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Population genomics of the endangered giant Galápagos tortoise

Etienne Loire1, Ylenia Chiari12, Aurélien Bernard1, Vincent Cahais1, Jonathan Romiguier1, Benoît Nabholz1, Joao Miguel Lourenço1 and Nicolas Galtier1*

Author Affiliations

1 Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France

2 CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal

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Genome Biology 2013, 14:R136  doi:10.1186/gb-2013-14-12-r136

Published: 16 December 2013

Abstract

Background

The giant Galápagos tortoise, Chelonoidis nigra, is a large-sized terrestrial chelonian of high patrimonial interest. The species recently colonized a small continental archipelago, the Galápagos Islands, where it has been facing novel environmental conditions and limited resource availability. To explore the genomic consequences of this ecological shift, we analyze the transcriptomic variability of five individuals of C. nigra, and compare it to similar data obtained from several continental species of turtles.

Results

Having clarified the timing of divergence in the Chelonoidis genus, we report in C. nigra a very low level of genetic polymorphism, signatures of a weakened efficacy of purifying selection, and an elevated mutation load in coding and regulatory sequences. These results are consistent with the hypothesis of an extremely low long-term effective population size in this insular species. Functional evolutionary analyses reveal a reduced diversity of immunity genes in C. nigra, in line with the hypothesis of attenuated pathogen diversity in islands, and an increased selective pressure on genes involved in response to stress, potentially related to the climatic instability of its environment and its elongated lifespan. Finally, we detect no population structure or homozygosity excess in our five-individual sample.

Conclusions

These results enlighten the molecular evolution of an endangered taxon in a stressful environment and point to island endemic species as a promising model for the study of the deleterious effects on genome evolution of a reduced long-term population size.