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. ; This project received funding from the European Union's Seventh Framework Programme for Research, Technological Development, and Demonstration under grant agreement no. FP7-PEOPLE-2011-IEF-298820 and ERC Consolidator Award 681396—Extinction Genomics to M.T.P.G. Portions of this manuscript were prepared while W.E.J. held a National Research Council Research Associateship Award at the Walter Reed Army Institute of Research (WRAIR).
Despite being heavily exploited, pangolins (Pholidota: Manidae) have been subject to limited research, resulting in a lack of reliable population estimates and standardised survey methods for the eight extant species. Camera trapping represents a unique opportunity for broad-scale collaborative species monitoring due to its largely nondiscriminatory nature, which creates considerable volumes of data on a relatively wide range of species. This has the potential to shed light on the ecology of rare, cryptic and understudied taxa, with implications for conservation decision-making. We undertook a global analysis of available pangolin data from camera trapping studies across their range in Africa and Asia. Our aims were (1) to assess the utility of existing camera trapping efforts as a method for monitoring pangolin populations, and (2) to gain insights into the distribution and ecology of pangolins. We analysed data collated from 103 camera trap surveys undertaken across 22 countries that fell within the range of seven of the eight pangolin species, which yielded more than half a million trap nights and 888 pangolin encounters. We ran occupancy analyses on three species (Sunda pangolin Manis javanica, white-bellied pangolin Phataginus tricuspis and giant pangolin Smutsia gigantea). Detection probabilities varied with forest cover and levels of human influence for P. tricuspis, but were low (<0.05) for all species. Occupancy was associated with distance from rivers for M. javanica and S. gigantea, elevation for P. tricuspis and S. gigantea, forest cover for P. tricuspis and protected area status for M. javanica and P. tricuspis. We conclude that camera traps are suitable for the detection of pangolins and large-scale assessment of their distributions. However, the trapping effort required to monitor populations at any given study site using existing methods appears prohibitively high. This may change in the future should anticipated technological and methodological advances in camera trapping facilitate greater sampling efforts and/or higher probabilities of detection. In particular, targeted camera placement for pangolins is likely to make pangolin monitoring more feasible with moderate sampling efforts. (c) 2019 The Authors. Published by Elsevier B.V. ; Fondation Segr~e; Biodiversity Monitoring Centre (Centre de Surveillance de la Biodiversit ~e) at the Faculty of Sciences of the University of Kisangani; Centre for International Forestry Research (CIFOR); Department of Science and Technology, Government of India (DST)Department of Science & Technology (India) [SR/S0/AS-100/2007]; Ministry of Education MalaysiaMinistry of Education, Malaysia [NRGS 2013/1088/02]; U.S. National Science FoundationNational Science Foundation (NSF) [BCS 1266389]; AXA Research Fellowship; Gordon and Betty Moore FoundationGordon and Betty Moore Foundation ; Thank you to the many individuals and institutions who generously made their data available for this study, and to the Zoological Society of London and donors to the IUCN SSC Pangolin Specialist Group for supporting the time of HK and CB during their research internships. The authors are grateful to Fondation Segr~e for supporting this research. AL would like to thank the Biodiversity Monitoring Centre (Centre de Surveillance de la Biodiversit ~e) at the Faculty of Sciences of the University of Kisangani and the Centre for International Forestry Research (CIFOR) for financial, academic and logistical support. AM would like to thank Agence Nationale des Parcs Nationaux and Centre National de la Recherche Scientifique et Technologique for kindly granting permission to conduct research in Gabon. CKO and TB would like to thank the Nouabal~e-Ndoki Foundation and Ministry of Forest Economy, Republic of Congo for kindly providing research permissions. GVG would like to gratefully thank the Department of Science and Technology, Government of India for their funding (DST. No. SR/S0/AS-100/2007), Mr. K. M. Selvan and Mr. S. Lyngdoh for their support in field data collection, and the Department of Environment & Forest, Government of Arunachal Pradesh for permissions. JAMwas supported by Ministry of Education Malaysia (NRGS 2013/1088/02). LAI acknowledges support from the U.S. National Science Foundation (BCS 1266389). ORW was supported by an AXA Research Fellowship. SE would like to thank R. Mueller and R. Roder for their input into data processing. Some data in this publication was provided by the Tropical Ecology Assessment and Monitoring (TEAM) Network, a collaboration between Conservation International, the Smithsonian Institution, and the Wildlife Conservation Society, and partially funded by these institutions, the Gordon and Betty Moore Foundation, and other donors.
