Abstract
Polymorphic short insertions and deletions (INDELs ≤ 50 bp) are
abundant, although less common than single nucleotide polymorphisms
(SNPs). Evidence from model organisms shows INDELs to be more strongly
influenced by purifying selection than SNPs. Partly for this reason,
INDELs are rarely used as markers for demographic processes or to detect
balancing or divergent selection. Here, we compared INDELs and SNPs in
the intertidal snail Littorina saxatilis, focusing on hybrid
zones between ecotypes. Using capture sequencing data, we computed INDEL
and SNP site frequency spectra (SFS) to compare the impact of purifying,
positive and balancing selection on these variant types. Because
signatures of selection may be confounded by GC-biased gene conversion
and polarization errors, we also examined their influence. We assessed
the impact of divergent selection by analysing allele frequency clines
across habitat boundaries. We show evidence that short INDELs are
affected more by purifying selection and less by positive selection than
SNPs, but part of the observed SFS difference can be attributed to
GC-biased gene conversion and polarization errors. We did not find a
difference in the impact of balancing or divergent selection between
short INDELs and SNPs. Short INDELs and SNPs were similarly distributed
across the genome and so are likely to respond to indirect selection in
the same way. A few regions likely affected by divergent selection were
revealed by INDELs and not by SNPs. Short INDELs can be useful genetic
markers helping to identify genomic regions under selective constraints
or important for adaptation and population divergence.