; p = 0.0107). Infant mortality was higher in hand-reared snow leopards (p<0.01) and male cheetahs (p = 0.0395) in the 1901-2011 dataset and lower in hand-reared female Siberian tiger and male snow leopard cubs (p = 0.0404; p = 0.0349) in the 2000-2011 dataset. The rearing of the mother and subsequent rearing of offspring showed a significant relationship for all species (p<0.01 for Siberian tiger and snow leopard cubs; p<0.001 for cheetah and snow leopard cubs). Taking into account the limited carrying capacity of zoos, the results of this study highlight that careful consideration should be taken when deciding whether or not to hand-rear individuals that are part of Species Survival Plans and European Endangered Species Programmes.