SUPPLEMENTARY TABLES

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1 Table S1. Sample information and genotyping summary statistics SUPPLEMENTARY TABLES Sample ID, species and race, sex and sampling locations are given, along with genotyping summary statistics. 'Hom Ref,' 'Het' and 'Hom' Alt refer to sites that were genotyped as homozygous for the reference genome allele, heterozygous and homozygous for an alternate allele, respectively. 'ts/tv' is the ratio of transitions to transversions for non-reference (alternate) genotypes. Sequence Read Archive accession numbers are given, along with the reference for the previous study that generated the sequence data, where relevant. Sample ID melp.hgc1 Species and race Sex Lat. Long. population depth Genotyped (Mb) % Hom Ref % Het % Hom Alt ts/tv Accession NA NA NA SRR ros.mk523 rosina M West SRS ros.mk524 rosina F West SRS ros.mk525 rosina M West SRS ros.mk589 rosina M West SRS ros.mk675 rosina M West SRS ros.mk676 rosina M West SRS ros.mk682 rosina M West SRS ros.mk683 rosina M West SRS ros.mk687 rosina F West SRS ros.mk689 rosina F West SRS ros.cj531 rosina M West ERR ros.cj533 rosina M West ERR ros.cj546 rosina M West ERR ros.cj2071 rosina M West ERR melp.cj18038 melp.cj18097 vul.cj14632 vulcanus F West ERR M West ERR M West ERS977709

2 vul.cs519 vul.cs10 vul.cs11 vulcanus vulcanus vulcanus M West ERS M West ERS M West ERS cyth.cj2856 cythera M West ERS cyth.cj2857 cythera M West ERS melc.cs3 melc.cs6 melc.cs25 melc.cs26 melc.cs27 M Colombia ERS M Colombia ERS M Colombia ERS M Colombia ERS M Colombia ERS moc.cs228 mocoa M East ERS moc.cs231 mocoa M East ERS moc.cs16 mocoa M East ERS moc.cs17 mocoa M East ERS ple.cj9156 plesseni F East ERS ple.cj16293 plesseni F East ERS mapl.cj16042 plessenix malleti M East ERS mal.cj16550 malleti M East ERS mal.cj17162 malleti F East ERS mal.cs21 malleti M East ERS mal.cs22 malleti M East ERS mal.cs24 malleti M East ERS ecu.cj9117 ecuadorensis M East ERS977695

3 ecu.cj9121 ama.jm216 ama.jm160 ama.jm293 ama.jm48 ecuadorensis amaryllis amaryllis amaryllis amaryllis M East ERS M East ERR F East ERR F East ERR M East ERR agl.jm108 aglaope M East ERR agl.jm112 aglaope M East ERR agl.jm569 aglaope M East ERR agl.jm572 aglaope M East ERR aman.cs2228 aman.cs2221 melg.cj9315 melg.cj9316 melg.cj9317 melg.cj13435 thel.cj13566 amandus amandus thelxiopeia M M East ERS East ERS M Guiana ERR M Guiana ERR M Guiana ERR M Guiana ERR M Guiana ERS mer.cj13715 meriana M Guiana ERS mer.cj13819 meriana M Guiana ERS cyd.cj553 cyd.cj560 H. cydno chioneus H. cydno chioneus M NA ERR M NA ERR cyd.cj564 H. cydno M NA ERR260297

4 cyd.cj565 tim.jm313 tim.jm57 tim.jm84 tim.jm86 chioneus H. cydno chioneus H. timareta thelxinoe H. timareta thelxinoe H. timareta thelxinoe H. timareta thelxinoe M NA ERR M NA ERR M NA ERR M NA ERR M NA ERR hec.jm273 H. hecale felix F NA ERR eth.jm67 par.jm371 ser.jm202 H. ethilla aerotome H. pardalinus ssp. nov. H. pardalinus sergestus M NA ERR M NA ERR M NA ERR wal.cj8687 H. wallacei M NA ERS bur.cj8560 H. burneyi M NA ERS hecu.cj8550 H. hecuba M NA ERS hier.cj8149 H. hierax M NA ERS dor.jc8684 H. doris M NA ERS era.cj2979 H. erato M NA ERS era.cj2980 H. erato M NA ERS era.cj2981 H. erato M NA ERS era.cj618 H. erato M NA ERS

5 Table S2. Comparing alternative genotyping approaches Summary statistics and estimated error rates for different genotyping approaches: with or without indel realignment or simultaneous genotyoing. ' 40/80 called' refers to the number of sites with high-quality genotype calls for at least 40 of the 80 samples. Indel realignment Called simultaneously Average calls per sample (%) 40/80 called 60/80 called 80/80 called ts/tv Est. error rate No No No Yes Yes No Yes Yes Table S3. Nucleotide diversity (π) and absolute divergence (d XY ), means with errors An extended version of Table 1, including the following site classes: All sites, intergenic, intronic, codon positions 1, 2 and 3, and 4D sites. Standard deviations and standard errors are given for all values. CV refers to the coefficient of variation, the ratio of the mean to the standard deviation. 'WG' values are for the whole genome and 'Z' values are specifically for the Z chromosome. site class region measure mean sd se CV All WG pi () All WG dxy ( cydno clade) All WG dxy ( silvaniform clade) All Z pi () All Z dxy ( cydno clade) All Z dxy ( silvaniform clade) Intergenic WG pi () Intergenic WG dxy ( cydno clade) Intergenic WG dxy ( silvaniform clade) Intergenic Z pi () Intergenic Z dxy ( cydno clade) Intergenic Z dxy ( silvaniform clade) Intron WG pi () Intron WG dxy ( cydno clade) Intron WG dxy ( silvaniform clade) Intron Z pi () Intron Z dxy ( cydno clade) Intron Z dxy ( silvaniform clade)

6 Codon 1 WG pi () Codon 1 WG dxy ( cydno clade) Codon 1 WG dxy ( silvaniform clade) Codon 1 WG dxy ( wallacei clade) Codon 1 WG dxy ( doris clade) Codon 1 WG dxy ( erato) Codon 1 Z pi () Codon 1 Z dxy ( cydno clade) Codon 1 Z dxy ( silvaniform clade) Codon 1 Z dxy ( wallacei clade) Codon 1 Z dxy ( doris clade) Codon 1 Z dxy ( erato) Codon 2 WG pi () Codon 2 WG dxy ( cydno clade) Codon 2 WG dxy ( silvaniform clade) Codon 2 WG dxy ( wallacei clade) Codon 2 WG dxy ( doris clade) Codon 2 WG dxy ( erato) Codon 2 Z pi () Codon 2 Z dxy ( cydno clade) Codon 2 Z dxy ( silvaniform clade) Codon 2 Z dxy ( wallacei clade) Codon 2 Z dxy ( doris clade) Codon 2 Z dxy ( erato) Codon 3 WG pi () Codon 3 WG dxy ( cydno clade) Codon 3 WG dxy ( silvaniform clade) Codon 3 WG dxy ( wallacei clade) Codon 3 WG dxy ( doris clade) Codon 3 WG dxy ( erato) Codon 3 Z pi () Codon 3 Z dxy ( cydno clade) Codon 3 Z dxy ( silvaniform clade) Codon 3 Z dxy ( wallacei clade) Codon 3 Z dxy ( doris clade) Codon 3 Z dxy ( erato)

7 4D WG pi () D WG dxy ( cydno clade) D WG dxy ( silvaniform clade) D WG dxy ( wallacei clade) D WG dxy ( doris clade) D WG dxy ( erato) D Z pi () D Z dxy ( cydno clade) D Z dxy ( silvaniform clade) D Z dxy ( wallacei clade) D Z dxy ( doris clade) D Z dxy ( erato) Table S4. Correlation Coefficients between all variables in the multiple regression main model r r pi d S D n gene density GC content pi d S D n gene density GC content Table S5. Summary of multiple regression with five explanatory variables for 4D site diversity, calculated for 100 kb windows, excluding H. erato (R 2 = 0.267; adjusted R 2 = 0.264; F 5,1461 = 106.2; p < 2.2e-16). Estimate Std. error SS RSS F 1, 1461 P (>F) Partial R 2 VIF Gene den < 2.2e rr e D n e d S < 2.2e GC cont e (Intercept) rr: recombination rate, D n : number of non-synonymous substitutions, d S : synonymous substitutions per synonymous site, SS: Sum of Squares, RSS: Residual Sum of Squares, VIF: variance inflation factor

8 Table S6. Summary of multiple regression with five explanatory variables for 4D site diversity, calculated for 100 kb windows using a after removal of the upper and lower 10 th percentile for a (R 2 = 0.321; adjusted R 2 = 0.318; F 5,1167 = 110.3; p < 2.2e-16). Estimate Std. error SS RSS F 1, 1167 P (>F) Partial R 2 VIF Gene den < 2.2e rr e a < 2.2e d S o < 2.2e GC cont (Intercept) a: number of adaptive substitutions Table S7. Summary of multiple regression with five explanatory variables for 4D site diversity, calculated for 100 kb windows, including only genes with minimal codon usage bias (R 2 = ; adjusted R 2 = 0.325; F 5,1393 = 135.5; p < 2.2e-16). Estimate Std. error SS RSS F 1, 1393 P (>F) Partial R 2 VIF Gene den < 2.2e rr e D n e d S < 2.2e GC cont (Intercept) Table S8. Summary of multiple regression with five explanatory variables for 4D site diversity, calculated for 100 kb windows, excluding chromosome ends, cut off = 0.9 (R 2 = 0.350; adjusted R 2 = 0.347; F 5,1330 = 143; p < 2.2e-16). Estimate Std. error SS RSS F 1, 1330 P (>F) Partial R 2 VIF Gene den < 2.2e rr e D n d S < 2.2e GC cont (Intercept)

9 Table S9. BLAST hits for genes in putative selective sweep regions For each gene in the two putative sweep intervals, the start and end positions on the Hmel1.1 scaffold and chromosome are given, along with details of the best blast hit in D. melanogaster, where applicable. Hmel1-1 Gene Start on scaffold End on scaffold Start on Chrom End on Chrom E-value hit Predictions/Assertions Chromosome 11 HE HMEL E-053 CG18003 FMN binding;glycolate oxidase activity HMEL CG11964 HMEL015154/5/ Gclc glutamate-cysteine ligase activity HMEL E-144 MED14 RNA polymerase II transcription cofactor activity HMEL E-007 CG15279 HMEL E-166 pbl cation:amino acid symporter activity; neurotransmitter transporter activity; neurotransmitter:sodium symporter activity GTPase activator activity; guanyl-nucleotide exchange factor activity; Rho guanylnucleotide exchange factor activity HMEL E-144 Ugt UDP-glucose:glycoprotein glucosyltransferase activity HMEL E-040 Tango11 HMEL Wnt5 frizzled-2 binding; receptor binding HMEL E-123 Taf6 protein heterodimerization activity HMEL E-167 Nup358 Ran GTPase binding; zinc ion binding HMEL E-008 CG8765 HMEL E-054 SelR peptide-methionine (R)-S-oxide reductase activity; zinc ion binding HMEL E-174 Pak ATP binding; protein serine/threonine kinase activity; receptor signaling protein serine/threonine kinase activity HMEL E-054 GCC185 identical protein binding; protein homodimerization activity HMEL E+000 Ef1alpha 100E GTP binding; GTPase activity; translation elongation factor activity

10 Chromosome 12 HE HMEL E-163 CG4678 metallocarboxypeptidase activity; serine-type carboxypeptidase activity; zinc ion binding HMEL E-033 Sod3 copper ion binding; superoxide dismutase activity; zinc ion binding HMEL E-059 RfC3 ATP binding; DNA binding; nucleoside-triphosphatase activity HMEL E-071 CG6379 methyltransferase activity; nucleic acid binding HMEL E-047 Ref1 mrna binding; nucleic acid binding; nucleotide binding; transcription coactivator activity HMEL E-044 CG7544 methyltransferase activity; nucleic acid binding HMEL E-021 Slbp mrna binding HMEL E-017 Hmg-2 DNA binding HMEL E-016 ebo Ran GTPase binding HMEL E-164 Cap-D2 HMEL E-070 CG5885 HMEL E-086 CG32447 G-protein coupled receptor activity; glutamate receptor activity HMEL E-048 CG12024

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