Table S2. Population samples from which the sequenced genomes originated. The number of sequenced individuals for each focal chromosome arm is given.


								Number of genomes for each euchromatic chromosome				
Population ID	Country	Locality	Date	Collector(s)	Latitude (negative=south)	Longitude (negative=west)	Elevation (m)	X	2	3	Comments	
CK	Congo	Kisangani	8/2010	J. Kennis	0.51	25.19	400	2	2	2		
CO	Cameroon	Oku	4/2004	J. Pool	6.25	10.43	2169	10	10	10	"3 additional chromosome 3 extractions exist, but derive from strains that were separately sequenced from haploid embryos"	
EA	Ethiopia	Gambella	12/2011	R. Corbett-Detig	8.25	34.59	525	4	4	4		
EB	Ethiopia	Bonga	12/2011	R. Corbett-Detig	7.26	36.25	1725	5	5	5		
ED	Ethiopia	Dodola	12/2008	J. Pool	6.98	39.18	2492	6	7	6		
EF	Ethiopia	Fiche	12/2011	R. Corbett-Detig	9.81	38.63	3070	5	5	5		
EG	Egypt	Cairo	1/2011	R. Corbett-Detig	30.10	31.32	25	3	2	2	contains heterozygous intervals (masked in consensus sequences)	
EM	Ethiopia	Masha	12/2011	R. Corbett-Detig	7.74	35.48	2260	3	3	3		
ER	Ethiopia	Debre Birhan	12/2011	R. Corbett-Detig	9.68	39.53	2840	5	5	5		
EZ	Ethiopia	Ziway	12/2008	J. Pool	7.93	38.72	1642	5	4	5		
FR	France	Lyon	7/2010	J. Pool	45.77	4.86	175	9	9	9		
GA	Gabon	Franceville	3/2002	B. Ballard & S. Charlat	-1.65	13.60	332	10	9	10	GA191 is missing chromosome 2 data due to heterozygosity	
GU	Guinea	DondŽ	6/2005	B. B. Sow	10.70	-12.25	801	5	5	7		
KM	Kenya	Malindi	7/2002	B. Ballard	-1.43	40.03	78	4	3	1	contains heterozygous intervals (masked in consensus sequences)	
KN	Kenya	Nyahururu	1/2009	J. Pool	0.04	36.36	2303	6	5	6		
KO	Kenya	Molo	1/2009	J. Pool	-0.25	35.73	2506	4	0	4		
KR	Kenya	Marigat	1/2009	J. Pool	0.47	35.98	1062	6	4	6		
KT	Kenya	Thika	1/2009	J. Pool	-1.04	37.08	1531	2	2	2		
NG	Nigeria	Maiduguri	9/2004	D. Gwary & B. Sastawa	11.85	13.16	295	6	6	6		
RAL	United States	Raleigh NC	2003	T. Mackay	35.76	-78.66	91	205	205	205	(sample sizes before heterozygosity and IBD masking)	
RC	Rwanda	Cyangugu	12/2008	J. Pool	-2.29	28.55	1602	2	2	2		
RG	Rwanda	Gikongoro	12/2008	J. Pool	-2.49	28.92	1927	27	27	27		
SB	South Africa	Barkly East	12/2011	J. Pool	-30.97	27.59	1800	5	5	5		
SD	South Africa	Dullstroom	12/2011	J. Pool	-25.42	30.10	2000	5	4	5	SD82 is missing chromosome 2 data due to heterozygosity	
SE	South Africa	Port Edward	12/2011	J. Pool	-31.06	30.22	50	3	3	3		
SF	South Africa	Fouriesburg	12/2011	J. Pool	-28.60	28.05	1800	5	4	5	SF7 is missing chromosome 2 data due to heterozygosity	
SP	South Africa	Phalaborwa	7/2010	R. Corbett-Detig	-23.94	31.14	350	7	7	7		
TZ	Tanzania	Uyole	12/2009	L. Nsemwa	-8.89	33.44	1800	3	3	3		
UG	Uganda	Namulonge	4/2005	J. Ogwang	0.53	32.60	1134	4	4	6		
UK	Uganda	Kisoro	1/2012	R. Corbett-Detig	-1.28	29.69	1925	5	4	5	UK120 is missing chromosome 2 data due to heterozygosity	
UM	Uganda	Masindi	7/2010	J. Pool	1.68	31.72	1170	3	3	3		
ZI	Zambia	Siavonga	7/2010	R. Corbett-Detig	-16.54	28.72	530	196	197	197	ZI382 is missing chromosome X due to heterozygosity	
ZK	Zimbabwe	Lake Kariba	5/1994	T. Mutangadura	-16.52	28.80	619	3	0	2	contains heterozygous intervals (masked in consensus sequences)	
ZL	Zambia	Livingstone	7/2010	R. Corbett-Detig	-17.86	25.86	900	1	1	1		
ZO	Zambia	Solwezi	7/2010	R. Corbett-Detig	-12.18	26.40	1380	2	2	2		
ZS	Zimbabwe	Sengwa	9/1990	R. Ramey	-18.16	28.22	865	4	4	4