. Author manuscript; available in PMC: 2020 Apr 18.

Published in final edited form as: Science. 2019 Oct 18;366(6463):eaax2083. doi: 10.1126/science.aax2083

Table 1. Top candidates for adaptive introgressed CNVs in Melanesians.

P values for selection and introgression scans are calculated from coalescent simulations. Only loci with selection test P values <0.01 are listed. Variant type is determined with respect to the human reference genome. The introgression statistic (f_D) is calculated separately for Neanderthals (NDL) and Denisovans (DNS). mCNV, multi-allelic CNV; DUP, bi-allelic duplication; DEL, bi-allelic deletion. V_ST is a measurement of copy number stratification. See tables S9 and S10 for all candidates.

Locus	Size (bp)	Type	Median CN (Melanesians)	Median CN (all others)	V_ST	P value selection (PBS)	P value, introgression (f_D) archaic ref: NDL	P value, introgression (f_D) archaic ref: DNS	Genes within 30 kbp
chr2:97699365–97907043	207,678	mCNV	48.722	39.147	0.487	<0.001^*	0.009^*	0.001^*	ANKRD36, FAHD2B
chr8:22886278–23003689^†	117,411	DUP	4.054	3.257	0.272	<0.001^*	0.003^*	0.055	TNFRSF10D/10C
chr14:73990658–74053946	63,288	mCNV	3.997	2.968	0.149	<0.001^*	0.008^*	0.013^*	ACOT1/2, HEATR4
chr3:177002637–177011375	8738	DEL	0.984	1.905	0.702	0.001^*	0.363	0.007^*	LINC00501
chr8:22981867–22988907	7040	DEL	1.160	2.163	0.428	0.001^*	<0.001^*	0.001^*	TNFRSF10D/10C
chr16:227l6041^:22783558^††	73,517	DUP	3.935	1.969	0.923	0.004^*	0.179	<0.001^*	MIR548AA2, MIR548D2
chr17:44170850–45157111	986,261	DUP	2.079	3.311	0.172	0.004^*	0.001^*	0.005^*	KANSL1, NSF(chr17q21)
chr1:1568057–1683771	115,714	mCNV	3.291	4.306	0.298	0.007^*	0.053	0.025^*	CDK11A/11B(chr1p36)
chr1:24520349–24523673	3324	DEL	0.790	1.898	0353	0.008^*	0.002^*	<0.001^*	IFNLR1

Significant test result.

^†

Newly identified genes: TNFRSF10D1 and TNFRSF10D2.

^††

Newly identified gene: NPIPB16.