The genome of the black-footed cat: Revealing a rich natural history and urgent conservation priorities for small felids

Habitat degradation and loss of genetic diversity are common threats faced by almost all of today's wild cats. Big cats, such as tigers and lions, are of great concern and have received considerable conservation attention through policies and international actions. However, knowledge of and conservation actions for small wild cats are lagging considerably behind. The black-footed cat, Felis nigripes, one of the smallest felid species, is experiencing increasing threats with a rapid reduction in population size. However, there is a lack of genetic information to assist in developing effective conservation actions. A de novo assembly of a high-quality chromosome-level reference genome of the black-footed cat was made, and comparative genomics and population genomics analyses were carried out. These analyses revealed that the most significant genetic changes in the evolution of the black-footed cat are the rapid evolution of sensory and metabolic-related genes, reflecting genetic adaptations to its characteristic nocturnal hunting and a high metabolic rate. Genomes of the black-footed cat exhibit a high level of inbreeding, especially for signals of recent inbreeding events, which suggest that they may have experienced severe genetic isolation caused by habitat fragmentation. More importantly, inbreeding associated with two deleterious mutated genes may exacerbate the risk of amyloidosis, the dominant disease that causes mortality of about 70% of captive individuals. Our research provides comprehensive documentation of the evolutionary history of the black-footed cat and suggests that there is an urgent need to investigate genomic variations of small felids worldwide to support effective conservation actions.

Erratum to: Mustela strandi (Mustelidae, Carnivora) from the Early Pleistocene of Crimea

An Erratum to this paper has been published: https://doi.org/10.1134/S0012496623050010

How genomic insights into the evolutionary history of clouded leopards inform their conservation

Clouded leopards (Neofelis spp.), a morphologically and ecologically distinct lineage of big cats, are severely threatened by habitat loss and fragmentation, targeted hunting, and other human activities. The long-held poor understanding of their genetics and evolution has undermined the effectiveness of conservation actions. Here, we report a comprehensive investigation of the whole genomes, population genetics, and adaptive evolution of Neofelis. Our results indicate the genus Neofelis arose during the Pleistocene, coinciding with glacial-induced climate changes to the distributions of savannas and rainforests, and signatures of natural selection associated with genes functioning in tooth, pigmentation, and tail development, associated with clouded leopards' unique adaptations. Our study highlights high-altitude adaptation as the main factor driving nontaxonomic population differentiation in Neofelis nebulosa. Population declines and inbreeding have led to reduced genetic diversity and the accumulation of deleterious variation that likely affect reproduction of clouded leopards, highlighting the urgent need for effective conservation efforts.

Langebaanweg's sabertooth guild reveals an African Pliocene evolutionary hotspot for sabertooths (Carnivora; Felidae)

Here, we describe and revise craniodental material from Langebaanweg 'E' Quarry (South Africa, early Pliocene, ∼5.2 Ma), which represents one of the largest and best-preserved collections of sabertooth felids from Mio-Pliocene deposits of Africa. Four taxa, including two new species, are recognized: Lokotunjailurus chinsamyae sp. nov., Adeilosmilus aff. kabir, Yoshi obscura, and Dinofelis werdelini sp. nov. The felid guild composition analyzed herein suggests the presence of a mosaic environment with open components in the region, and shows a potential relationship with that of Yuanmou, suggesting a similar environment and/or dispersal route/event. The reassessment of the rich early Pliocene felids from Langebaanweg is a step toward understanding the transition and evolution of the felids in the southern hemisphere during the late Miocene to early Pliocene.

Mustela palerminea (Mustelidae, Carnivora) from the Early Pleistocene of Crimea

The mandibles of two individuals of Mustela palerminea (Petenyi, 1864) are described  from the Lower Pleistocene deposits of the Taurida cave in Crimea (Late Villafranchian, 1.8-1.5 Ma). This extinct mustelid species was a typical representative of the Villafranchian faunas of Europe. It is the first record of M. palerminea in Russia.

Mustela strandi (Mustelidae, Carnivora) from the Early Pleistocene of Crimea

The dentary of Mustela strandi Kormos, 1934 is described from the Lower Pleistocene deposits (Late Villafranchian, 1.8-1.5 Ma) of the Taurida cave in Crimea. It is the first finding of M. strandi in Russia. This extinct mustelid species is rarely found in the Lower and Middle Pleistocene of Central Europe.

Origin of adaptations to open environments and social behaviour in sabretoothed cats from the northeastern border of the Tibetan Plateau

The iconic sabretooth Homotherium is thought to have hunted cooperatively, but the origin of this behaviour and correlated morphological adaptations are largely unexplored. Here we report the most primitive species of Amphimachairodus (Amphimachairodus hezhengensis sp. nov.), a member of Machairodontini basal to Homotherium, from the Linxia Basin, northeastern border of the Tibetan Plateau (9.8-8.7 Ma). The long snout, laterally oriented and posteriorly located orbit of Amphimachairodus suggest a better ability to observe the surrounding environment, rather than targeting single prey, pointing to an adaptation to the open environment or social behaviour. A pathological forepaw of Amphimachairodus provides direct evidence of partner care. Our analyses of trait evolutionary rates support that traits correlated with killing behaviour and open environment adaptation evolved prior to other traits, suggesting that changes in hunting behaviour may be the major evolutionary driver in the early evolution of the lineage. A. hezhengensis represents one of the most important transitions in the evolution of Machairodontini, leading to adaptation in open environments and contributing to their further dispersal and radiation worldwide. This rapid morphological change is likely to be correlated with increasingly arid environments caused by the rise of the Tibetan Plateau, and competition from abundant large carnivores in this area.

Parallelism and lineage replacement of the late Miocene scimitar-toothed cats from the old and New World

In contrast to large-scale convergence/parallelism, the small-scale convergence/parallelism of sabertooth adaptation within closely related genera and species has been seldom investigated. Here, we describe and analyze the rich material of Nimravides catocopis, and provide evidence using a new phylogenetic analysis that Nimravides was endemic to North America. The late Miocene (10.5-6.5 Ma) Nimravides represents a lineage that shows clearly parallelism with the contemporary Old World lineage of Machairodus-Amphimachairodus.The Old World lineage experienced a higher evolutionary rate of cranial trait than the New World one did. The low density of Amphimachairodus at its first appearance in North America suggests that the derived traits did not provide a direct competitive advantage over Nimravides, but allowed Amphimachairodus to survive the significant faunal change in the early-late Hemphillian (∼6.5 Ma) in North America, a process that probably can be applied to most replacement of closely related lineages.

The first complete cranium of Homotherium (Machairodontinae, Felidae) from the Nihewan Basin (northern China)

The Nihewan Basin is famous for producing a rich Early Pleistocene fauna, the most classic and standard for the Early Pleistocene of northern China, as well as rich paleolithic remains, documenting the early presence of humans. Many fossil Carnivora, including the scimitar toothed cat Homotherium, were found from this basin, but no complete material of this cat was known, which hampers a deep study of its taxonomy. Here, we report a complete cranium of Homotherium, found in Shigou, a recently discovered locality in the Nihewan Basin. The morphology of the cranium supports its assignment to Homotherium crenatidens teilhardipiveteaui, a terminal evolutionary stage of the species with a Palearctic distribution. Our analyses suggest that Homotherium evolved largely contemporarily in different regions of Eurasia, suggesting a continuous gene flow within the continent, and the subspecies delimitation should be more chronological than geographical.

Information in morphological characters

The construction of morphological character matrices is central to paleontological systematic study, which extracts paleontological information from fossils. Although the word information has been repeatedly mentioned in a wide array of paleontological systematic studies, its meaning has rarely been clarified nor specifically defined. It is important, however, to establish a standard to measure paleontological information because fossils are hardly complete, rendering the recognition of homologous and homoplastic structures difficult. Here, based on information theory, we show the deep connections between paleontological systematic study and communication system engineering. Information is defined as the decrease of uncertainty and it is the information in morphological characters that allows distinguishing operational taxonomic units (OTUs) and reconstructing evolutionary history. We propose that concepts in communication system engineering such as source coding and channel coding, correspond to the construction of diagnostic features and the entire character matrices in paleontological studies. The two coding strategies should be distinguished following typical communication system engineering, because they serve dual purposes. With character matrices from six different vertebrate groups, we analyzed their information properties including source entropy, mutual information, and channel capacity. Estimation of channel capacity shows character saturation of all matrices in transmitting paleontological information, indicating that, due to the presence of noise, oversampling characters not only increases the burden in character scoring, but also may decrease quality of matrices. We further test the use of information entropy, which measures how informative a variable is, as a character weighting criterion in parsimony-based systematic studies. The results show high consistency with existing knowledge with both good resolution and interpretability.

The Earliest Ursine Bear Demonstrates the Origin of Plant-Dominated Omnivory in Carnivora

In Carnivora, increases in body size often lead to dietary specialization toward hypercarnivory. Ursine bears (Tremarctos and Ursus), however, are the only omnivorous Carnivora that evolved large body sizes (i.e., >50 kg). Traits contributing to their gigantism, and how those traits evolved, have never been studied. Here we propose that special dental characters of Ursinae (parallel buccal and lingual ridges) permit a sagittally oriented mastication associated with increasing emphasis on plant foods. This pattern can be traced back to a new early diverging bear of plant-dominated omnivorous diet, Aurorarctos tirawa gen. et sp. nov. from the late Middle Miocene of North America, which was supported as the earliest known ursine bear by phylogenetic analysis. The anatomical transition to increased masticatory efficiency, probably together with the ability to hibernate, helped bears break prior ecological limitations on body size and led to the evolution of a distinctive lineage of herbivorous-omnivorous, large-bodied Carnivora.