Table 1.

Heritability analysis of natural selection metrics

		Top 2% of scores (genome wide)		Top 1% of scores (genome wide)		Top 0.5% of scores (genome wide)
Metric	Ref.	Enrichment	2-sided P value	Enrichment	2-sided P value	Enrichment	2-sided P value
Background selection (B statistic)	[29]	1.801	0.001	2.341	9.90×10−4	2.365	0.002
Positive selection (CLR)	[28]	0.408	6.53×10−5	0.173	5.80×10−7	0.259	0.016
Positive selection (CMS)	[88]	0.054	0.001	−0.037	0.006	−0.039	0.007
Positive selection (XP-EEH)	[87]	0.621	0.342	0.383	0.303	0.125	0.268
Positive selection (iHS)	[86]	0.973	0.946	0.980	0.974	1.633	0.557
Neanderthal posterior probability (LA)	[89]	0.807	0.347	0.800	0.462	0.858	0.745

Partitioned LDSR regression results for SNPs thresholded by extreme values (defined as top percentiles versus all other SNPs) of each natural selection metric. All tests have been adjusted for 58 ‘baseline’ annotations, which include categories such as LoF intolerant, recombination coldspot and conserved (Methods). Enrichment values below 1 indicate a depletion of h²_SNP in an annotation category (less contribution than expected for a given number of SNPs). Negative enrichments should be considered zero (no contribution to h²_SNP by these SNPs). Bold values indicate results surviving correction after adjusting for all tests (Bonferroni a = 0.05/18 = 0.0028).