(a) Copadichromis sp. “Virginalis kajose”

	Lake Malombe	Lake Malawi
Population code	LM	CT	CH	NO	NK	MI	SB	NKU
Sample size	21	10	12	11	10	12	11	11
Number haplotypes	7	5	5	6	7	6	3	6
Number polymorphic sites	22	17	6	5	22	15	15	19
Gene diversity	0.810 ± 0.004	0.667 ± 0.027	0.788 ± 0.008	0.727 ± 0.021	0.867 ± 0.011	0.682 ± 0.022	0.473 ± 0.026	0.873 ± 0.005
Average pairwise difference	6.981	3.4000	2.136	1.200	4.867	3.045	2.873	7.673
Nucleotide diversity (average over loci)	0.02161 ± 0.00002	0.01053 ± 0.00004	0.00659 ± 0.00001	0.00370 ± 0.00001	0.01507 ± 0.00005	0.00943 ± 0.00003	0.00889 ± 0.00004	0.02375 ± 0.00003