Additional file 5 of Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti

Additional file 5: Figure S5. All Applied Introgression Tests. Patterson’s D was used to assess introgression between a potential introgressing clade and pair of putative sister clades, with an outgroup used to determine derived alleles for the other three clades; 5a) introgression into individual colonies was compared by applying Patterson’s D statistic to each colony as compared to the other two colonies of the same subspecies (e.g we examined Aaf introgression into Kenya_Aaa vs Thai_Aaa + USA_Aaa using Ae. mascarensis as the outgroup). Specific tests applied are given in figures i,iii,v, and the results for each shown in figs ii,iv,vi. Significance was tested by block jackknifing. 5b) The same test was applied to introgression between mascarensis and any individual population (i-iv), as well as between Ae mascarensis and all Aaf or Aaa populations (v-vi); all inter-specific tests used Ae albopictus as the outgroup. 5c) Significant introgression was detected in between Aaf and Kenya_Aaa, between Aaa and Kenya_Aaf, indicating bidirectional introgression between the two subspecies in Kenya. Martin’s fD statistic was applied to identify specific introgressed loci in these two populations and was also applied to testing for Aaf introgression into the ‘hybrid’ population in this region. 5d) significant introgression was also detected between Ae. mascarensis and global Aaa populations. Notably one fD peaks at the distal end of chromosome 2q appeared to have introgressed between Aaa and Kenya_Aaf and Aaa and Ae mascarensis.