ArticleNature genetics2025
A likelihood-based framework for demographic inference from genealogical trees.
Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 20 papers.
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20 citing papers in PubMed.
- ARGscape: a modular, interactive tool for manipulation of spatiotemporal ancestral recombination graphs.Bioinformatics (Oxford, England) · 2026Article
- Recent advances in methods to characterize archaic introgression in modern humans.Genome research · 2026Review
- Likelihoods for a general class of ARGs under the SMC.Genetics · 2026Article
- The promise and challenge of spatial inference with the full ancestral recombination graph under Brownian motion.G3 (Bethesda, Md.) · 2025Article
- Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.Molecular ecology · 2025Article
- Inference of complex demographic history using composite likelihood based on whole-genome genealogies.bioRxiv : the preprint server for biology · 2025Article
- Recent Statistical Innovations in Human Genetics.Annals of human genetics · 2025Review
- Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes.Nature genetics · 2025Article
- A genealogy-based approach for revealing ancestry-specific structures in admixed populations.American journal of human genetics · 2025Article
- Physics-Inspired Single-Particle Tracking Accelerated with Parallelism.bioRxiv : the preprint server for biology · 2025Article
- Evaluating ARG-estimation methods in the context of estimating population-mean polygenic score histories.Genetics · 2025Article
- Likelihoods for a general class of ARGs under the SMC.bioRxiv : the preprint server for biology · 2025Article
- A genealogy-based approach for revealing ancestry-specific structures in admixed populations.bioRxiv : the preprint server for biology · 2025Article
- tskit_arg_visualizer: interactive plotting of ancestral recombination graphs.Bioinformatics advances · 2025Article
- Inference and applications of ancestral recombination graphs.Nature reviews. Genetics · 2025Review
- Constructing ancestral recombination graphs through reinforcement learning.Frontiers in genetics · 2025Article
- Evaluating ARG-estimation methods in the context of estimating population-mean polygenic score histories.bioRxiv : the preprint server for biology · 2024Article
- Tree sequences as a general-purpose tool for population genetic inference.bioRxiv : the preprint server for biology · 2024Article
- Article
- A general and efficient representation of ancestral recombination graphs.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
- Erratum issued
- Update of
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8 authors.
Funding
Abstract
The demographic history of a population underlies patterns of genetic variation and is encoded in the gene-genealogical trees of the sampled haplotypes. Here we propose a demographic inference framework called the genealogical likelihood (gLike). Our method uses a graph-based structure to summarize the relationships among all lineages in a gene-genealogical tree with all possible trajectories of population memberships through time and derives the full likelihood across trees under a parameterized demographic model. We show through simulations and empirical applications that for populations that have experienced multiple admixtures, gLike can accurately estimate dozens of demographic parameters, including ancestral population sizes, admixture timing and admixture proportions, and it outperforms conventional demographic inference methods using the site frequency spectrum. Taken together, our proposed gLike framework harnesses underused genealogical information to offer high sensitivity and accuracy in inferring complex demographies for humans and other species.
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