New evidence for habitat-specific selection in Wadden Sea Zostera marina populations revealed by genome scanning using SNP and microsatellite markers

Abstract

Eelgrass Zostera marina is an ecosystem-engineering species of outstanding importance for coastal soft sediment habitats that lives in widely diverging habitats. Our Wrst goal was to detect divergent selection and habitat adaptation at the molecular genetic level; hence, we compared three pairs of permanently submerged versus intertidal populations using genome scans, a genetic markerbased approach. Three diVerent statistical approaches for outlier identiWcation revealed divergent selection at 6 loci among 46 markers (6 SNPs, 29 EST microsatellites and 11 anonymous microsatellites). These outlier loci were repeatedly detected in parallel habitat comparisons, suggesting the inXuence of habitat-speciWc selection. A second goal was to test the consistency of the general genome scan approach by doubling the number of gene-linked microsatellites and adding single nucleotide polymorphism (SNP) loci, a novel marker type for seagrasses, compared to a previous study. Reassuringly, results with respect to selection were consistent among most marker loci. Functionally interesting marker loci were linked to genes involved in osmoregulation and water balance, suggesting diVerent osmotic stress, and reproductive processes (seed maturation), pointing to diVerent life history strategies. The identiWed outlier loci are valuable candidates for further investigation into the genetic basis of natural selection.

Eelgrass Zostera marina populations in northern Norwegian fjords are genetically isolated and diverse

“…Although the presence of distinct subgroups within the Sørk -josen and Medby sites suggests that ecotypic differentiation is possible, demonstration of local habitat selection (Stockwell et al 2003) requires experimental support, which putatively neutral microsatellite loci cannot provide. However, genome scans of common garden and reciprocal transplant experiments have revealed selection between intertidal and subtidal, and depth-associated genotypes of Z. marina (Oetjen & Reusch 2007, Oetjen et al 2010, Winters et al 2011, illustrating that ecotypic differentiation is common.…”

“…Meadows may be heterogeneous as a consequence of temporal admixture events of repeated recruitment through time (originally proposed by Petit et al 2003for oaks, Becheler et al 2010; limited dispersal of pollen and seeds, leading to patchiness (Hämmerli & Reusch 2003); and local habitat selection (Oetjen & Reusch 2007, Oetjen et al 2010, Winters et al 2011. Alternatively, they can be homogeneous as a consequence of dominance by a few large genets/clones (Reusch et al 1999, Coyer et al 2008) and limited recruitment (Duarte et al 2006).…”

Genetic distance predicts trait differentiation at the subpopulation but not the individual level in eelgrass,Zostera marina

“…We delineated genotypes and estimated relatedness using 11 microsatellite loci selected from a pool of >30 loci developed specifically for Z. marina (Abbott & Stachowicz, 2016; Oetjen, Ferber, Dankert & Reusch, 2010; Oetjen & Reusch, 2007; Reusch, 2000; Reusch, Stam & Olsen, 1999). We identified a total of 219 unique genotypes from the 260 ramets we collected.…”

Bioinformatics Applied to Proteomics

“…We do not intend to give a comprehensive overview of all available methods and technical advances potentially useful for identifying functional DNA polymorphisms, but rather we explore briefly some of promising recent developments of genomic tools from which proteomics taken its rise during the last twenty years, applicable also to non model organisms. The genome scan, became one of the most promising molecular genetics (Oetjen et al, 2010). Genome scans use a large number of molecular markers coupled with statistical tests in order to identify genetic loci influenced by selection (Stinchombe & Hoekstra, 2008).…”