Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations
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RESEARCH ARTICLE
Open Access
Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations Eeva Jansson1* , Francois Besnier1, Ketil Malde1, Carl André2, Geir Dahle1 and Kevin A. Glover1,3
Abstract Background: Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results: After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~ 1% within Scandinavia. SNPs showing large divergence (FST > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (mean FST_173_loci = 0.065, FST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions: Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further. Keywords: Assignment, Ctenolabrus rupestris, Marker validation, Population genomics, Resequencing, SNP
Background Thanks to the rapid development of whole-genome sequencing methods during the last decade [36, 93], genome wide data is now relatively cost-effective to produce and is becoming increasingly commonplace to study evolutionary questions even for non-model organisms * Correspondence: [email protected] 1 Institute of Marine Research, P. O. Box 1870, Nordnes, 5817 Bergen, Norway Full list of author information is available at the end of the article
[22]. For the conservation and management of wild populations, studies employing high-throughput sequencing technologies may provide better estimates than traditional population genetics tools for key parameters such as effective population size, genetic struc
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