Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans

Amélia Viricel 1, * Eric Pante 1 Willy Dabin 2 Benoit Simon-Bouhet 1
* Auteur correspondant
2 PELAGIS - Observatoire PELAGIS UMS 3462
LIENSs - LIttoral ENvironnement et Sociétés - UMR 7266, CNRS - Centre National de la Recherche Scientifique : UMS3462
Abstract : Restriction site-Associated DNA tag (RAD-tag) sequencing has become a popular approach to generate thousands of SNPs used to address diverse questions in population genomics. Comparatively, the suitability of RAD-tag genotyping to address evolutionary questions across divergent species has been the subject of only a few recent studies. Here, we evaluate the applicability of this approach to conduct genome-wide scans for polymorphisms across two cetacean species belonging to distinct families: the short-beaked common dolphin (Delphinus delphis; n = 5 individuals) and the harbor porpoise (Phocoena phocoena; n = 1 individual). Additionally, we explore the effects of varying two parameters in the Stacks analysis pipeline on the number of loci and level of divergence obtained. We observed a 34% drop in the total number of loci that were present in all individuals when analyzing individuals from the distinct families compared to analyses restricted to intra-specific comparisons (i.e., within D. delphis). Despite relatively stringent quality filters, 3,595 polymorphic loci were retrieved from our inter-familial comparison. Cetaceans have undergone rapid diversification and the estimated divergence time between the two families is relatively recent (14 to 19 My). Thus, our results showed that, for this level of divergence, a large number of orthologous loci can still be genotyped using this approach, which is on par with two recent in silico studies. Our findings constitute one of the first empirical investigations using RAD-tag sequencing at this level of divergence and highlights the great potential of this approach in comparative studies and to address evolutionary questions.
Type de document :
Article dans une revue
Molecular Ecology Resources, Wiley/Blackwell, 2014, 14 (3), pp.597-605. 〈10.1111/1755-0998.12206〉
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Soumis le : samedi 23 novembre 2013 - 12:57:13
Dernière modification le : jeudi 11 janvier 2018 - 06:25:39
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Amélia Viricel, Eric Pante, Willy Dabin, Benoit Simon-Bouhet. Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans. Molecular Ecology Resources, Wiley/Blackwell, 2014, 14 (3), pp.597-605. 〈10.1111/1755-0998.12206〉. 〈hal-00908459〉

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