Geographical variation in and evolutionary history of the Sunda clouded leopard (Neofelis diardi) (Mammalia: Carnivora: Felidae) with the description of a new subspecies from Borneo.

Recent morphological and molecular studies led to the recognition of two extant species of clouded leopards; Neofelis nebulosa from mainland southeast Asia and Neofelis diardi from the Sunda Islands of Borneo and Sumatra, including the Batu Islands. In addition to these new species-level distinctions, preliminary molecular data suggested a genetic substructure that separates Bornean and Sumatran clouded leopards, indicating the possibility of two subspecies of N. diardi. This suggestion was based on an analysis of only three Sumatran and seven Bornean individuals. Accordingly, in this study we re-evaluated this proposed subspecies differentiation using additional molecular (mainly historical) samples of eight Bornean and 13 Sumatran clouded leopards; a craniometric analysis of 28 specimens; and examination of pelage morphology of 20 museum specimens and of photographs of 12 wild camera-trapped animals. Molecular (mtDNA and microsatellite loci), craniomandibular and dental analyses strongly support the differentiation of Bornean and Sumatran clouded leopards, but pelage characteristics fail to separate them completely, most probably owing to small sample sizes, but it may also reflect habitat similarities between the two islands and their recent divergence. However, some provisional discriminating pelage characters are presented that need further testing. According to our estimates both populations diverged from each other during the Middle to Late Pleistocene (between 400 and 120 kyr). We present a discussion on the evolutionary history of Neofelis diardi sspp. on the Sunda Shelf, a revised taxonomy for the Sunda clouded leopard, N. diardi, and formally describe the Bornean subspecies, Neofelis diardi borneensis, including the designation of a holotype (BM.3.4.9.2 from Baram, Sarawak) in accordance with the rules of the International Code of Zoological Nomenclature.

Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens.

Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1-4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6-8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a ∼7x nuclear genome and a ∼38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (∼22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11-14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage.

Convergent evolution in feeding types: salivary gland mass differences in wild ruminant species.

In the ongoing debate about divergent evolutionary morphophysiological adaptations of grazing and browsing ruminants, the size of the salivary glands has received special attention. Here, we report the most comprehensive dataset on ruminant salivary glands so far, with data on the Glandula parotis (n=62 species), Gl. mandibularis (n=61), Gl. buccalis ventralis (n=44), and Gl. sublingualis (n=30). All four salivary gland complexes showed allometric scaling with body mass (BM); in all cases, the 95% confidence interval for the allometric exponent included 0.75 but did not include 1.0 (linearity); therefore, like other parameters linked to the process of food intake, salivary gland mass appears to be correlated to metabolic body weight (BM0.75), and comparisons of relative salivary gland mass between species should rather be made on the basis of BM0.75 than as a percentage of BM. In the subsequent analyses, the percentage of grass (%grass) in the natural diet was used to characterize the feeding type; the phylogenetic tree used for a controlled statistical evaluation was entirely based on mitochondrial DNA information. Regardless of phylogenetic control in the statistical treatment, there was, for all four gland complexes, a significant positive correlation of BM and gland mass, and a significant negative correlation between %grass in the natural diet and gland mass. If the Gl. parotis was analyzed either for cervid or for bovid species only, the negative correlation of gland mass and %grass was still significant in either case; an inspection of certain ruminant subfamilies, however, suggested that a convergent evolutionary adaptation can only be demonstrated if a sufficient variety of ruminant subfamilies are included in a dataset. The results support the concept that ruminant species that ingest more grass have smaller salivary glands, possibly indicating a reduced requirement for the production of salivary tannin-binding proteins.