Pooled population resequencing of clam shrimp (Eulimnadia texana) from different vernal pools reveals signatures of local adaptation

Vernal pool clam shrimp (Eulimnadia texana) are a promising model due to ease of culturing, short generation time, modest genome size, and obligate desiccated diapaused eggs. We collected Illumina data (Poolseq) from eleven pooled wild vernal pool clam shrimp populations. We hypothesized that restricted gene flow between vernal pools, separated by distances of 0.36 to 253 km, in concert with Poolseq data from each population, could be used to identify genes important in local adaptation. We adapted Bayenv2 to genome-wide Poolseq data and detected thirteen genomic regions showing a strong excess of population subdivision relative to a genome-wide background. We identified a set of regions that appear to be significantly diverged in allele frequency, above what is expected based on the relationships amongst the populations. Regions identified as significant were on average 9.5 kb in size and harbored 3.8 genes. We attempted to identify correlations between allele frequencies at each genomic region and environmental variables that may influence local adaptation in the sequences populations, but found that there were too many confounding environmental variables to draw strong conclusions. One such genomic region harbored an ortholog of Drosophila melanogaster CG10413, a gene predicted to have sodium/potassium/chloride activity. Finally, we demonstrate that the identified regions could not have been found with less powerful statistics, i.e. FST, or with a less contiguous genome assembly.