TABLE 1.

Sample details and summary statistics for the 55,267 ddRAD SNPs for each sample organized and summarized by watershed

	Geographic region (admixture zone)	N	Pi	H O	H E	P LD	P HWD	F IS
Albert Nile
01-DUK†-NW	Northwest	20	0.177	0.207	0.172	0.200	0.121	−0.1691,2,3
02-ORB†-NW	Northwest	12	0.175	0.163	0.167	0.186	0.037	0.0811,2,3
		32	0.179	0.189	0.176	0.192	0.117	−0.0501,2,3
Achwa River
03-NGO	Northwest	12	0.169	0.139	0.162	0.176	0.093	0.2061,2,3
04-BOL	Northwest/Northeast (“b”)	20	0.162	0.180	0.158	0.174	0.051	−0.1041,2,3
05-CHU	Northwest/Northeast (“b”)	13	0.145	0.133	0.139	0.140	0.042	0.0951,2,3
		45	0.162	0.155	0.160	0.138	0.141	0.0551,2,3
Okole River
06-ACA	Northwest/Northeast (“b”)	18	0.163	0.175	0.158	0.167	0.053	−0.0711,2,3
07-APU	Northwest/Northeast (“b”)	10	0.170	0.190	0.161	0.199	0.026	−0.1151,2,3
08-OCA	Northwest/Northeast (“b”)	20	0.163	0.172	0.158	0.159	0.047	−0.0521,2,3
09-UWA	Northwest/West (“a”)	15	0.185	0.153	0.178	0.222	0.057	0.1901,2,3
		63	0.172	0.171	0.170	0.158	0.178	0.0141,2,3
Lake Kyoga
10-OCU†-NE	Northeast	20	0.146	0.148	0.142	0.132	0.048	0.000
11-OT†-NE	Northeast	14	0.143	0.142	0.137	0.121	0.024	0.0091,2,3
12-BN	Northeast/South (“d”)	12	0.161	0.154	0.154	0.144	0.040	0.0591,2,3
		46	0.156	0.148	0.155	0.130	0.103	0.0671,2,3
Lake Albert
13-MF†-w	West	10	0.155	0.147	0.147	0.185	0.021	0.0631,2,3
14-MS†-w	West	11	0.160	0.129	0.153	0.134	0.085	0.2301,2,3
		21	0.165	0.137	0.160	0.164	0.120	0.1861,2,3
Kafu River
15-KAF	West/South (“c”)	20	0.158	0.129	0.154	0.114	0.117	0.2121,2,3
Lake Victoria
16-JN	West/South (“c”)	5	0.108	0.106	0.096	0.056	0.004	0.0311,2,3
17-NB	Northeast/South (“d”)	5	0.100	0.101	0.089	0.048	0.004	0.003
18-WAM†-s	South	14	0.132	0.137	0.127	0.074	0.020	−0.0351,2,3
		24	0.134	0.122	0.131	0.087	0.043	0.1011,2,3

Geographic region of origin and assignment to admixture zones “a”–“d” if applicable (Beadell et al., 2010; Echodu et al., 2013; Opiro et al., 2017), sample size (N) and statistics from stacks v.1.34 software (Catchen et al., 2013) including sample-wide nucleotide diversity in the 55,267 representative SNPs (Pi; one SNP per ddRAD fragment), sample-wide observed heterozygosity (H_O), and sample-wide expected heterozygosity (H_E), statistics from plink version 1.9 (Purcell et al., 2007) including the proportion of locus pairs in linkage disequilibrium in this sample (P_LD) and the proportion of loci in Hardy–Weinberg disequilibrium in this sample (P_HWD), and sample-wide inbreeding fixation index (F_IS) calculated in the “hierFSTAT” R package (Goudet and Jombart, 2015). F_IS values are marked with ¹ if significantly different from zero with p < 0.02 based on 1,000 bootstrap replicates, with ^1,2 if p < 0.02 after Benjamini–Hochberg correction for multiple testing, and with ^1,2,3 if p < 0.02 after Bonferroni correction for multiple testing (Supporting Information Table S4). Samples that were used to represent the four pure genetic backgrounds are marked † followed by the abbreviation of the genetic cluster it represents (northwest: NW, northeast: NE, west: W, south: S).