Development of SNP markers for population structure and phylogeography characterization in little owl ( Athene noctua )
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TECHNICAL NOTE
Development of SNP markers for population structure and phylogeography characterization in little owl (Athene noctua) using a genotyping- by-sequencing approach I. Pellegrino1 • L. Boatti1 • M. Cucco1 • F. Mignone1 • T. N. Kristensen2 N. Mucci3 • E. Randi3 • A. Ruiz-Gonzalez4,5 • C. Pertoldi2,6
•
Received: 28 October 2015 / Accepted: 7 December 2015 / Published online: 18 December 2015 Ó Springer Science+Business Media Dordrecht 2015
Abstract Single nucleotide polymorphisms (SNPs) are becoming the most utilized markers in population genetics studies. Reduced representation genome techniques, as genotyping-by-sequencing (GBS), allow identifying great numbers of polymorphisms that are useful to analyze genetic diversity in non-model organisms. In this investigation, we implemented a GBS protocol and different bioinformatics tools to identify a novel SNP panel and investigate the genetic structure and variability in populations of little owl (Athene noctua) sampled from seven geographical regions in Europe (Balkans, north-west Europe, north, central and south Italy, Spain and Portugal). We obtained a total of 22,185 putative SNPs and 1306 indels. After the filtering procedure, 7175 SNP loci and 53 individuals met the stringent quality control measures. Neutrality test identified 281 candidate loci under positive selection, which were used for population genetic analyses.
& I. Pellegrino [email protected] 1
Department of Science and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy
2
Department of Bioscience, Aarhus University, Ny Munkegade 114-116, 8000 Aarhus C, Denmark
3
Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale, Ozzano dell’Emilia, Bologna, Italy
4
Department of Zoology and Animal Cell Biology, University of the Basque Country, UPV/EHU; C/Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
5
Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country, UPV/EHU; Avda. Miguel de Unamuno, 3, 01006 Vitoria-Gasteiz, Spain
6
Aalborg Zoo, Mølleparkvej 63, 9000 Aalborg, Denmark
The selected SNP panel allowed an accurate description of the genetic structure of the little owl. Keywords Athene noctua SNP Genotyping-bysequencing Population genetics
Text Genotyping-by-sequencing (GBS), a highly multiplexed, high-throughput, and low-cost method, is one of the simplest reduced representation genome approaches developed so far (Davey et al. 2011; Elshire et al. 2011). SNPs markers obtained through GBS and other procedures implemented in next-generation sequencing (NGS) platforms, are widely used in phylogenetics and phylogeographic studies and to estimate genome-wide diversity in populations of non-model species (Ekblom and Galindo 2010; Garrick et al. 2015). The large numbers of markers per individual enables the characterization of population genetic diversity and structure using a limited number of samples (Willing et al. 2012). Association ana
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