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Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods. Relaxed clock analyses support the long-fuse model of diversification and highlight the importance of including multiple fossil calibrations that are spread across the tree. Molecular time trees and diversification analyses suggest important roles for the Cretaceous Terrestrial Revolution and Cretaceous-Paleogene (KPg) mass extinction in opening up ecospace that promoted interordinal and intraordinal diversification, respectively. By contrast, diversification analyses provide no support for the hypothesis concerning the delayed rise of present-day mammals during the Eocene Period.

Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300–100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations. Pumas are experiencing increased isolation as human persecution and habitat loss fragment the populations of this once widespread species. Here, the authors estimate the genomic consequences of this isolation by analyzing the genomes of ten pumas from across North and South America.

Melanism in the cat family has been associated with functions including camouflage, thermoregulation and parasite resistance. Here we investigate a new hypothesis proposing that the evolution of melanism in cats has additionally been influenced by communication functions of body markings. To evaluate this hypothesis, we assembled a species-level data set of morphological (body marks: white marks on the backs of ears) and ecological (circadian activity: arrhythmic/nocturnal, and environmental preference: open/closed) characteristics that could be associated with communication via body markings, and combined these data with a dated molecular phylogeny. Next, we tested the association between melanism and communication, first by relating species' body marks with their ecological conditions, using a Bayesian implementation of the threshold model. Second, to explore the evolution of characteristics potentially influencing melanism in cat species, we modeled their evolution relative to melanism using models of coordinated vs. independent character changes. Our results suggest that white marks are associated with intraspecific communication between individuals that have non-melanistic phenotypes, as well as towards melanistic individuals (without white marks). The absence of white marks in a melanistic individual tends to be a limiting condition for intraspecific visual communication at night, resulting in an evolutionary dilemma for these species, i.e. to be almost invisible at night, but not to communicate visually. The comparative analysis of several evolutionary models indicated more support for the evolution of melanism being coordinated with the evolution of arrhythmic activity and white marks on the backs of ears.

The margay (Leopardus wiedii) is a small Neotropical arboreal wild cat. This species is thought to be forest-dependent, although few studies so far have directly evaluated the relationships between spatiotemporal aspects of its ecology and landscape characteristics. The aim of this study was to estimate margay population density and activity patterns in six areas with different habitat types and levels of anthropogenic disturbance in the southernmost Atlantic Forest of Brazil. Our working hypothesis was that density and activity patterns differed between areas in response to differences in forest cover and anthropogenic disturbance. Margay records were obtained using camera trapping, during spring and summer from 2017 to 2019. In all areas, the sampling scheme consisted of 20 un-baited stations, set 1km apart, each containing two paired cameras. We assessed the potential effects of environmental variables, including anthropogenic factors, on margay density, rate of detection and space use by comparing nine spatial capture-recapture (SCR) models. Activity patterns of the margay, its potential prey, and competitors were described and compared using the date and time of the records. We obtained 66 records of margay. Two of the six sampled areas were excluded from subsequent analyses due to the small number of records. The density estimated by the top-ranked model varied from 9.6±6.4 individuals/100km2 in the area with the highest human disturbance to 37.4±15.1 individuals/100km2 in a less disturbed area. Margay densities responded positively to vegetation cover, supporting the hypothesis of forest dependence by the species. Both the margay and their potential prey (small rodents and marsupials) were found to be mostly nocturnal. Margay activity also overlapped with that of the ocelot, Leopardus pardalis, and with mammals associated with human presence (wild boar, cattle, domestic dogs and cats). This is the first multi-area study on patterns of density and activity of the margay in the Brazilian Atlantic Forest. We concluded that the margay is mostly nocturnal, and while its densities are positively influenced by forest cover and negatively influenced by human disturbance, the activity pattern of the species does not seem to change across landscapes with distinct levels of human modification. Margay populations seem to be able to persist under moderate levels of habitat modification, highlighting the importance of preserving even small native forest remnants in the highly fragmented Atlantic Forest.

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.

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.

Competing hypotheses for the timing of the placental mammal radiation focus on whether extant placental orders originated and diversified before or after the Cretaceous-Tertiary (K/T) boundary. Molecular studies that have addressed this issue suffer from single calibration points, unwarranted assumptions about the molecular clock, and/or taxon sampling that lacks representatives of all placental orders. We investigated this problem using the largest available molecular data set for placental mammals, which includes segments of 19 nuclear and three mitochondrial genes for representatives of all extant placental orders. We used the Thorne/Kishino method, which permits simultaneous constraints from the fossil record and allows rates of molecular evolution to vary on different branches of a phylogenetic tree. Analyses that used different sets of fossil constraints, different priors for the base of Placentalia, and different data partitions all support interordinal divergences in the Cretaceous followed by intraordinal diversification mostly after the K/T boundary. Four placental orders show intraordinal diversification that predates the K/T boundary, but only by an average of 10 million years. In contrast to some molecular studies that date the rat-mouse split as old as 46 million years, our results show improved agreement with the fossil record and place this split at 16-23 million years. To test the hypothesis that molecular estimates of Cretaceous divergence times are an artifact of increased body size subsequent to the K/T boundary, we also performed analyses with a \"K/T body size\" taxon set. In these analyses, interordinal splits remained in the Cretaceous.

Carnivores play a vital role in ecosystem health and are thus an important focus for conservation management. Non‐invasive methods have gained traction for carnivore monitoring as carnivores are often elusive and wide‐ranging, making visual counts particularly difficult. Faecal mini‐barcoding combines field collection of scats with genetic analysis for species identification. Here, we assessed the applicability of a mini‐barcode based on the mitochondrial ATP6 gene in southern Africa. We predicted amplification success based on in silico evaluation of reference sequences from 34 of the 42 terrestrial carnivore species existing in southern Africa, including the Congo clawless otter (Aonyx congicus) for which we contributed a mitochondrial assembly. We further tested amplification success on available reference samples of 23 species. We expanded the existing ATP6 mini‐barcode reference database by contributing additional sequences for 22 species, including the Cape genet (Genetta tigrina) and the side‐striped jackal (Lupulella adusta) for which no complete mini‐barcode sequences were available on GenBank, and compiled a representative reference dataset of 61 unique sequences as a tool for species identification. As a proof of principle, we applied the ATP6 mini‐barcode to a small scat‐based carnivore survey conducted in Namibia 13 years prior, which showed a 95% identification success and detected six species among 157 samples collected. With southern Africa's mammalian carnivores facing escalating threats, this robust mini‐barcode offers a vital tool for accurate species identification from non‐invasive samples, enabling crucial monitoring and conservation efforts. We evaluated the effectiveness of a mitochondrial mini‐barcode based on the ATP6 gene to identify terrestrial carnivores in southern Africa, both theoretically and through PCR amplification. We provide a curated reference dataset composed of previously published and newly generated sequences, including three species for which no reference sequence was available for this marker. We applied the mini‐barcode to a field survey in an African thornbush savannah with a 95% identification success.

The jaguar (Panthera onca) is an iconic top predator that is threatened by habitat loss and fragmentation, along with an emerging expansion of poaching for the illegal trade of live individuals and their parts. To address the need for tools that improve surveillance and monitoring of its remaining populations, we have developed a genome‐enabled single nucleotide polymorphism (SNP) panel targeting this species. From a dataset of 58 complete jaguar genomes, we identified and selected highly informative SNPs for geographic traceability, individual identification, kinship, and sexing. Our panel, named “Jag‐SNP”, comprises 459 SNPs selected from an initial pool of 13,373,949 markers based on the inter‐biome FST, followed by rigorous filtering and addition of eight sex‐linked SNPs. We then randomly selected subsets of this panel and identified an 84‐SNP set that exhibited a similar resolving power. With both the 459‐SNP panel and its 84‐SNP subset, samples were assigned with 98% success to their biomes of origin and 65%–69% of them were assigned to within 500 km of their origin. Furthermore, ca. 10–18 SNPs within these panels were sufficient to distinguish individuals, whereas 6 sex‐linked SNPs perfectly separated males and females. We used whole‐genome data from an additional 18 jaguars to further test these panels, which provided insights into kinship relationships and allowed inference of geographic origin of samples collected outside the spatial scope of the original sample set. These results support the strong potential of these panels as an efficient tool for application in forensic, genetic, ecological, behavioral and conservation projects targeting jaguars. RESUMO O manejo da vida selvagem exige ferramentas poderosas para monitorar e proteger a biodiversidade à medida que esta diminui rapidamente. Nesse sentido, a área da genômica trouxe novas possibilidades para o desenvolvimento de ferramentas baseadas em polimorfismos de nucleotídeo único (SNPs), que melhoram as estimativas genéticas em relação a marcadores tradicionais, como os microssatélites. A aplicação de painéis de SNPs selecionados e otimizados a partir de grandes conjuntos de dados genômicos tem um grande potencial no contexto dos esforços de conservação de espécies esquivas e ameaçadas, como a onça‐pintada (Panthera onca), o maior felídeo das Américas e espécie guarda‐chuva para conservação da biodiversidade. Neste estudo, a partir de um conjunto de dados de 58 genomas completos de onças‐pintadas do Brasil, identificamos e selecionamos SNPs altamente informativos para rastreabilidade geográfica, identificação individual, parentesco e sexagem. Através de uma rigorosa filtragem, foram escolhidos 459 SNPs dentre 13.373.949 marcadores, com base no FST inter‐bioma, para compor um painel junto de outros 8 SNPs ligados ao sexo. Deste painel, selecionamos subconjuntos de forma aleatória e identificamos um com apenas 84 SNPs que apresentou um poder de resolução semelhante ao painel completo. Quanto à atribuição de origem geográfica, tanto o painel geral quanto o subconjunto atingiram uma acurácia de 98% relativa ao bioma de origem das amostras e 65–69% delas foram atribuídas a um raio de até 500 km da sua origem. Para identificação individual, observamos que 10–18 SNPs dentre os marcadores selecionados são suficientes para diferenciar indivíduos, enquanto 6 SNPs ligados ao sexo são capazes de separar corretamente machos e fêmeas. Por fim, através de uma validação in silico, também foi possível recuperar corretamente as relações de parentesco entre os indivíduos testados, ressaltando a versatilidade desses marcadores e seu potencial para o desenvolvimento de ensaios de genotipagem como ferramenta para perguntas forenses, genéticas e ecológicas envolvendo onças‐pintadas. We have developed a genome‐enabled single nucleotide polymorphism (SNP) panel for use in jaguar geographic traceability, individual identification, kinship, and sexing. Our panel, named “Jag‐SNP”, comprises 459 SNPs selected from an initial pool of 13,373,949 markers based on the inter‐biome FST, followed by rigorous filtering and addition of eight sex‐linked SNPs. We demonstrated that the panel and much smaller subsets of these markers can be successfully applied to all their target goals, supporting their effectiveness as multipurpose tools for forensic, genetic, ecological, behavioral and conservation projects targeting jaguars.