Table 1 Tests for introgression across the α- and β-globin gene clusters, 26 HIF-pathway genes, and genome-wide RAD-Seq analysis of 81,957 SNPs.

From: Adaptive introgression of the beta-globin cluster in two Andean waterfowl

	Dinvestigate		Dtrios					F_ST within species		F_ST between species
Locus	D	_fD	D_trios	ABBA	BABA	z-score	P value	Speckled teal	Yellow-billed pintail	Low vs. Low	High vs. High
ACE	−0.013	−0.012	0.022	13.1	12.6	1.287	0.099	0.079	0.016	0.364	0.380
ANGPT1	0.026	0.014	0.003	25.6	25.4	0.048	0.481	0.059	0.016	0.568	0.585
ANGPT2	0.011	0.003	0.006	5.2	5.2	0.210	0.417	0.060	0.000	0.557	0.622
ARNT	0.178	0.009	0.047	0.1	0.1	0.220	0.413	0.190	−0.018	0.567	0.585
ARNT2	−0.008	0.005	0.004	25.2	25.0	0.266	0.395	0.057	−0.003	0.499	0.501
ARNTL	0.374	0.050	0.292	0.2	0.1	2.333	0.010	0.112	0.128	0.745	0.654
CLOCK	−0.040	−0.003	0.060	0.8	0.7	0.490	0.312	0.134	0.018	0.666	0.773
CUL2	−0.152	−0.010	0.017	1.4	1.4	0.183	0.428	0.082	0.012	0.507	0.554
EGLN1	0.052	0.005	0.023	12.7	12.1	0.186	0.426	0.596*	0.403*	0.589	0.879
EGLN3	−0.128	−0.017	0.086	1.5	1.3	1.334	0.091	0.266	−0.058	0.681	0.698
EPAS1 (HIF2α)	0.064	0.006	0.063	19.1	16.8	0.851	0.197	0.508*	0.444*	0.525	0.865
HIF1A	0.096	0.017	0.015	1.5	1.4	0.115	0.454	0.189	0.193	0.527	0.530
HSP90AA1	0.476	0.009	0.348	0.1	0.0	0.951	0.171	0.182	0.106	0.708	0.705
MTOR	0.093	0.038	0.052	21.4	19.3	0.854	0.197	0.082	0.019	0.476	0.465
NOS1	−0.046	−0.041	0.005	32.6	32.2	0.422	0.336	0.068	0.024	0.302	0.376
NOS2	−0.200	0.127	0.049	2.7	2.4	0.640	0.261	0.042	0.142	0.622	0.569
P4HA1	0.025	0.021	0.016	15.3	14.9	0.887	0.188	0.051	0.005	0.446	0.466
P4HA2	0.081	0.137	0.040	20.2	18.7	2.286	0.011	0.090	−0.012	0.372	0.269
P4HA3	0.075	0.101	0.033	6.8	6.4	0.666	0.253	0.027	0.032	0.252	0.294
PDHA1	−0.303	−1.746	0.051	6.2	5.6	0.854	0.196	0.030	0.039	0.484	0.554
PPARA (α)	0.088	0.014	0.042	1.1	1.0	0.000	1.000	0.179	0.022	0.878	0.883
PPARD (δ)	0.042	0.041	0.013	4.0	3.9	0.408	0.342	0.042	0.017	0.215	0.284
PPARG (γ)	0.000	0.000	0.030	0.2	0.2	0.095	0.462	0.092	−0.018	0.778	0.764
TCEB3	0.037	0.029	0.022	5.6	5.4	0.896	0.185	0.032	−0.017	0.283	0.367
THRB	−0.054	−0.024	0.017	12.4	12.0	1.093	0.137	0.062	0.017	0.485	0.493
VEGF	−0.018	−0.006	0.012	4.5	4.4	0.177	0.430	0.264	0.029	0.469	0.533
*β-globin cluster*	*0.775*	*0.683*	*0.203*	*43.7*	*28.9*	*4.586*	*0.000002*	0.425*	0.363*	*0.163*	*0.277*
α-globin cluster	−0.038	−0.005	0.006	3.4	3.3	0.057	0.477	0.338*	0.003	0.558	0.664
RAD-Seq	0.002	0.001	0.006	581.3	574.0	2.442	0.007	0.062	0.008	0.410	0.473

We used D-statistics (ABBA–BABA) to test if shared polymorphism between non-sister taxa (high-altitude speckled teal and high-altitude yellow-billed pintail) signifies adaptive introgression, or alternatively incomplete lineage sorting (ILS). The null expectation for equal ABBA:BABA proportions under ILS is that D = 0, whereas a significantly positive or negative D corresponds to introgression. Results are derived from 20 jacknife replicates in Dsuite (Malinsky et al. 2021) using the Dinvestigate and Dtrios programs showing the number of SNPs supporting either ABBA or BABA patterns; the averaging Dtrios performs over the 20 replicates results in non-integer ABBA and BABA values. Only the β-globin cluster shown in bold text has a z-score >3.3 standard deviations corresponding to a P value for two-tailed test <0.001, with more ABBA patterns than expected by chance, reflecting introgression between the high-altitude populations. At right is the average pairwise F_ST for each locus, between populations within each species (low- vs. high-altitude) and between each species (low altitude vs. low altitude and high altitude vs. high altitude, respectively). The rows given in italic denote divergently-selected candidate loci with high F_ST outliers marked with asterisks (between populations within species) relative to background F_ST from the genome-wide analysis.

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Table 1 Tests for introgression across the α- and β-globin gene clusters, 26 HIF-pathway genes, and genome-wide RAD-Seq analysis of 81,957 SNPs.

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