High genetic diversity and low differentiation reflect the ecological versatility of the African leopard

[1]  Panthera pardus , 2022, CABI Compendium.

[2]  Huanming Yang,et al.  The evolutionary history of extinct and living lions , 2020, Proceedings of the National Academy of Sciences.

[3]  Knut Reinert,et al.  GenMap: ultra-fast computation of genome mappability , 2020, Bioinform..

[4]  M. Hofreiter,et al.  Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena , 2020, Science Advances.

[5]  K. Guschanski,et al.  Conservation Genomic Analyses of African and Asiatic Cheetahs (Acinonyx jubatus) Across Their Current and Historic Species Range , 2020, bioRxiv.

[6]  Molecular Genetic Variation , 2020, Definitions.

[7]  Brendan L. O’Connell,et al.  Puma genomes from North and South America provide insights into the genomic consequences of inbreeding , 2019, Nature Communications.

[8]  T. Mahmood,et al.  Range contraction of snow leopard (Panthera uncia) , 2019, PloS one.

[9]  A. Albrechtsen,et al.  Evaluation of Model Fit of Inferred Admixture Proportions , 2019, bioRxiv.

[10]  Anders Albrechtsen,et al.  Testing for Hardy–Weinberg equilibrium in structured populations using genotype or low‐depth next generation sequencing data , 2019, Molecular ecology resources.

[11]  A. Albrechtsen,et al.  Allele frequency‐free inference of close familial relationships from genotypes or low‐depth sequencing data , 2018, bioRxiv.

[12]  John M. Gaspar,et al.  NGmerge: merging paired-end reads via novel empirically-derived models of sequencing errors , 2018, BMC Bioinformatics.

[13]  N. Schmidt,et al.  The Muskox Lost a Substantial Part of Its Genetic Diversity on Its Long Road to Greenland , 2018, Current Biology.

[14]  F. Gillet,et al.  A genome-wide data assessment of the African lion (Panthera leo) population genetic structure and diversity in Tanzania , 2018, PloS one.

[15]  R. Wayne,et al.  Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction , 2018, Science Advances.

[16]  B. Nickel,et al.  Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations , 2018, bioRxiv.

[17]  A. Albrechtsen,et al.  Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data , 2018, Genetics.

[18]  Emmanuel Paradis,et al.  ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R , 2018, Bioinform..

[19]  G. Amato,et al.  Historical mitochondrial diversity in African leopards (Panthera pardus) revealed by archival museum specimens , 2018, Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis.

[20]  D. Díez-del-Molino,et al.  Quantifying Temporal Genomic Erosion in Endangered Species. , 2017, Trends in ecology & evolution.

[21]  Graham M. Hughes,et al.  Genome-wide signatures of complex introgression and adaptive evolution in the big cats , 2017, Science Advances.

[22]  E. Grosholz,et al.  Trophic sensitivity of invasive predator and native prey interactions: integrating environmental context and climate change , 2017 .

[23]  M. Tress,et al.  Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx , 2016, Genome Biology.

[24]  Yun Sung Cho,et al.  Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly , 2016, Genome Biology.

[25]  P. Elkan,et al.  Multi-locus Analyses Reveal Four Giraffe Species Instead of One , 2016, Current Biology.

[26]  D. Rödder,et al.  Home ranges, activity patterns and habitat preferences of leopards in Luambe National Park and adjacent Game Management Area in the Luangwa Valley, Zambia , 2016, Mammalian Biology.

[27]  M. Farhadinia,et al.  Leopard (Panthera pardus) status, distribution, and the research efforts across its range , 2016, PeerJ.

[28]  S. Puechmaille.  The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem , 2016, Molecular ecology resources.

[29]  Jameal F. Samhouri,et al.  Ecosystem context and historical contingency in apex predator recoveries , 2016, Science Advances.

[30]  M. Diekhans,et al.  Genomic legacy of the African cheetah, Acinonyx jubatus , 2015, Genome Biology.

[31]  K. Vrieling,et al.  Autosomal and mtDNA Markers Affirm the Distinctiveness of Lions in West and Central Africa , 2015, PloS one.

[32]  B S Weir,et al.  Genetic assignment of large seizures of elephant ivory reveals Africa’s major poaching hotspots , 2015, Science.

[33]  J. Fattebert,et al.  Density-Dependent Natal Dispersal Patterns in a Leopard Population Recovering from Over-Harvest , 2015, PloS one.

[34]  Matthew Stephens,et al.  Visualizing spatial population structure with estimated effective migration surfaces , 2014, Nature Genetics.

[35]  Anders Albrechtsen,et al.  ANGSD: Analysis of Next Generation Sequencing Data , 2014, BMC Bioinformatics.

[36]  T. Korneliussen,et al.  Estimating Individual Admixture Proportions from Next Generation Sequencing Data , 2013, Genetics.

[37]  Yun Sung Cho,et al.  The tiger genome and comparative analysis with lion and snow leopard genomes , 2013, Nature Communications.

[38]  F. Achard,et al.  State and evolution of the African rainforests between 1990 and 2010 , 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.

[39]  Philip L. F. Johnson,et al.  Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse , 2013, Nature.

[40]  Arcadi Navarro,et al.  Great ape genetic diversity and population history , 2013, Nature.

[41]  J. Fattebert,et al.  Long-Distance Natal Dispersal in Leopard Reveals Potential for a Three-Country Metapopulation , 2013 .

[42]  Sven Rahmann,et al.  Snakemake--a scalable bioinformatics workflow engine. , 2012, Bioinformatics.

[43]  E. Lorenzen,et al.  Comparative phylogeography of African savannah ungulates 1 , 2012, Molecular ecology.

[44]  Jun Wang,et al.  SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data , 2012, PloS one.

[45]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[46]  Zhigang Jiang,et al.  Mitogenomic analysis of the genus Panthera , 2011, Science China Life Sciences.

[47]  David Reich,et al.  Testing for ancient admixture between closely related populations. , 2011, Molecular biology and evolution.

[48]  R. Durbin,et al.  Inference of Human Population History From Whole Genome Sequence of A Single Individual , 2011, Nature.

[49]  S. O’Brien,et al.  Evolution of a Major Drug Metabolizing Enzyme Defect in the Domestic Cat and Other Felidae: Phylogenetic Timing and the Role of Hypercarnivory , 2011, PloS one.

[50]  Josyf Mychaleckyj,et al.  Robust relationship inference in genome-wide association studies , 2010, Bioinform..

[51]  J. Ragle,et al.  IUCN Red List of Threatened Species , 2010 .

[52]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[53]  Anit Raja Banerjee,et al.  An Introduction to Conservation Genetics , 2010, The Yale Journal of Biology and Medicine.

[54]  Philip L. F. Johnson,et al.  A Draft Sequence of the Neandertal Genome , 2010, Science.

[55]  Alkes L. Price,et al.  Reconstructing Indian Population History , 2009, Nature.

[56]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[57]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[58]  Alejandro A. Schäffer,et al.  Database indexing for production MegaBLAST searches , 2008, Bioinform..

[59]  C. Eckert,et al.  Genetic variation across species’ geographical ranges: the central–marginal hypothesis and beyond , 2008, Molecular ecology.

[60]  Jean L. Chang,et al.  Initial sequence and comparative analysis of the cat genome. , 2007, Genome research.

[61]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[62]  G. Kerley,et al.  Prey preferences of the leopard (Panthera pardus) , 2006 .

[63]  S. Steppan,et al.  Evolution of hypercarnivory: the effect of specialization on morphological and taxonomic diversity , 2004, Paleobiology.

[64]  J. Damuth,et al.  Cope's Rule, Hypercarnivory, and Extinction in North American Canids , 2004, Science.

[65]  Sander,et al.  TROPHIC LEVELS ARE DIFFERENTIALLY SENSITIVE TO CLIMATE , 2003 .

[66]  S. O’Brien,et al.  Conservation genetics of the Far Eastern leopard (Panthera pardus orientalis). , 2002, The Journal of heredity.

[67]  P. Arctander,et al.  Population structure of the African savannah elephant inferred from mitochondrial control region sequences and nuclear microsatellite loci , 2002, Heredity.

[68]  S. O’Brien,et al.  Phylogenetics, genome diversity and origin of modern leopard, Panthera pardus , 2001, Molecular ecology.

[69]  J. L. Gittleman,et al.  Predicting extinction risk in declining species , 2000, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[70]  Erik Meijer,et al.  Delete-m Jackknife for Unequal m , 1999, Stat. Comput..

[71]  George R. Hughes,et al.  Wild Cats – Status Survey and Conservation Action Plan , 1998, Biodiversity & Conservation.

[72]  S. O’Brien,et al.  Phylogeographic Subspecies Recognition in Leopards (Panthera pardus): Molecular Genetic Variation , 1996 .

[73]  R. Frankham.  Effective population size/adult population size ratios in wildlife: a review. , 1995, Genetical research.

[74]  J. Hill,et al.  The Mammals of the Indomalayan Region: A Systematic Review , 1992 .

[75]  C. Groves,et al.  A revised taxonomy of the Felidae : The final report of the Cat Classification Task Force of the IUCN Cat Specialist Group , 2017 .

[76]  Sven Rahmann,et al.  Genome analysis , 2022 .

[77]  R. Nowak,et al.  Walker's mammals of the world , 1968 .