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).