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Lescroart J, Bonilla-Sánchez A, Napolitano C, Buitrago-Torres DL, Ramírez-Chaves HE, Pulido-Santacruz P, Murphy WJ, Svardal H, Eizirik E. Extensive Phylogenomic Discordance and the Complex Evolutionary History of the Neotropical Cat Genus Leopardus. Mol Biol Evol 2023; 40:msad255. [PMID: 37987559 PMCID: PMC10701098 DOI: 10.1093/molbev/msad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023] Open
Abstract
Even in the genomics era, the phylogeny of Neotropical small felids comprised in the genus Leopardus remains contentious. We used whole-genome resequencing data to construct a time-calibrated consensus phylogeny of this group, quantify phylogenomic discordance, test for interspecies introgression, and assess patterns of genetic diversity and demographic history. We infer that the Leopardus radiation started in the Early Pliocene as an initial speciation burst, followed by another in its subgenus Oncifelis during the Early Pleistocene. Our findings challenge the long-held notion that ocelot (Leopardus pardalis) and margay (L. wiedii) are sister species and instead indicate that margay is most closely related to the enigmatic Andean cat (L. jacobita), whose whole-genome data are reported here for the first time. In addition, we found that the newly sampled Andean tiger cat (L. tigrinus pardinoides) population from Colombia associates closely with Central American tiger cats (L. tigrinus oncilla). Genealogical discordance was largely attributable to incomplete lineage sorting, yet was augmented by strong gene flow between ocelot and the ancestral branch of Oncifelis, as well as between Geoffroy's cat (L. geoffroyi) and southern tiger cat (L. guttulus). Contrasting demographic trajectories have led to disparate levels of current genomic diversity, with a nearly tenfold difference in heterozygosity between Andean cat and ocelot, spanning the entire range of variability found in extant felids. Our analyses improved our understanding of the speciation history and diversity patterns in this felid radiation, and highlight the benefits to phylogenomic inference of embracing the many heterogeneous signals scattered across the genome.
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Affiliation(s)
- Jonas Lescroart
- Department of Biology, University of Antwerp, Antwerp, Belgium
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Alejandra Bonilla-Sánchez
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
- Faculty of Exact and Natural Sciences, University of Antioquia, Medellín, Colombia
| | - Constanza Napolitano
- Department of Biological Sciences and Biodiversity, University of Los Lagos, Osorno, Chile
- Institute of Ecology and Biodiversity, Concepción, Chile
- Cape Horn International Center, Puerto Williams, Chile
- Andean Cat Alliance, Villa Carlos Paz, Argentina
| | - Diana L Buitrago-Torres
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Héctor E Ramírez-Chaves
- Department of Biological Sciences, University of Caldas, Manizales, Colombia
- Centro de Museos, Museo de Historia Natural, University of Caldas, Manizales, Colombia
| | | | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, Netherlands
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
- Instituto Pró-Carnívoros, Atibaia, Brazil
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Tirelli FP, Trigo TC, Queirolo D, Kasper CB, Bou N, Peters F, Mazim FD, Martínez-Lanfranco JA, González EM, Espinosa C, Favarini M, da Silva LG, Macdonald DW, Lucherini M, Eizirik E. High extinction risk and limited habitat connectivity of Muñoa’s pampas cat, an endemic felid of the Uruguayan Savanna ecoregion. J Nat Conserv 2021. [DOI: 10.1016/j.jnc.2021.126009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Trindade FJ, Rodrigues MR, Figueiró HV, Li G, Murphy WJ, Eizirik E. Genome-wide SNPs clarify a complex radiation and support recognition of an additional cat species. Mol Biol Evol 2021; 38:4987-4991. [PMID: 34320647 PMCID: PMC8557425 DOI: 10.1093/molbev/msab222] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Phylogenetic reconstruction and species delimitation are often challenging in the case of recent evolutionary radiations, especially when postspeciation gene flow is present. Leopardus is a Neotropical cat genus that has a long history of recalcitrant taxonomic problems, along with both ancient and current episodes of interspecies admixture. Here, we employ genome-wide SNP data from all presently recognized Leopardus species, including several individuals from the tigrina complex (representing Leopardus guttulus and two distinct populations of Leopardus tigrinus), to investigate the evolutionary history of this genus. Our results reveal that the tigrina complex is paraphyletic, containing at least three distinct species. While one can be assigned to L. guttulus, the other two remain uncertain regarding their taxonomic assignment. Our findings indicate that the “tigrina” morphology may be plesiomorphic within this group, which has led to a longstanding taxonomic trend of lumping these poorly known felids into a single species.
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Affiliation(s)
- Fernanda J Trindade
- PUCRS, Escola de Ciências da Saúde e da Vida, Laboratório de Biologia Genômica e Molecular, Porto Alegre, RS, Brazil
| | - Maíra R Rodrigues
- PUCRS, Escola de Ciências da Saúde e da Vida, Laboratório de Biologia Genômica e Molecular, Porto Alegre, RS, Brazil.,USP, Department of Genetics and Evolutionary Biology, Institute of Biosciences, São Paulo, Brazil
| | - Henrique V Figueiró
- PUCRS, Escola de Ciências da Saúde e da Vida, Laboratório de Biologia Genômica e Molecular, Porto Alegre, RS, Brazil.,Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USA
| | - Gang Li
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843-4458, USA.,College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843-4458, USA
| | - Eduardo Eizirik
- PUCRS, Escola de Ciências da Saúde e da Vida, Laboratório de Biologia Genômica e Molecular, Porto Alegre, RS, Brazil.,Instituto Pró-Carnívoros, Atibaia, SP, Brazil
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Bou N, Soutullo Á, Hernández D, Mannise N, González S, Bartesaghi L, Pereira J, Merino M, Espinosa C, Trigo TC, Cosse M. Population structure and gene flow of Geoffroy’s cat ( Leopardus geoffroyi) in the Uruguayan Savanna ecoregion. J Mammal 2021. [DOI: 10.1093/jmammal/gyab043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Felids are among the species most threatened by habitat fragmentation resulting from land-use change. In the Uruguayan Savanna ecoregion, about 30% of natural habitats have been lost, large felids have been eradicated from most of the region, and the impact of anthropogenic threats over the smaller species that remain is unknown. To develop management strategies, it is important to enhance knowledge about species population structure and landscape connectivity, particularly when land-use change will continue and intensify in the next years. In this study, we evaluate the population structure and gene flow of Geoffroy’s cat in the Uruguayan Savanna ecoregion. We generated a matrix of 11 microsatellite loci for 70 individuals. Based on Bayesian approaches we found that within the Uruguayan Savanna, Geoffroy’s cat shows high levels of genetic variability and no population structure. However, we observed genetic differences between individuals from the Uruguayan Savanna and those from the contiguous ecoregion, the Argentinian Humid Pampa. Four first-generation migrants from Humid Pampa were identified in the Uruguayan Savanna, suggesting a stronger gene flow in the west-east direction. We detected a past bottleneck followed by a subsequent recovery in Geoffroy’s cat populations in both ecoregions. These results lay the groundwork to understand the population dynamics and conservation status of Geoffroy’s cat in the Uruguayan Savanna ecoregion, and provide baseline data to establish population monitoring.
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Affiliation(s)
- Nadia Bou
- Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable-Ministerio de Educación y Cultura, Avenida Italia 3318, 11600 Montevideo, Uruguay
| | - Álvaro Soutullo
- Departamento de Ecología y Gestión Ambiental, Centro Universitario Regional del Este, Universidad de la República, Calle Tacuarembó esquina Bvar. Artigas, 20000 Maldonado, Uruguay
| | - Daniel Hernández
- Laboratorio de Control Ambiental, Polo Educativo Tecnológico Arrayanes, Camino de los Arrayanes km 7, 20200 Piriápolis, Uruguay
| | - Natalia Mannise
- Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable-Ministerio de Educación y Cultura, Avenida Italia 3318, 11600 Montevideo, Uruguay
| | - Susana González
- Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable-Ministerio de Educación y Cultura, Avenida Italia 3318, 11600 Montevideo, Uruguay
| | - Lucía Bartesaghi
- Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable-Ministerio de Educación y Cultura, Avenida Italia 3318, 11600 Montevideo, Uruguay
| | - Javier Pereira
- Grupo de Genética y Ecología en Conservación y Biodiversidad, División Mastozoología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Angel Gallardo 470, Ciudad de Buenos Aires, C1405DJR, Argentina
| | - Mariano Merino
- Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, CICPBA, Monteagudo 2772, Pergamino, Provincia de Buenos Aires, B2700KIZ, Argentina
| | - Caroline Espinosa
- Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, prédio 43435, Bairro Agronomia, 91501-970Porto Alegre, RS, Brazil
| | - Tatiane C Trigo
- Setor de Mastozoologia, Museu de Ciências Naturais, Secretaria de Meio Ambiente e Infraestrutura, Rua Dr. Salvador França, 1427, CEP 90.690-000 - Porto Alegre, RS, Brazil
| | - Mariana Cosse
- Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable-Ministerio de Educación y Cultura, Avenida Italia 3318, 11600 Montevideo, Uruguay
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Nascimento FOD, Cheng J, Feijó A. Taxonomic revision of the pampas cat Leopardus colocola complex (Carnivora: Felidae): an integrative approach. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe pampas cat Leopardus colocola has been subject to conflicting classifications over the years. Currently, one polytypic species with seven subspecies is recognized, but integrative taxonomic study for this debated group has never been done. Here, we combine the broadest morphological coverage of the pampas cat to date with molecular data and ecological niche models to clarify its species composition and test the validity of recently proposed subspecies. The multiple lines of evidence derived from morphology, molecular, biogeography and climatic niche datasets converged on the recognition of five monotypic species: L. braccatus, L. colocola, L. garleppi (including thomasi, budini, steinbachi, crespoi and wolffsohni as synonyms), L. munoai and L. pajeros (including crucina as synonym). These five species are morphologically diagnosable based on skin and skull traits, have evolved in distinct climatic niche spaces and were recovered in molecular species delimitation. Contrary to previous taxonomic arrangements, we do not recognize subspecies in pampas cats. To objectively define the two most controversial species, we designate neotypes for L. colocola and L. pajeros. The diversification of pampas cats is associated with Middle Pleistocene glaciations, but additional genetic samples from the central Andean region are still needed to conclusively reconstruct its evolutionary history.
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Affiliation(s)
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
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Gómez Fernández MJ, Fameli A, Rojo Gómez J, Pereira JA, Mirol P. Phylogeographical spatial diffusion analysis reveals the journey of Geoffroy’s cat through the Quaternary glaciations of South America. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blz207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractLeopardus geoffroyi is a small feline with a widespread distribution in a broad array of habitats. Here we investigate its evolutionary history to characterize the phylogeographical patterns that led to its present distribution using mitochondrial DNA from 72 individuals collected throughout its entire range. All haplotypes conformed to a monophyletic group, including two clades with a central/marginal disposition that is incongruent to the proposed subspecies. Spatial diffusion analysis showed the origin of the species within the oldest and more diverse central clade. A Bayesian Skyline Plot combined with a dispersal through time plot revealed two population increases at 190 000–170 000 and 45 000–35 000 years ago, the latter period accompanied by an increase in the dispersal rate. Species distribution models showed similar patterns between the present and Last Interglacial Period, and a reduction of high-probability areas during the Last Glacial Maximum (LGM). Molecular evidence confirms L. geoffroyi as a monotypic species whose origin is located in Central Argentina. The last glaciation had little effect on the pattern of distribution of the species: the population and range expansion that started before the LGM, although probably being halted, continued after the glaciation and resulted in the presence of this felid in the far south of Patagonia.
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Affiliation(s)
- María Jimena Gómez Fernández
- Grupo de Genética y Ecología en Conservación y Biodiversidad, División Mastozoología, Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’, CONICET. Buenos Aires, Argentina
| | - Alberto Fameli
- Grupo de Genética y Ecología en Conservación y Biodiversidad, División Mastozoología, Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’, CONICET. Buenos Aires, Argentina
| | - Julio Rojo Gómez
- Grupo de Genética y Ecología en Conservación y Biodiversidad, División Mastozoología, Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’, CONICET. Buenos Aires, Argentina
| | - Javier A Pereira
- Grupo de Genética y Ecología en Conservación y Biodiversidad, División Mastozoología, Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’, CONICET. Buenos Aires, Argentina
| | - Patricia Mirol
- Grupo de Genética y Ecología en Conservación y Biodiversidad, División Mastozoología, Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’, CONICET. Buenos Aires, Argentina
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Bou N, Cuyckens G, González E, Meneghel M. Conservation planning in Uruguay based on small felids (Leopardus spp.) as umbrella species. STUDIES ON NEOTROPICAL FAUNA AND ENVIRONMENT 2019. [DOI: 10.1080/01650521.2019.1669421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Nadia Bou
- Genética de la Conservación - Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - G.A.E. Cuyckens
- Instituto de Ecorregiones Andinas, (CONICET - UNJu), San Salvador de Jujuy, Argentina
- Centro de Estudios Territoriales Ambientales y Sociales (CETAS), Universidad Nacional de Jujuy (UNJu), San Salvador de Jujuy, Jujuy, Argentina
| | - E.M. González
- Sección Mastozoología, Museo Nacional de Historia Natural (MNHN), Montevideo, Uruguay
| | - M. Meneghel
- Laboratorio de Sistemática e Historia Natural de Vertebrados, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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