Population structuring: lessons from Genotyping by Sequencing in the East Atlantic peacock wrasse
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1
Universitat de Barcelona, Genètica, Microbiologia i Estadística and IrBio, Spain
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2
Centre d'Estudis Avançats de Blanes, Spain
The assessment of marine biodiversity, including genetic structuring is one of the major goals of population management and conservation biology. One of the flagships of the new genomics era, favoured by Next-Generation-Sequencing (NGS) technologies, is the possibility to easily obtain Single Nucleotide Polymorphisms (SNP) markers in ecological-model species without reference genomes. SNPs feature important advantages with respect to more ‘traditional’ markers such as microsatellites; reproducibility between laboratories, high density of markers, and potential for annotation, among others. However, a method of genome reduction is necessary for species with medium to large genomes to ensure sequence depth for SNP identification by NGS. This can be achieved using Restriction site Associated DNA sequencing such as the Genotyping-by-Sequencing (GBS) approach.
The East Atlantic peacock wrasse (Symphodus tinca) is an endemic fish of the Mediterranean and the Black Seas, thus inhabiting a wide environmental range. We genotyped 176 individuals collected in 6 populations of the southern Adriatic region with GBS. A total of 51,221 putative SNPs were identified among our samples and 4,162 polymorphic SNPs retained over all samples after applying all filters. The most likely number of genetic groups identified was three. Two strong barriers to gene flow were observed, the main one differentiating Tremiti Islands, in the northwest, from all the other samples (Fst range 0.013-0.021, P< 0.001) and the second one separating east and south-west localities (Fst range 0.004-0.006, P< 0.001). Some potential migrants from other unsampled areas were detected in the northernmost and southernmost localities. We identified 81 outlier SNPs to be potentially under directional selection. Both selective and neutral SNPs (FST = 0.1350 and FST = 0.0046, respectively) showed significant structuring although outlier SNPs showed deeper differentiation. Some of the adaptive SNPs could be related to environmental factors as revealed with a BlastN search against the genome of the Nile Tilapia (Oreochromis niloticus). Most convincing evidence of selection was obtained for one SNP located within the nptx2b gene, involved in the regulation of the circadian rhythm, as it matched a regulatory position involved in intron splicing and its frequency varied with latitude.
The use of neutral and putatively selected markers suggest that although individuals may physically move from one population to the other local conditions may be different enough to prevent the genetic homogenisation of these populations through selection. Consequently, the differences found in outlier loci should also be taken into account when defining species management units because the degree of genetic structuring is clearly deeper than suggested by only neutral markers. This is especially relevant when planning networks of Marine Protected Areas. Overall, our study clearly indicates that GBS is a good approach for population genomic studies of non-model organisms and emphasizes the novelties that it brings, particularly to marine organisms. The change from population genetics to population genomics studies increases the ability to identify genomic areas under selection enhancing knowledge on how dispersal and local adaption, as inferred through neutral and outlier SNPs, shape biodiversity structuring.
Acknowledgements
This research has been funded by project CHALLENGEN (CTM2013-48163) of the Spanish Government.
Keywords:
Symphodus tinca,
snps,
Population Genomics,
outlier loci,
Dispersal
Conference:
XIX Iberian Symposium on Marine Biology Studies, Porto, Portugal, 5 Sep - 9 Sep, 2016.
Presentation Type:
Oral Presentation
Topic:
2. GLOBAL CHANGES, INVASIVE SPECIES AND CONSERVATION
Citation:
Carreras
C,
Ordóñez
V,
Macpherson
E and
Pascual
M
(2016). Population structuring: lessons from Genotyping by Sequencing in the East Atlantic peacock wrasse.
Front. Mar. Sci.
Conference Abstract:
XIX Iberian Symposium on Marine Biology Studies.
doi: 10.3389/conf.FMARS.2016.05.00081
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Received:
29 Apr 2016;
Published Online:
02 Sep 2016.
*
Correspondence:
Dr. Marta Pascual, Universitat de Barcelona, Genètica, Microbiologia i Estadística and IrBio, Barcelona, 08028, Spain, martapascual@ub.edu