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

• Published in: Molecular Ecology Resources
• Main Authors: Viricel, Amélia, Pante, Eric, Dabin, Willy, Simon-Bouhet, Benoit
• Other Authors: LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Observatoire pour la Conservation de la Mégafaune Marine (PELAGIS), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), CPER Poitou-Charente 2007-2013, Action Internationales et Rayonnement de l'Université de La Rochelle, UMR 7266 LIENSs CNRS-Université de La Rochelle
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2014
• Subjects: RAD sequencing; phylogenetics; genomics; inter-familial divergence; Delphinidae; Phocoenidae; [SDV.BID]Life Sciences [q-bio]/Biodiversity; Phocoena phocoena
• Online Access: https://hal.science/hal-00908459; https://hal.science/hal-00908459/document; https://hal.science/hal-00908459/file/mer_viricel_rad_phocoena_25Oct13.pdf; https://doi.org/10.1111/1755-0998.12206

International audience 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.