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).