Table 2. Features of the published admixture graphs (AGs) that support inferences in the original studies and the level of their support in our re-analysis.

The table lists key features whose support we assessed in sets of alternative well-fitting and temporally plausible models generated by findGraphs. Since this assessment had to be performed manually, only in two cases (marked by asterisks) all models fitting better and non-significantly worse than the published one were scrutinized; in other cases only a subset of best-fitting models was examined (see the respective sections in Appendix 2 for details).

Study	Groups/admixture events	Features of the published model supported by all temporally plausible alternative models generated by findGraphs that we scrutinized	Features of the published model lacking universal support among temporally plausible alternative models generated by findGraphs
Bergström et al., 2020	7/3*	Early divergence of domesticated dog lineages (prior to the date of the Karelian dog, 10,900 ya).	Siberian (Baikal), American, and East Mediterranean dog lineages are unadmixed, and the West European (Germany Early Neolithic), East European (Karelia), and dogs of Southeast Asian origin (New Guinea singing dog) are admixed.
Lazaridis et al., 2014	7/4	Present-day Europeans represent a mixture of three ancestral sources related to the following groups: Mal’ta (MA1), West European hunter–gatherers, and early European farmers.	N/A
Shinde et al., 2019	8/3*	(1) Iranian farmer-related ancestry in the Indus Periphery group is not derived from the Hajji Firuz Neolithic or Tepe Hissar Chalcolithic groups. (2)There is Asian-related ancestry in the Indus Periphery group.	N/A
	8/4	(2) There is Asian ancestry in the Indus Periphery group.	(1) Iranian farmer-related ancestry in the Indus Periphery group is not derived from the Hajji Firuz Neolithic or Tepe Hissar Chalcolithic groups.
Librado et al., 2021	10/8 or 9	(2) DOM2 and C-PONT are sister groups (they form a clade). (4) There is gene flow from a deep-branching ghost group to the NEO-ANA group.	(1) NEO-ANA-related admixture is absent in the DOM2 group. (3) There is no gene flow connecting the CWC group and the cluster associated with Yamnaya horses and horses of the later Sintashta culture whose ancestry is maximized in the Western Steppe (DOM2, C-PONT, TURG). (5) Tarpan is a mixture of a CWC-related and a DOM2-related lineage.
Hajdinjak et al., 2021	12/8	(3) The Vestonice16 lineage is a mixture of a Sunghir-related and a BK1653-related lineage.	(1) There are gene flows from the lineage found in the ~45,000- to 43,000-year-old Bacho Kiro Initial Upper Paleolithic (IUP)-associated lineage to the Ust’-Ishim, Tianyuan, and GoyetQ116-1 lineages. (2) The ~35,000-year-old Bacho Kiro Cave individual BK1653 belonged to a population that was related, but not identical, to that of the GoyetQ116-1 individual.
Lipson et al., 2020b	12/11	N/A	(1) A lineage maximized in present-day West African groups (Lemande, Mende, and Yoruba) also contributed some ancestry to the ancient Shum Laka individual and to present-day Biaka and Mbuti. (2) Another ancestry component in Shum Laka is a deep-branching lineage maximized in the rainforest hunter–gatherers Biaka and Mbuti. (3) ‘Super-archaic’ ancestry (i.e., diverging at the modern human/Neanderthal split point or deeper) contributed to Biaka, Mbuti, Shum Laka, Lemande, Mende, and Yoruba. (4) A ghost modern human lineage (or lineages) contributed to Agaw, Mota, Biaka, Mbuti, Shum Laka, Lemande, Mende, and Yoruba.
Wang et al., 2021	12/8	N/A	Admixture from a source related to Andamanese hunter–gatherers is almost universal in East Asians, occurring in the Jomon, Tibetan, Upper Yellow River Late Neolithic, West Liao River Late Neolithic, Taiwan Iron Age, and China Island Early Neolithic (Liangdao) groups.
Sikora et al., 2019 ‘West’	13/6	N/A	The Mal’ta (MA1_ANE) lineage received gene flow from the Caucasus hunter–gatherer (CaucasusHG_LP or CHG) lineage.
Sikora et al., 2019 ‘East’	14/6	(2) European-related ancestry in the Kolyma, USR1, and Clovis lineages is closer to Mal’ta than to Yana.	(1)The Mal’ta (MA1_ANE) and Yana (Yana_UP) lineages received gene flow from a common East Asian-associated source diverging before the ones contributing to the Devil’s Cave (DevilsCave_N), Kolyma (Kolyma_M), USR1 (Alaska_LP), and Clovis (Clovis_LP) lineages. (3)The Devil’s Cave lineage received no European-related gene flows, and Kolyma has less European-related ancestry than ancient Americans (USR1 and Clovis).