Complex signatures of genomic variation of two non-model marine species in a homogeneous environment
Date
2018-05-09
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
Background: Genomic 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.
Results: Using 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.
Conclusions: Our 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.
Description
CITATION: Nielsen, E. S, et al. 2018. Complex signatures of genomic variation of two non-model marine species in a homogeneous environment. BMC Genomics, 19:347, doi:10.1186/s12864-018-4721-y.
The original publication is available at https://bmcgenomics.biomedcentral.com
The original publication is available at https://bmcgenomics.biomedcentral.com
Keywords
Granular limpet (Scutellastra granularis) -- Genomics, Cape urchin (Parechinus angulosus) -- Genomics, Homogeneous spaces, DNA (RAD) sequencing
Citation
Nielsen, E. S, , et al. 2018. Complex signatures of genomic variation of two non-model marine species in a homogeneous environment. BMC Genomics, 19:347, doi:10.1186/s12864-018-4721-y