Can genomic analysis actually estimate past population size? DOI Creative Commons
Jaya Bansal, Richard A. Nichols

Trends in Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Genomic data can be used to reconstruct population size over thousands of generations, using a new class algorithms [sequentially Markovian coalescent (SMC) methods]. These analyses often show recent decline in Ne (effective size), which at face value implies conservation or demographic crisis: crash and loss genetic diversity. This interpretation is frequently mistaken. Here we outline how SMC methods work, why they generate this misleading signal, suggest simple approaches for exploiting the rich information produced by these algorithms. In most species, genomic patterns reflect major changes species' range subdivision tens hundreds years. Consequently, collaboration between geneticists, palaeoecologists, palaeoclimatologists, geologists crucial evaluating outputs

Language: Английский

Likelihoods for a general class of ARGs under the SMC DOI Creative Commons
Gertjan Bisschop, Jerome Kelleher, Peter L. Ralph

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 27, 2025

Ancestral recombination graphs (ARGs) are the focus of much ongoing research interest. Recent progress in inference has made ARG-based approaches feasible across range applications, and many new methods using inferred ARGs as input have appeared. This on long-standing problem ARG proceeded two distinct directions. First, Bayesian under Sequentially Markov Coalescent (SMC), is now practical for tens-to-hundreds samples. Second, approximate models heuristics can scale to sample sizes three orders magnitude larger. Although these heuristic reasonably accurate metrics, one significant drawback that they estimate do not topological properties required compute a likelihood such SMC present-day formulations. In particular, typically precise details about events, which currently likelihood. this paper we present backwards-time formulation derive straightforward definition general class model. We show does require events be estimated, robust presence polytomies. discuss possibilities opens.

Language: Английский

Citations

0
Can genomic analysis actually estimate past population size? DOI Creative Commons
Jaya Bansal, Richard A. Nichols

Trends in Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Genomic data can be used to reconstruct population size over thousands of generations, using a new class algorithms [sequentially Markovian coalescent (SMC) methods]. These analyses often show recent decline in Ne (effective size), which at face value implies conservation or demographic crisis: crash and loss genetic diversity. This interpretation is frequently mistaken. Here we outline how SMC methods work, why they generate this misleading signal, suggest simple approaches for exploiting the rich information produced by these algorithms. In most species, genomic patterns reflect major changes species' range subdivision tens hundreds years. Consequently, collaboration between geneticists, palaeoecologists, palaeoclimatologists, geologists crucial evaluating outputs

Language: Английский

Citations

0