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

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 (N_e): GONE2, for inferring recent changes in N_e when a genetic map is available, and currentNe2, which estimates contemporary N_e 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 F_ST 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 N_e underestimation.