Open Access Highly Accessed Research article

Whole mitochondrial genome scan for population structure and selection in the Atlantic herring

Amber GF Teacher125*, Carl André3, Juha Merilä4 and Christopher W Wheat1

Author Affiliations

1 Department of Biosciences, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland

2 Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Treliever Road, Penryn, Cornwall, TR10 9EZ, UK

3 Department of Marine Ecology – Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden

4 Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland

5 Current address: Centre for Ecology and Conservation, Biosciences, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Treliever Road, Penryn, Cornwall, TR10 9EZ, UK

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BMC Evolutionary Biology 2012, 12:248  doi:10.1186/1471-2148-12-248

Published: 22 December 2012

Abstract

Background

Marine fish, such as the Atlantic herring (Clupea harengus), often show a low degree of differentiation over large geographical regions. Despite strong environmental gradients (salinity and temperature) in the Baltic Sea, population genetic studies have shown little genetic differentiation among herring in this area, but some evidence for environmentally-induced selection has been uncovered. The mitochondrial genome is a likely target for selection in this system due to its functional role in metabolism.

Results

We sequenced whole mitochondrial genomes for herring from throughout the Baltic region (n=98) in order to investigate evidence for geographical structuring, selection, and associations between genetic and environmental variation. Three well-supported clades that predate the formation of the Baltic Sea were identified, but geographic structuring of this variation was weak (ΦST = 0.036). There was evidence for significant positive selection, particularly in the ND2, ND4 and ND5 genes, and amino acids under significant selection in these genes explained some of the clade formation. Despite uncovering evidence for selection, correlations between genetic diversity or differentiation with environmental factors (temperature, salinity, latitude) were weak.

Conclusions

The results indicate that most of the current mtDNA diversity in herring predates the formation of the Baltic Sea, and that little structuring has evolved since. Thus, fisheries management units in this region cannot be determined on the basis of mtDNA variability. Preliminary evidence for selection underlying clade formation indicates that the NADH complex may be useful for examining adaptation and population structuring at a broader geographical scale.

Keywords:
Baltic sea; Clupea harengus; Fisheries; Genome; Mitochondria; Selection; Phylogeography