ArticleMolecular biology and evolution2020
Inferring the Demographic History of Inbred Species from Genome-Wide SNP Frequency Data.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Evolutionary Consequences of Repeated Loss of Distyly in Linum.Genome biology and evolution · 2026Article
- Gene-level complexity explains genome-wide variation in the distribution of fitness effects.Molecular biology and evolution · 2026Article
- CoalMiner: a coalescent model generator forbioRxiv : the preprint server for biology · 2026Article
- Population genomic signatures of founding events in autonomously self-fertilizing plants: a test with Impatiens capensis.The New phytologist · 2026Article
- Estimating the Reduction in Genetic Diversity from Background Selection under Non-equilibrium Demography and Partial Selfing.Molecular biology and evolution · 2026Article
- Genetic rescue of Florida panthers reduced homozygosity but did not swamp ancestral genotypes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Population Genomics of Giant Mice from the Faroe Islands: Hybridization, Colonization, and a Novel Challenge to Identifying Genomic Targets of Selection.Genome biology and evolution · 2025Article
- Quantifying the Evolution of SNPs That Affect RNA Secondary Structure in Arabidopsis thaliana Genes.Molecular biology and evolution · 2025Article
- Modeling Biases from Low-Pass Genome Sequencing to Enable Accurate Population Genetic Inferences.Molecular biology and evolution · 2025Article
- Whole Genomes Inform Genetic Rescue Strategy for Montane Red Foxes in North America.Molecular biology and evolution · 2024Article
- Modeling biases from low-pass genome sequencing to enable accurate population genetic inferences.bioRxiv : the preprint server for biology · 2024Article
- Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum.Molecular biology and evolution · 2024Article
- The genomic footprint of whaling and isolation in fin whale populations.Nature communications · 2023Article
- Demographic history inference and the polyploid continuum.Genetics · 2023Article
- The meaning of wild: Genetic and adaptive consequences from large-scale releases of domestic mallards.Communications biology · 2023Article
- Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations.eLife · 2023Article
- dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra.bioRxiv : the preprint server for biology · 2023Article
- Review
- Review
- Demographic modelling helps track the rapid and recent divergence of a conifer species pair from Central Mexico.Molecular ecology · 2022Article
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Authors and funding
3 authors.
Funding
Abstract
Demographic inference using the site frequency spectrum (SFS) is a common way to understand historical events affecting genetic variation. However, most methods for estimating demography from the SFS assume random mating within populations, precluding these types of analyses in inbred populations. To address this issue, we developed a model for the expected SFS that includes inbreeding by parameterizing individual genotypes using beta-binomial distributions. We then take the convolution of these genotype probabilities to calculate the expected frequency of biallelic variants in the population. Using simulations, we evaluated the model's ability to coestimate demography and inbreeding using one- and two-population models across a range of inbreeding levels. We also applied our method to two empirical examples, American pumas (Puma concolor) and domesticated cabbage (Brassica oleracea var. capitata), inferring models both with and without inbreeding to compare parameter estimates and model fit. Our simulations showed that we are able to accurately coestimate demographic parameters and inbreeding even for highly inbred populations (F = 0.9). In contrast, failing to include inbreeding generally resulted in inaccurate parameter estimates in simulated data and led to poor model fit in our empirical analyses. These results show that inbreeding can have a strong effect on demographic inference, a pattern that was especially noticeable for parameters involving changes in population size. Given the importance of these estimates for informing practices in conservation, agriculture, and elsewhere, our method provides an important advancement for accurately estimating the demographic histories of these species.
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