Ae.aegypti_Ne_genepop_files

Aedes aegypti microsatellite alleles and SNP-chip genotypes from a worldwide sample of populations in "genepop" format, used in estimates of Ne for this paper. Details of the "genepop" format can be found at http://genepop.curtin.edu.au. For the microsatellite genotyping, we used the protocol described in (Brown et al, 2011) for 12 loci; A1, B2, B3, A9, AC2, CT2, AG2, AC4, AC1, AC5, AG1, and AG4. Briefly, amplifications were performed using standard PCR protocol (35 cycles at 54˚C) with fluorescently labeled M13 primers (6-FAM and HEX) in 10.0 μl reaction volumes using the Type-it Microsatellite PCR Master Mix (Qiagen), then diluted, multiplexed, and submitted for fragment analysis with GS 500 ROX internal size standard (Applied Biosystems, Foster City, CA, USA) on an Applied Biosystems 3730xl DNA Genetic Analyzer at the DNA Analysis Facility on Science Hill at Yale. Alleles were scored using GeneMapper v4.0 (Applied Biosystems).
For the SNP-chip genotyping, 167 samples were analyzed on the Axiom_aegypti1 SNP-chip (Evans et al, 2015) at the Functional Genomics Core at University of North Carolina, Chapel Hill, using manufacturer protocols. Raw data were processed and converted into genotype calls following Evans et al. (2015) using Genotyping Console v4.2 (Affymetrix, Santa Clara, CA, USA) and SNPolisher v1.4 (Affymetrix) in the R environment with the call threshold set to 95%. SNPs were pruned to remove any linked SNPs in PLINK v1.7 (Purcell et al, 2007) with the command “--indep 100 10 2”, which recursively removed SNPs within a sliding window of 100 SNPs wide, shifting 10 SNPs per step, with a variance inflation factor (i.e. VIF) threshold of 2.