Accounting for population structure and data quality in demographic inference with linkage disequilibrium methods

Enrique Santiago (), Carlos Köpke and Armando Caballero
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Enrique Santiago: Facultad de Biología, Universidad de Oviedo
Carlos Köpke: Plasma Labs Enterprises SL
Armando Caballero: Universidade de Vigo, Facultade de Bioloxía

Nature Communications, 2025, vol. 16, issue 1, 1-10

Abstract: Abstract Linkage disequilibrium methods for demographic inference usually rely on panmictic population models. However, the structure of natural populations is generally complex and the quality of the genotyping data is often suboptimal. We present two software tools that implement theoretical developments to estimate the effective population size (Ne): GONE2, for inferring recent changes in Ne when a genetic map is available, and currentNe2, which estimates contemporary Ne even in the absence of genetic maps. These tools operate on SNP data from a single sample of individuals, and provide insights into population structure, including the FST index, migration rate, and subpopulation number. GONE2 can also handle haploid data, genotyping errors, and low sequencing depth data. Results from simulations and laboratory populations of Drosophila melanogaster validated the tools in different demographic scenarios, and analysis were extended to populations of several species. These results highlight that ignoring population subdivision often leads to Ne underestimation.

Date: 2025
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DOI: 10.1038/s41467-025-61378-w

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