SNP annotation and gene ontology
To obtain functional annotations for candidate loci, we used the LastZ
pairwise alignment tool v1.04.00 (R. S. Harris, 2007) to find
homologous M. ochrogaster positions. To do this, we used a 20,000
bp scaffold surrounding each candidate locus as a query in LastZ and the
default options for calculating pairwise alignments. Only alignments
with a bit score greater than 1,000 and a query coverage of at least
50% were considered. If multiple alignments passed this filter, the
alignment with the longest length and highest bit score was selected as
the best match. If the loci were on protein-coding regions, we used the
UniProt database to examine gene function and find gene ontology (GO)
terms. We performed an enrichment analysis using topGO (Alexa &
Rahnenführer, 2010) in the ”biological processes” category. We compared
our list of candidate genes with all genes with a SNP. We used Fisher’s
exact test and the elim algorithm to account for correlation in
the topology of the GO graph, and reported the GO terms with a p-value
< 0.01 and at least 4 associated genes (Table S6).