Divergence mapping
Outlier analyses identified 311 (4.0%) SNPs as candidates for positive selection (out of a total of 7,716 SNPs; P > 0.995). LOSITAN was also used to identify neutral loci, which we defined using a conservative threshold range of probabilities between 0.10 and 0.90. There were 350 (4.5%) and 4 (< 0.1%) SNPs below and above this range, respectively (i.e. candidates for balancing and positive selection, respectively), and 7,051 neutral loci (91.4% of 7716 loci) that fell within these probability levels.
A total of 7385 out of 7716 loci (95.7%) and 7366 out of 7716 loci (95.4%) aligned to the Pacific Lamprey female and male genome assemblies, respectively, and 4916 out of 7716 loci (63.7%) aligned to the male gametic sea lamprey genome. The alignment to the Pacific lamprey male genome was used to order the loci by scaffold position, and in cases in which only alignments to the other assemblies were available we interpolated values to estimate relative positions. Manhattan plot was used to visualize the distribution of the outlier SNPs in both the Pacific lamprey and sea lamprey male genome assemblies (Fig. 1), and alignments were generated between Pacific lamprey male and female genomes (Fig. S3). These results illustrated that 65% of the outlier loci are localized to each of the following four chromosomes:01, 02, 04, and 22; which share homology with sea lamprey chromosomes 03, 06, 05, and 12, respectively (Fig. 1). The patterns of synteny within these four chromosomes indicated large regions of inversions that overlapped with concentrations of outlier SNPs (e.g., chromosomes 01 and 02, Fig. S3) and may be polymorphic within Pacific lamprey given the differences between male and female genome assemblies. The same inversion patterns on chromosomes 01 and 02 were present between species (male assemblies, Fig. S3).