Table 1S: Additional Genomes, Accession Numbers and Locations

Table 1S: Additional genomes, accession numbers and locations

Species Accession number Sample localities Drosophila simulans AF 200833.1 Moorea, Tahiti AF 200834.1 Papeete, Tahiti AF 200835.1 Honolulu, Hawaii AF 200836.1 Honolulu, Hawaii AF 200837.1 Noumea, New Caledonia AF 200838.1 Noumea, New Caledonia AF 200839.1 Nanyuki, Kenya AF 200840.1 Watsonville, CA, USA AF 200841.1 Riverside, CA, USA AF 200842.1 Ansirabe, Madagascar AF 200843.1 Joffreville, Madagascar AF 200844.1 Mahe, Seychelles AF 200845.1 St. Pierre, Reunion Is. AF 200847.1 St. Dennis, Reunion Is.

Drosophila melanogaster JQ 686694.1 Bermuda FJ 190106.1 New South Wales, Australia JX 266575.1 Barcelona, Spain FJ 190107.1 Texas, USA FJ 190108.1 Benin, Africa JX 266576.1 Hawaii (USA, Tucson Stock Center). JX 266577.1 Israel FJ 190109.1 Jume, Japan JX 266578.1 Madang, Papua New Guinea FJ 190110.1 Mysore, India AF 200828.1 Roseburg, OR, USA JQ 686698.1 Roseburg, OR, USA JX 266579.1 Puerto Montt, Chile JQ 686696.1 Israel JQ 686697.1 Madeira, Portugal JX 266580.1 Sweden, Europe JQ 686693.1 - FJ 190105.1 - AF 200829.1 Sengwa, Africa

1 Table 2S: Sequence for Drosophila –virilis radiation used in bayesian analyses

Accession number Species COI COII ND2

D. aracataca DQ471599 JF736116 DQ471526

D. bromeliae KF632602 AF478418 KF632702

D. grimshawi GU597459 GU597491 BK006341

D. littoralis JN019910 FJ447340 DQ471458

D. virilise JQ679111 HQ110559 BK006340

D. robusta EU390725 GU597482 AY750082

D. melânica EU390737 EU390748 AY750064

D. hydei KJ463782 AF145888 HQ110576

D. mercatorum HG798344 DQ202028 DQ471460

D. replete DQ471533 KF601933 DQ471464

D. mojavensis DQ383726 AY437280 BK006339

D. mulleri DQ437708 EU555337 DQ202112

D. buzzati KF632603 AF146169 KF632703

D. nannoptera DQ471531 AF183971 KF632708

D. immigrans KJ671605 KF601931 HQ110577

2 Table 3S: Length and A-T content for the A-T rich region of different Drosophilidae species

Species A-T rich region length (bp) References A-T content (%)** D. incompta 733 This study 92 % D. obscura 1,149 Saito et al. 2005 92 % D. madeirensis 936 Brehm et al. 2001 92.7 % D. guanche 953 Brehm et al. 2001 92.9 % D. teissieri 1,090 Monnerot et al. 1990 92.9 % Clary and D. yakuba 1,077 92.9 % Wolstenholme (1987) D. mauritiana 1,090 Tsujino et al. 2002 95.5 % Clary and D. virilis 1,029 90.1 % Wolstenholme (1987) D. albomicans 872 Saito et al. 2005 88.8 % Z. indianus 842 Silva et al. 2009 94.3 % Note: “**” indicates that these values are from Silva et al. (2009).

3 Table 4S: Comparative mitochondrial diversity measures between Drosophila species

Species Gene π (SD) Reference D. buzzatii COI Between 0.00039 ± 0.00028 De Brito et al. 2002 D. pachea COI and 0.008260.007 ± 0.004± 0.00190 Hurtado et al. 2004 D. mettleri COI 0.002 ± 0.001 Hurtado et al. 2004 D. nigrospiracula COI 0.0002 ± 0.000 Hurtado et al. 2004 D. arizonae COI ne Reed et al. 2007 D. mojavensis COI ne Reed et al. 2007 D. virilis COI + COII 0.00185 +- 0.00114 Mirol et al. 2008 D. gouveai COII 0.019 +- 0.002 Moraes et al. 2009 D. borborema COI 0.0024 (± 0.0017) Franco and Manfrin (2013) D. seriema COI 0.0111 (± 0.0059) Franco and Manfrin (2013) D. gouveai COI 0.0107 (± 0.0057) Franco and Manfrin (2013) D. serido COI 0.0070 (± 0.0039) Franco and Manfrin (2013) Abbreviation: π (SD) = nucleotide diversity (standard deviation); ne = non-estimated.