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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

Additional files

Additional file 1: Figure S1:

Mitochondrial DNA genealogy in C. nigra. The tree was built based on a 705-long fragment of the control region from 89C. nigra individuals. Sequence accession numbers and island of origin of each turtle are provided. The three major clades identified by Caccone et al. [18] are indicated. The five individuals analyzed in this study appear in red.

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Additional file 2:

Details about sampling, sequencing, assembly, SNP calling, gene expression, gene ontology, and phylogenomic analyses.

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Additional file 3: Table S1:

Contrasting GO-slim term-specific selective pressure between C. nigra and E. orbicularis. list of GO-slim ‘Biological process’ terms, with the number of associated contigs, their average πNS ratio and its normalized version (z-score) in C. nigra vs. E. orbicularis.

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Additional file 4: Table S2:

C. nigra and E. orbicularis coding sequences associated to GO-slim terms ‘immune process’ and ‘response to stress’. list of predicted contigs associated to the ‘immune process’ and ‘response to stress’ terms in either C. nigra or E. orbicularis, their functional annotation, length, coverage, πN, and πS.

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