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).