Complex signatures of genomic variation of two non-model marine species in a homogeneous environment

Erica S Nielsen,Robert J Toonen,Romina Henriques,Baocheng Guo,Sophie Von Der Heyden,Ingrid S S Knapp

doi:10.1186/s12864-018-4721-y

Abstract

BackgroundGenomic tools are increasingly being used on non-model organisms to provide insights into population structure and variability, including signals of selection. However, most studies are carried out in regions with distinct environmental gradients or across large geographical areas, in which local adaptation is expected to occur. Therefore, the focus of this study is to characterize genomic variation and selective signals over short geographic areas within a largely homogeneous region. To assess adaptive signals between microhabitats within the rocky shore, we compared genomic variation between the Cape urchin (Parechinus angulosus), which is a low to mid-shore species, and the Granular limpet (Scutellastra granularis), a high shore specialist.ResultsUsing pooled restriction site associated DNA (RAD) sequencing, we described patterns of genomic variation and identified outlier loci in both species. We found relatively low numbers of outlier SNPs within each species, and identified outlier genes associated with different selective pressures than those previously identified in studies conducted over larger environmental gradients. The number of population-specific outlier loci differed between species, likely owing to differential selective pressures within the intertidal environment. Interestingly, the outlier loci were highly differentiated within the two northernmost populations for both species, suggesting that unique evolutionary forces are acting on marine invertebrates within this region.ConclusionsOur study provides a background for comparative genomic studies focused on non-model species, as well as a baseline for the adaptive potential of marine invertebrates along the South African west coast. We also discuss the caveats associated with Pool-seq and potential biases of sequencing coverage on downstream genomic metrics. The findings provide evidence of species-specific selective pressures within a homogeneous environment, and suggest that selective forces acting on small scales are just as crucial to acknowledge as those acting on larger scales. As a whole, our findings imply that future population genomic studies should expand from focusing on model organisms and/or studying heterogeneous regions to better understand the evolutionary processes shaping current and future biodiversity patterns, particularly when used in a comparative phylogeographic context.

Highlights

Genomic tools are increasingly being used on non-model organisms to provide insights into population structure and variability, including signals of selection
In line with our predictions, we found relatively low numbers of outlier Single nucleotide polymorphism (SNP) within each species, and identified outlier genes associated with different selective pressures than those previously identified in marine taxa occurring in regions with larger environmental gradients [11,12,13,14,15,16]
Regardless of the processes that have shaped the array of private SNPs within the study species, our results indicate that the northern west coast of South Africa may possibly be a reservoir of genomic diversity for marine invertebrates not found elsewhere

Summary

Introduction

Genomic tools are increasingly being used on non-model organisms to provide insights into population structure and variability, including signals of selection. Most studies are carried out in regions with distinct environmental gradients or across large geographical areas, in which local adaptation is expected to occur. The focus of this study is to characterize genomic variation and selective signals over short geographic areas within a largely homogeneous region. The majority of studies directed at identifying genes under selection do so with model organisms, and over large areas with strong environmental gradients, where local adaptation is to be expected (see for example [11,12,13,14,15,16]). Fewer studies characterize genetic differentiation over relatively small and/or environmentally homogeneous regions ( see [17, 18] for microhabitat examples), leaving genome-wide variation of species within these types of environments unexplored. Comparative approaches provide opportunities to test whether different species respond to the same environmental drivers in similar ways, or whether signals of selection differ across species and their populations [24, 25], and the scales at which selection acts [17]

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