Association mapping
The 308 SNP loci on the GT-seq panel were aligned to reference genomes using BOWTIE2. There were 306 that were assigned to a single location on the Pacific lamprey male genome (99.4%), covering 70 different chromosomes with an average of 4.4 loci per chromosome (range 1 – 22). Marker locations were based on the alignments of marker sequences to the Pacific lamprey male and female genomes, homologous scaffolds of the sea lamprey genome, and positions on the previously published Pacific lamprey linkage map (Smith et al. 2018).
Adjusted P -values from the association testing described above were log transformed (-LOG10) and plotted by consensus genome position on the Pacific lamprey male genome. We tested correlation of association tests -LOG10(P) with F ST from the rangewide divergence to understand whether trait associations may explain the high divergence observed at the rangewide scale for the subset of markers shared between datasets. Among the 308 SNPs, there were 230 neutral SNPs, 41 adaptive markers SNPs, and a set of 31 “intermediate” SNPs that did not fit definitions of putatively neutral and putatively adaptive (divergence mapping). Finally, four loci were species diagnostic (Hess et al. 2015), and 2 loci were duplicated. Therefore, there were 302 unique markers available for these association analyses. These markers included 38 SNPs that were mostly adaptive loci that were categorized into the following 4 groups of statistically linked loci: A (N=10), B (N=13), C (N=7), and D (N=8, Hess et al.2013).