What is an ancestral recombination graph?

Written by: Dylan Highland
Reviewed by: Keaka Farleigh, Ph.D.
Date: September, 15th, 2026.
Date last modified: September, 16th, 2026

Purpose

To help you understand what an ancestral recombination graph (ARG) is and what it is used for.

What is an ancestral recombination graph?

An ancestral recombination graph (ARG) is a powerful phylogenetic framework that is used in population genomics studies to represent the evolutionary and genealogical history of a given set of genomic data (Brandt et al. 2024). While traditional phylogenetic approaches often consider the genome a single entity when inferring relationships between groups, ARGs account for genetic recombination by allowing different genomic regions to have distinct genealogical histories. This property of ARGs allows us to disentangle intricate evolutionary forces such as selection and gene flow that occur across the genome. Specifically, an ARG represents the relationships among sampled haplotypes across the genome as a series of local genealogies connected by recombination events. These genealogies describe how haplotypes coalesce through time and we can use them to estimate the time to the most recent common ancestor between lineages (TMRCA_B), as well as the time to the most recent common ancestor within a lineage (TMRCA_W).

ARGs have a variety of applications in population genetics, including characterizing patterns of ancestry and genetic variation across the genome. For example, ARGs can be used to investigate the distribution of mutations and genetic variants, signatures of natural selection, and patterns of introgression between populations or species (Lewanski et al. 2024). By retaining information about local genealogies and their relationships across the genome, ARGs can provide insights into evolutionary processes that may be difficult to distinguish using individual gene trees or summary statistics alone.

Using ARGs to identify signatures of natural selection and introgression

Because forces of natural selection cause shifts in allele frequencies over time, we can use ARGs to estimate coalescence times of sampled haplotypes, and further, the mode of selection that operates there. For example, under positive selection a given allele is swept to fixation (assuming a complete sweep) within a population; therefore, we would expect to see more recent coalescence times than predicted under neutrality (Hejase et al. 2020). Conversely, an allele that is maintained by balancing selection at intermediate frequencies for long stretches of time would appear to have older coalesence times than a neutral site (Rasmussen et al. 2014). Additionally, ARGs can also be used to detect introgression events between species, as this process introduces alleles into the recipient population post divergence, reducing the coalescence time between lineages, TMRCA_B (Hubisz et al. 2020).

Using ARGHelpR to identify signatures of natural selection and introgression

You can use ARGHelpR to signatures of natural selection and introgression. Please see this article for a tutorial and explaination of how ARGHelpR works.

Literature Cited

Brandt, D. Y., Huber, C. D., Chiang, C. W., & Ortega-Del Vecchyo, D. (2024). The promise of inferring the past using the ancestral recombination graph. Genome biology and evolution, 16(2), evae005.

Hejase, H. A., Salman-Minkov, A., Campagna, L., Hubisz, M. J., Lovette, I. J., Gronau, I., & Siepel, A. (2020). Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. Proceedings of the National Academy of Sciences, 117(48), 30554-30565.

Hubisz, M. J., Williams, A. L., & Siepel, A. (2020). Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLoS genetics, 16(8), e1008895.

Lewanski, A. L., Grundler, M. C., & Bradburd, G. S. (2024). The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics. Plos Genetics, 20(1), e1011110.

Rasmussen, M. D., Hubisz, M. J., Gronau, I., & Siepel, A. (2014). Genome-wide inference of ancestral recombination graphs. PLoS genetics, 10(5), e1004342.