Table 1.

Summary of sample information. Coverage denotes the mean depth of genomic coverage and chosen coverage range (in square brackets) of sites analyzed in each population. Mapped sites: Sites covered by at least one read. Deviating sites are biallelic sites (minor allele frequency > 0.05) with read numbers for the two parental alleles deviating significantly from 1 : 1 after Benjamini–Hochberg procedure (FDR = 0.05). Sites with more than two alleles are not used in our analysis.

Samples	Mapped sites	Coverage (X)	Biallelic sites	Deviating sites
Alexandrina	168,224,903	98 [40–200]	1,540,667	288
Coleridge	166,329,006	84 [20–150]	1,491,775	252
Hawea	165,334,107	51 [20–120]	1,416,048	35
Hayes	168,826,070	139 [50–250]	1,538,123	667
Johnson	168,204,869	125 [50–250]	1,523,441	572
Ohau	168,392,915	102 [50–200]	1,539,681	340
Pukaki	168,109,981	94 [50–200]	1,536,485	238
Sullivan’s Dam	167,880,110	88 [50–200]	1,525,683	224
Moke	164,531,082	43 [20–100]	1,509,765	41
Tekapo	166,918,220	78 [30–150]	1,494,053	175
Von	166,794,759	82 [30–150]	1,488,926	196
Wakatipu	167,805,336	107 [50–200]	1,513,257	411
Wanaka	164,530,961	42 [20–100]	1,370,378	14
Kapoai	175,278,062	48[20–100]	2,059,905	147