Remote, oceanic islands such as the Galápagos are often seen as natural laboratories for the study of species evolution. One of this archipelago’s most striking inhabitants, the giant Galápagos tortoise (Chelonoidis nigra) is renowned for its influence on the thinking of Charles Darwin and its contribution to the development of evolutionary theory. Nicolas Galtier and colleagues from Montpellier University, France, have now applied 21st century methods of transcriptome assembly and phylogenetic analysis to explore the genomic consequences of island evolution on the C. nigra population, as published in a recent Genome Biology study.

Giant Galápagos tortoise (C. nigra) on Isabela Island, Galápagos Archipelago. Image source: Flickr, brian.gratwicke

Galtier and colleagues analysed the transcriptomic variability of five individuals of C. nigra from three distinct subspecies, comparing it to similar data obtained from several continental relatives, including the red-footed tortoise Chelonoidis carbonaria from South America and the Spanish pond turtle Mauremys leprosa. By generating a phylogenetic tree of eight turtle species, based on a dataset of 248 orthologous genes, they first confirmed previous conclusions on the placement of C. nigra.

Next, the researchers looked at the relative effects of natural selection and genetic drift on these species. This was measured by calculating the ratio of non-synonymous genetic mutations to synonymous genetic mutations. The former results in changes in the amino acid sequence that are often not retained unless the organism is under a selective pressure to adapt. The calculated ratios differed significantly across taxa, with C. nigra showing the highest ratio of all due to a greater amount of non-synonymous mutations. Further investigation of coding sequence polymorphisms however revealed that this trait was unlikely to be due to increased adaptation but rather an accelerated rate of genetic drift. The diminished effect of natural selection uncovered was in line with the demographics of C. nigra– a species isolated on an island with a long-term, reduced population size, resulting in decreased genetic diversity.

Tree topology of eight turtle species created using maximum-likelihood coding sequence analysis. dN/dS (ratio of non-synonymous substitutions to synonymous substitutions). Image source: Loire et al, Genome Biology, 2013, 14:R136

Functional evolutionary analyses were used to investigate the selective pressure on gene sets of C. nigra and C. carbonaria. Most genes in C. nigra exhibited ‘relaxed selection’, with traits that were adaptive in their original environment being maintained, with slow signs of decay, even though of little benefit in the current environment. Two notable exceptions were genes relating to immunity and stress. Increased selection for stress response genes may reflect the highly fluctuating climate of the Galápagos islands, which often experience periods of drought, as well as the giant tortoise’s longevity – both exerting a selective pressure on these genes. In contrast the significant loss of genetic diversity in immunity genes may reflect the island isolation of C. nigra, where the chances of encountering new pathogens is reduced, so diminishing the need to maintain a highly tuned and energetically costly acquired immune response.

These findings not only have important conservation implications, shedding light on the molecular evolution of an endangered taxon in a stressful environment, but also indicate that island endemic species may be good models for the exploration of genetic drift on genomic patterns, gene function and adaptation.

 

Written by Elizabeth Moylan, Biology Editor for BioMed Central.

 

Research

Highly AccessedOpen Access

Population genomics of the endangered giant Galápagos tortoise

Loire E, Chiari Y, Bernard A, Cahais V, Romiguier J, Nabholz B, Lourenço JM and Galtier N

Genome Biology 2013, 14:R136


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