Gene flow in the anemone Anthopleura elegantissima limits signatures of local adaptation across an extensive geographic range

Species inhabiting marine environments face a wide range of environmental conditions that vary spatially across several orders of magnitude. The selective pressures that these conditions impose on marine organisms, in combination with potentially high rates of gene flow between distant populations, make it difficult to predict the extent to which these populations can locally adapt. Here, I identify how selection and gene flow influence the population genetic structure of the anemone Anthopleura elegantissima along the Pacific coast of North America. Isolation-by-distance is the dominant pattern across the range of this species, with a genetic break near Pt. Conception, CA. Furthermore, demographic modeling suggests that this species was historically confined to southerly latitudes before expanding northward. Outlier analyses identify 24 loci under selection (out of ~1,100), but the same analysis on simulated genetic data generated using the most likely demographic model erroneously identified the same number of loci under selection, if not more. Taken together, these results suggest that demographic processes are the dominant force shaping population genetic patterns in A. elegantissima along the Pacific coast of North America. I discuss these patterns in terms of the evolutionary history of A. elegantissima, the potential for local adaptation, and their consequences with respect to interactions with the endosymbiont Breviolum muscatinei across their geographic range.
Methods
Individuals were collected from Washington state to Baja California. After DNA extraction, RAD-seq libraries were produced using sbfI  and random shearing to achieve the desired insert size. Individuals were sequenced on the Illumina 2500 and 4000 platforms. Subsequent SNP calls were made using the STACKS software pipeline after aligning reads to a draft A. sola genome assembly. Finally, loci were screened for contamination by BLASTing all loci to a database of bacteria and dinoflagellate genomes and were excluded if they had positive BLAST match e-values of 1 or less. All remaining loci were included in subsequent analyses and are included in the dataset uploaded here. Raw reads and the draft genome assembly are available on NCBI Bioproject PRJNA632874.