Open Access Highly Accessed Research article

Population history, phylogeography, and conservation genetics of the last Neotropical mega-herbivore, the lowland tapir (Tapirus terrestris)

Benoit de Thoisy12*, Anders Gonçalves da Silva3, Manuel Ruiz-García4, Andrés Tapia56, Oswaldo Ramirez7, Margarita Arana7, Viviana Quse8, César Paz-y-Miño9, Mathias Tobler10, Carlos Pedraza11 and Anne Lavergne2

Author Affiliations

1 Association Kwata, BP 672, 97335 Cayenne cedex, French Guiana

2 Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana

3 CSIRO Marine and Atmospheric Research, GPO Box 1538, Hobart, TAS 7001, Australia

4 Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá DC., Colombia

5 Centro Tecnológico de Recursos Amazónicos, Centro Fátima, Casilla 16-01-800 Puyo-Pastaza, Ecuador

6 Programa de Maestría en Biodiversidad de Áreas Tropicales y su Conservación MBATC, CSIC/UCE/UIMP, Quito, Ecuador

7 Unidad de Biología Integrativa, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú

8 Facultad de Ciencias Veterinarias de Esperanza, Universidad Nacional del Litoral, Buenos Aires, Argentina

9 Instituto de Investigaciones Biomédicas, Universidad de las Américas, Avenida Granados y Colimes, Quito, Ecuador

10 Andes to Amazon Biodiversity Program, Botanical Research Institute of Texas, Fort Worth, TX 76102, USA

11 Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogota, Colombia

For all author emails, please log on.

BMC Evolutionary Biology 2010, 10:278  doi:10.1186/1471-2148-10-278

Published: 14 September 2010



Understanding the forces that shaped Neotropical diversity is central issue to explain tropical biodiversity and inform conservation action; yet few studies have examined large, widespread species. Lowland tapir (Tapirus terrrestris, Perissodactyla, Tapiridae) is the largest Neotropical herbivore whose ancestors arrived in South America during the Great American Biotic Interchange. A Pleistocene diversification is inferred for the genus Tapirus from the fossil record, but only two species survived the Pleistocene megafauna extinction. Here, we investigate the history of lowland tapir as revealed by variation at the mitochondrial gene Cytochrome b, compare it to the fossil data, and explore mechanisms that could have shaped the observed structure of current populations.


Separate methodological approaches found mutually exclusive divergence times for lowland tapir, either in the late or in the early Pleistocene, although a late Pleistocene divergence is more in tune with the fossil record. Bayesian analysis favored mountain tapir (T. pinchaque) paraphyly in relation to lowland tapir over reciprocal monophyly, corroborating the inferences from the fossil data these species are sister taxa. A coalescent-based analysis rejected a null hypothesis of allopatric divergence, suggesting a complex history. Based on the geographic distribution of haplotypes we propose (i) a central role for western Amazonia in tapir diversification, with a key role of the ecological gradient along the transition between Andean subcloud forests and Amazon lowland forest, and (ii) that the Amazon river acted as an barrier to gene flow. Finally, the branching patterns and estimates based on nucleotide diversity indicate a population expansion after the Last Glacial Maximum.


This study is the first examining lowland tapir phylogeography. Climatic events at the end of the Pleistocene, parapatric speciation, divergence along the Andean foothill, and role of the Amazon river, have similarly shaped the history of other taxa. Nevertheless further work with additional samples and loci is needed to improve our initial assessment. From a conservation perspective, we did not find a correspondence between genetic structure in lowland tapir and ecogeographic regions proposed to define conservation priorities in the Neotropics. This discrepancy sheds doubt into this scheme's ability to generate effective conservation planning for vagile species.