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Human Ancestries Simulation and Inference: a Review of Ancestral Recombination Graph Samplers

Patrick Fournier, Fabrice Larribe

TL;DR

This review comprehensively catalogs ARG sampling software across three decades, analyzing 32 samplers on the axes of performance, usability, and biological realism. It highlights a spectrum from exact, model-based samplers like ms and ARGweaver to fast, heuristic inference tools such as Relate, tsinfer, and Threads, emphasizing trade-offs between realism and scalability. A consistent pattern is the selective exclusion of certain event types (notably type B coalescences and type 2 recombinations) to boost speed, particularly in inference-focused tools. The authors emphasize msprime's impact as a scalable, Python-friendly backbone and advocate for continued development toward fast, user-friendly, and interoperable ARG software, with an eye toward broader access and replicability in population genetics research.

Abstract

There is little debate about the importance of the ancestral recombination graph in population genetics. An important theoretical tool, the main obstacle to its widespread usage is the computational cost required to match the ever-increasing scale of the data being analyzed. Many of these difficulties have been overcome in the past two decades, which have consequently seen the development of increasingly sophisticated ARG simulation and inference software. Nonetheless, challenges remain, especially in the area of ancestry inference. This paper is a comprehensive review of ARG samplers that have emerged in the past three decades to meet the need for scalable and flexible ancestry simulation and inference solutions. It specifically focuses on their performance, usability, and the biological realism of the underlying algorithm, and aims primarily to provide a technical overview of the field for researchers seeking to write their own coalescent-with-recombination sampler. As a complement to this article, we have compiled links to software, source code and documentation and made them available at https://www.patrickfournier.ca/arg-samplers-review/graph.

Human Ancestries Simulation and Inference: a Review of Ancestral Recombination Graph Samplers

TL;DR

This review comprehensively catalogs ARG sampling software across three decades, analyzing 32 samplers on the axes of performance, usability, and biological realism. It highlights a spectrum from exact, model-based samplers like ms and ARGweaver to fast, heuristic inference tools such as Relate, tsinfer, and Threads, emphasizing trade-offs between realism and scalability. A consistent pattern is the selective exclusion of certain event types (notably type B coalescences and type 2 recombinations) to boost speed, particularly in inference-focused tools. The authors emphasize msprime's impact as a scalable, Python-friendly backbone and advocate for continued development toward fast, user-friendly, and interoperable ARG software, with an eye toward broader access and replicability in population genetics research.

Abstract

There is little debate about the importance of the ancestral recombination graph in population genetics. An important theoretical tool, the main obstacle to its widespread usage is the computational cost required to match the ever-increasing scale of the data being analyzed. Many of these difficulties have been overcome in the past two decades, which have consequently seen the development of increasingly sophisticated ARG simulation and inference software. Nonetheless, challenges remain, especially in the area of ancestry inference. This paper is a comprehensive review of ARG samplers that have emerged in the past three decades to meet the need for scalable and flexible ancestry simulation and inference solutions. It specifically focuses on their performance, usability, and the biological realism of the underlying algorithm, and aims primarily to provide a technical overview of the field for researchers seeking to write their own coalescent-with-recombination sampler. As a complement to this article, we have compiled links to software, source code and documentation and made them available at https://www.patrickfournier.ca/arg-samplers-review/graph.
Paper Structure (58 sections, 1 equation, 2 figures, 1 table)

This paper contains 58 sections, 1 equation, 2 figures, 1 table.

Table of Contents

  1. Introduction
  2. Vocabulary
  3. ARG vs Coalescent-With-Recombination
  4. Location vs Position
  5. Recombination, Chromosomal Crossover and Gene Conversion
  6. Simulation vs. Inference
  7. Typology
  8. Model vs Heuristic
  9. Sampled Events
  10. Coalescence events
  11. Recombination events
  12. Inferred vs Simulated
  13. Programming Language
  14. Interface
  15. Review of Samplers
  16. ...and 43 more sections

Figures (2)

  • Figure 1: Examples of coalescence events.
  • Figure 2: Examples of recombination events.