Table 2.
Overview of methods for characterizing local patterns of introgression
| Method | Requires polarized data | Control panel | Target panel | Source panel | Additional requirements | Introgression map |
|---|---|---|---|---|---|---|
| IBDmix | No. | N/A | Phased or unphased genotypes for at least 10 individuals. | Phased or unphased genotypes. | Genotyping error rates for the target and source panels. | Per individual from a single source. |
| Data: Neanderthal introgression maps from Li et al. (2024). | ||||||
| diCal-ADMIX | Yes. | Phased genotypes. | Phased genotypes. | Phased or pseudo-haploid genotypes. | Point estimates of the mutation and recombination rates and the demographic history of the control, target, and source panels. | Per haplotype from a single source. |
| Data: Neanderthal introgression maps from Steinrücken et al. (2018). | ||||||
| ArchaicSeeker2.0 | Yes. | Phased genotypes. | Phased genotypes. | Phased or unphased genotypes (per source of introgression). | Ancestral state sequence, outgroup sequence, recombination map, and a population tree (in Newick format) with branch lengths that includes the control, target, and source panels. | Per haplotype from multiple sources. |
| Protocol: Zhang et al. (2022); Data: Introgression maps from Yuan et al. (2021). | ||||||
| admixfrog | No. | Phased or unphased genotypes for at least one individual. | Phased or unphased genotypes (for high-coverage data) or Binary Alignment Map (for low-coverage data). | Phased or unphased genotypes for at least one individual (per source of introgression). | Panel of phased or unphased genotypes representing the source of contamination, initial number of bases to determine if a read is deaminated, initial sequencing error rate, and initial contamination rate (for low-coverage data). | Per individual from multiple sources. |
| Data: Neanderthal introgression maps from Iasi et al. (2024). | ||||||
| CRF | Yes. | Phased genotypes for modern humans and unphased genotypes for archaic humans. | Phased genotypes. | Unphased genotypes. | Recombination map and demographic history of the control, target, and source panels to simulate training data for parameter estimation. | Per haplotype from multiple sources. |
| Data: Introgression maps from Sankararaman et al. (2016). | ||||||
| IntroUNET | No. | Phased or unphased genotypes (only when the source of introgression is unknown). | Phased or unphased genotypes. | Phased or unphased genotypes. | Demographic history of the target and source panels or the demographic history of the control, target, and source panels (only when the source of introgression is unknown). | Per haplotype (for phased data) or per individual (for unphased data) from a single source. |
| N/A | ||||||
| SPrime | No. | Phased or unphased genotypes for at least 15 individuals. | Phased or unphased genotypes for at least 15 individuals. | Phased or unphased genotypes (only for computing matching rates). | Recombination map. | Per population from an unknown source. |
| Protocol: Zhou and Browning (2021); Data: Introgression maps from Browning et al. (2018). | ||||||
| sstar | Yes. | Phased or unphased genotypes for at least 10 individuals. | Phased or unphased genotypes for at least 10 individuals. | Phased or unphased genotypes (optional). | Point estimate of the recombination rate or recombination map and demographic history of the control, target, and source panels. | Per individual from an unknown source or multiple sources (per optional source panel). |
| N/A | ||||||
| ArchIE | Yes. | Phased genotypes for at least 50 individuals. | Phased genotypes for at least 50 individuals. | N/A | Demographic history of the control, target, and source panels. | Per haplotype from an unknown source. |
| Data: Introgression maps from Durvasula and Sankararaman (2020). | ||||||
| hmmix | Yes. | Phased or unphased genotypes. | Phased or unphased genotypes. | Phased or unphased genotypes (optional). | Point estimate of the mutation rate or mutation map, point estimate of the recombination rate, and estimates of: split times between the control and target panels and the control and source panels, time of the gene flow event, and admixture proportion. | Per haplotype (for phased data) or per individual (for unphased data) from an unknown source. |
| Data: Introgression maps from Skov et al. (2018). | ||||||
| DAIseg | Yes. | Phased or unphased genotypes. | Phased or unphased genotypes. | Phased or unphased genotypes per source (optional). | Point estimate of the mutation rate or mutation map, point estimate of the recombination rate, and estimates of: split times between the control and target panels and the control and source panels, time of the gene flow events, and associated admixture proportion per gene flow event. | Per haplotype (for phased data) or per individual (for unphased data) from multiple unknown sources. |
| Data: Introgression maps from Planche et al. (2025). | ||||||
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For each method, we provide a link to its documentation, note whether polarizing ancestral states is required, and describe the data requirements for a control panel (assumed to lack any genetic contributions from the source panel), a target panel (the putative recipient), and a source panel (the putative donor). We also provide any additional data requirements, the resolution of the inferred introgression maps (e.g., population-, individual-, or haplotype-level, and the number of possible sources), and links to publicly available resources (located in the second row per method) including published protocols and data sets. Note that the methods appear in the order in which they are referenced in the text, and all associated URL links are provided in the “Data sets” section.
