3.3 Complete set of SNPs and species-specific SNPs
A total of 5,702 SNPs were detected after stringent filtering and of
those, 2,127 (37.3%) were polymorphic in I. elegans but
invariable in I. graellsii , and 1,711 (30.0%) were polymorphic
in I. graellsii but invariable in I. elegans . Of the
remaining, 1,421 (24.9%) were polymorphic in both species, 62 (1.1%)
fixed for the same allele in allopatric I. elegans and I.
graellsii, and 381 (6.7%) species-specific, i.e., alternatively fixed
between I. elegans and I. graellsii individuals from the
allopatric populations (Supplementary Table S3). Note that our set of
species-specific alleles, which was determined by comparing 43
allopatric I. elegans and 25 allopatric I. graellsiiindividuals, might not represent entirely fixed alleles, but represent
alleles with highly skewed frequencies between our species groups (see
Fitzpatrick, 2012; Jordan et al., 2017).