Table 1. Published graphs in the context of automatically found graphs.
We compared graphs from eight publications to alternative graphs inferred on the same or very similar data (see Supplementary file 1 for details).
| Publication | Figure in the original publication | Groups (populations) | Admixture events | SNPs used | Publ. model: worst residual, SE | Distinct alternative topologies found | Significantly better fitting topologies, % | Non-significantly better fitting topologies, % | Non-significantly worse fitting topologies, % | Significantly worse fitting topologies, % | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Bergström et al., 2020 | 1e | 7 | 3 | 312,282 | 2.1 | 221 | 0.5 | 2.3 | 16.7 | 80.5 | |
| Lazaridis et al., 2014 | 3 | 7 | 4 | 642,247 | 2.2 | 306 | 1.0 | 12.1 | 80.7 | 6.2 | |
| Shinde et al., 2019 | 3 | 8* | 3 | 2,49,009 | 2.6 | 143 | 0.0 | 2.8 | 3.5 | 93.7 | |
| Librado et al., 2021 | 3b | 10* | 3 | 1,767,419 | 23.9 | 324 | 6.8 | 15.7 | 24.1 | 53.4 | |
| Ext 5d | 4 | 14.1 | 535 | 0.0 | 0.0 | 4.5 | 95.5 | ||||
| Ext 5e | 5 | 6.9 | 784 | 0.0 | 0.3 | 28.4 | 71.3 | ||||
| Hajdinjak et al., 2021 | 2d | 12 | 8 | 263,698 | 4.8 | 1988 | 15.7 | 55.7 | 6.6 | 22.0 | |
| Lipson et al., 2020b | Ext 4 | 12 | 11† | 211,738 | 2.3 | 2000 | 0.0 | 11.9 | 77.1 | 10.4 | |
| Wang et al., 2021 | Ext 6 | 12 | 8 | 203,753 | 3.8 | 1778 | 12.6 | 84.3 | 3.1 | 0.0 | |
| Sikora et al., 2019 | 3f (left) | 13 | 6† | 344,903 | 3.8 | 894 | 0.3 | 17.1 | 34.6 | 48.0 | |
| 3f (right) | 14 | 6† | 613,509 | 4.2 | 2785 | 0.1 | 0.9 | 9.8 | 89.2 |
Publication: Last name of the first author and year of the relevant publication.
Figure in the original publication: Figure number in the original paper where the AG is presented.
Groups (populations): The number of populations in each graph.
Admixture events: The number of admixture events in each graph.
SNPs used: The number of single-nucleotide polymorphisms (SNPs; with no missing data at the group level) used for fitting the AGs. For all case studies, we tested the original data (SNPs, population composition, and the published graph topology) and obtained model fits very similar to the published ones. However, for the purpose of efficient topology search, we in some cases adjusted settings for f3-statistic calculation, population composition, or graph complexity as noted in the footnotes, in Supplementary file 1, and discussed in the text.
Publ. model: Worst residual, SE: The worst f-statistic residual of the published graph fitted to the SNP set shown in the ‘SNPs used’ column, measured in standard errors (SE).
Distinct alternative topologies found: The number of distinct newly found topologies differing from the published one.
Significantly better fitting topologies, %: The percentage of distinct alternative topologies that fit significantly better than the published graph according to the bootstrap model comparison test (two-tailed empirical p-value <0.05). If the number of distinct topologies was very large, a representative sample of models (1/20 to 1/3 of models evenly distributed along the log-likelihood spectrum) was compared to the published one instead, and the percentages in this and following columns were calculated on this sample.
Non-significantly better fitting topologies, %: The percentage of distinct topologies that fit non-significantly (nominally) better than the published graph according to the bootstrap model comparison test (two-tailed empirical p-value ≥0.05).
Non-significantly worse fitting topologies, %: The percentage of distinct topologies that fit non-significantly (nominally) worse than the published graph according to the bootstrap model comparison test (two-tailed empirical p-value ≥0.05).
Significantly worse fitting topologies, %: The percentage of distinct topologies that fit significantly worse than the published graph according to the bootstrap model comparison test (two-tailed empirical p-value <0.05).
The population composition was modified, see Supplementary file 1 and the text.
Certain gene flows were removed from the published model for simplicity, see Supplementary file 1 and the text.