Details of datasets included on Dryad from: High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment. Ford Antonia; Dasmahapatra Kanchon; Rüber Lukas; Gharbi Karim; Cezard Timothée; Day Julia. Table S2. Data subsets and respective analyses conducted on RAD data,,,,,, ,Description ,Sequences,Sites (n),Variable sites (%),Analyses,Figure /Table A,Full alignment of all mapped; quality filtered sites with sequence data for >1 individual,n=92 (ref. O. niloticus; 7 O. amphimelas; 84 Alcolapia),"28,560,698",1.91,p-distance,SI 11 B,Full alignment of all mapped; quality filtered sites; reduced taxa,n=25 (ref. O. niloticus; 4 O. amphimelas; 20 Alcolapia),"26,135,098",1.71,RAxML; GTRGAMMA model,2A;B C,Full alignment excluding reads not mapped to assigned linkage groups ,n=92 (ref. O. niloticus; 7 O. amphimelas; 84 Alcolapia),"22,249,264",1.82,"LD; f4; FST (EggLib method); Sliding-window FST",4; Table1 SI 2; D,Variable sites (SNPs) across full alignment ,n=92 (ref. O. niloticus; 7 O. amphimelas; 84 Alcolapia),"544,916",100,RAxML; GTRGAMMA model,2C E,SNPs across full alignment; excluding ambiguous bases,n=92 (ref. O. niloticus; 7 O. amphimelas; 84 Alcolapia),"363,983",100,RAxML GTRGAMMA model; corrected for ascertainment bias,SI 3 F,Biallelic unlinked SNPs 12 populations (n=4 per population); no missing data,n=48 (38 A. alcalica; 12 A. grahami; 19 A. latilabris; 15 A. ndalalani),"1,266",100,SNAPP,SI 5 G,Full alignment; de novo assembled; filtered sites,n=91 (7 O. amphimelas; 84 Alcolapia),"436,839",1.33,RAxML; GTRGAMMA model,SI 4A H,SNPs from de novo assembled alignment,n=91 (7 O. amphimelas; 84 Alcolapia),"5,832",100,RAxML; GTRGAMMA model,SI 4B J,SNPs from de novo; no ambiguous bases ,n=91 (7 O. amphimelas; 84 Alcolapia),"1,898",100,RAxML GTRGAMMA model; _ASC model,SI 4C K,Combined mapped and de novo reads; SNPs,n=91 (7 O. amphimelas; 84 Alcolapia),"550,748",100,RAxML GTRGAMMA model,SI 4D L,Combined mapped and de novo reads; SNPs; no ambiguous bases,n=91 (7 O. amphimelas; 84 Alcolapia),"182,909",100,RAxML GTRGAMMA model; _ASC model,SI 4E M,Biallelic SNPs across Alcolapia,n=84 (38 A. alcalica; 12 A. grahami; 19 A. latilabris; 15 A. ndalalani),"246,336",100,STRUCTURE; SplitsTree,2D; SI 6 N,Biallelic unlinked SNPs across Alcolapia ,n=84 (38 A. alcalica; 12 A. grahami; 19 A. latilabris; 15 A. ndalalani),"2,297",100,STRUCTURE ,3; SI 6 P,A. alcalica biallelic SNPs ,n=38 A. alcalica,"173,964",100,STRUCTURE ,SI 8 Q,A. alcalica biallelic SNPs; unlinked,n=38 A. alcalica,"2,222",100,STRUCTURE ,SI 8 R,Biallelic SNPs; max missing data 10%,n=84 (38 A. alcalica; 12 A. grahami; 19 A. latilabris; 15 A. ndalalani),"31,555",100,FST (Arlequin),Table SI 3 S,Biallelic SNPs; MAF >0.1; max. missing data 25%,n=16 (8 A. alcalica; 8 A. grahami),"23,264",100,Bayescan,Table 2 T,Biallelic SNPs; MAF >0.1; max. missing data 25%,n=16 (8 A. alcalica; 8 A. latilabris),"30,841",100,Bayescan,Table 2 U,Biallelic SNPs; MAF >0.1; max. missing data 25%,n=16 (8 A. alcalica; 8 A. ndalalani),"28,026",100,Bayescan,Table 2 V,Biallelic SNPs; MAF >0.1; max. missing data 25%,n=16 (8 A. latilabris; 8 A. ndalalani),"22,946",100,Bayescan,Table 2 W,Biallelic SNPs; MAF >0.1; max. missing data 25%,n=14 (7 A. alcalica; 7 O. amphimelas),"82,474",100,Bayescan,Table 2 X,Biallelic unlinked SNPs; sympatric Alcolapia,n=24 (8 A. alcalica; 8 A. latilabris; 8 A. ndalalani),"2,227",100,STRUCTURE,SI 7