Conservation Genetics

, Volume 17, Issue 1, pp 125–139 | Cite as

Effects of habitat deterioration on the population genetics and conservation of the jaguar

  • S. Roques
  • R. Sollman
  • A. Jácomo
  • N. Tôrres
  • L. Silveira
  • C. Chávez
  • C. Keller
  • D. Mello do Prado
  • P. Carignano Torres
  • C. Jorge dos Santos
  • X. Bernardes Garcia da Luz
  • W. E. Magnusson
  • J. A. Godoy
  • G Ceballos
  • F. Palomares
Research Article


Over the past century, human activities and their side effects have significantly threatened both ecosystems and resident species. Nevertheless, the genetic patterns of large felids that depend heavily on large and well-conserved continuous habitat remain poorly studied. Using the largest-ever contemporary genetic survey of wild jaguars (Panthera onca), we evaluated their genetic diversity and population structure in natural (Brazilian Amazon) and highly modified habitats (e.g. Cerrado, Caatinga) including those close to the northern (Yucatan, Mexico) and southern (Pantanal) edge of the species’ distribution range. Data from our set of microsatellites revealed a pronounced genetic structure, with four genetically differentiated geographic areas. Geographic distance was not the only factor influencing genetic differentiation through the jaguar range. Instead, we found evidence of the effects of habitat deterioration on genetic patterns: while the levels of genetic diversity in the Amazon forest, the largest continuum habitat for the species, are high and consistent with panmixia across large distances, genetic diversity near the edge of the species distribution has been reduced through population contractions. Mexican jaguar populations were highly differentiated from those in Brazil and genetically depauperated. An isolated population from the Caatinga showed the genetic effects of a recent demographic decline (within the last 20–30 years), which may reflect recent habitat degradation in the region. Our results demonstrate that the jaguar is highly sensitive to habitat fragmentation especially in human-dominated landscapes, and that in Brazil, the existing but limited genetic connectivity in the central protected areas should be maintained. These conclusions have important implications for the management of wide-ranging species with high dispersal and low population density. The restoration of ecological connectivity between populations over relatively large scales should be one of the main priorities for species conservation.


Felid Elusive Habitat deterioration Connectivity Conservation 



This study was carried out with the support of the project BIOCON 05—100/06 of the Fundación BBVA, the project CGL2010-16902 of the Spanish Ministry of Research and Innovation, the project CGL2013-46026-P of MINECO, the excellence project RNM 2300 of the Junta de Andalucía, and projects UAM-PTC-333 and PROMEP/103.5/12/3823. Sampling in the Mexican areas under the license SGPA/DGVS/549 provided by Martín Vargas of the Dirección General de Vida Silvestre (Semarnat). Faecal samples were exported from Mexico to Spain under the export licences no MX33790 and MX42916 of the Secertaria de Medio Ambiente/CITES. Sampling in Brazil was carried out in RAPELD sites installed or maintained by the Brazilian Program for Biodiversity Research (PPBio) and under licenses #131/2005 CGFAU/LIC, 13883-1 SISBIO and 15664-1 SISBIO of the Instituto Brasileiro do Meio Ambiente—IBAMA. Faecal samples were exported from Brazil to Spain for genetic analysis under IBAMA/CGEN Autorização de Acesso license #063/05 and IBAMA/CITES export licenses #0123242BR and 08BR002056/DF”. We thank the management of the Edén Ecological Reserve (Marco Lazcano) and El Zapotal Ecological Reserve (Pronatura Península de Yucatán: Juan Carlos Faller and María Andrade) for their logistical support. We are grateful to J.S. Lópes and J. Tavares for the collection of most of the field samples in Brazil. Julia Martínez, Gloria Clemencia Amaya, Juan Carlos Faller, Meredic Calleja and Ana Alicia Morales helped with the fieldwork in Brazil and Mexico, as well as the local reserve staff of El Zapotal and El Edén (Mexico). L. Soriano and A. Piriz provided technical advice on multiple issues, and A. García, E. Marmesat, and B. Gutiérrez assisted in the analysis of samples. Logistical support was provided by Laboratorio de Ecología Molecular, Estación Biológica de Doñana, CSIC (LEM-EBD). The Spanish Ministry of Education and Sciences supported the visit of S. Roques in Mexico. We thank Manuela Gonzalez-Suarez and Philip Hedrick for an early revision of the manuscript.

Supplementary material

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Supplementary material 1 (XLS 37 kb)
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Supplementary material 2 (XLS 74 kb)
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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • S. Roques
    • 1
  • R. Sollman
    • 2
  • A. Jácomo
    • 2
  • N. Tôrres
    • 2
    • 6
  • L. Silveira
    • 2
  • C. Chávez
    • 3
  • C. Keller
    • 4
  • D. Mello do Prado
    • 4
  • P. Carignano Torres
    • 4
  • C. Jorge dos Santos
    • 4
  • X. Bernardes Garcia da Luz
    • 4
  • W. E. Magnusson
    • 4
  • J. A. Godoy
    • 7
  • G Ceballos
    • 5
  • F. Palomares
    • 1
  1. 1.Department of Conservation BiologyEstación Biológica de Doñana (EBD-CSIC)SevilleSpain
  2. 2.Jaguar Conservation Fund/Instituto Onça-PintadaMineirosBrazil
  3. 3.División de Ciencias Biológicas y de la Salud, Departamento de Ciencias AmbientalesUniversidad Autónoma Metropolitana-Unidad LermaLerma de VilladaMexico
  4. 4.Instituto Nacional de Pesquisas da Amazônia - INPAManausBrazil
  5. 5.Instituto de EcologíaUniversidad Nacional Autonoma de MexcioMexicoMexico
  6. 6.Biology InstitutionFederal University of Uberlândia – UFUUberlândiaBrazil
  7. 7.Department of Integrative Ecology, Estación Biológica de Doñana(EBD-CSIC)SevilleSpain

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