ArticleG3 (Bethesda, Md.)2017
Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories.
Article in G3 (Bethesda, Md.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
What it found
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Who cites it
44 citing papers in PubMed.
- Inferring the demographic history of Chinese and Indian rhesus macaque (Macaca mulatta) populations from PacBio HiFi long-read sequencing data.Molecular biology and evolution · 2026Article
- Combining Population Genomics With Ancient DNA to Understand Island Colonisation History of the Madagascar Turtle Dove.Molecular ecology · 2026Article
- A Dominant Founder Lineage Has Possible Fitness Costs for the Endangered Mexican Grey Wolf.Molecular ecology · 2026Article
- GHIST 2024: The First Genomic History Inference Strategies Tournament.Molecular biology and evolution · 2025Article
- Accelerated Bayesian inference of population size history from recombining sequence data.Nature genetics · 2025Article
- Estimating Recent and Historical Effective Population Size of Marine and Freshwater Sticklebacks.Molecular ecology · 2025Article
- Article
- Population History Across Timescales in an Urban Archipelago.Genome biology and evolution · 2025Article
- Demographic History, Genetic Load, and the Efficacy of Selection in the Globally Invasive Mosquito Aedes aegypti.Genome biology and evolution · 2025Article
- Domestication history and genetic changes for the newly evolved flower color in the ornamental plantHorticulture research · 2025Article
- Ignoring population structure in hominin evolutionary models can lead to the inference of spurious admixture events.Nature ecology & evolution · 2025Article
- Population history across timescales in an urban archipelago.bioRxiv : the preprint server for biology · 2025Article
- Inferring the Demographic History of Aye-Ayes (Daubentonia madagascariensis) from High-Quality, Whole-Genome, Population-Level Data.Genome biology and evolution · 2025Article
- Inferring the demographic history of aye-ayes (bioRxiv : the preprint server for biology · 2024Article
- Genomic divergence and mutation load in thePlant diversity · 2024Article
- Genetic load and viability of a future restored northern white rhino population.Evolutionary applications · 2024Article
- Past volcanic activity predisposes an endemic threatened seabird to negative anthropogenic impacts.Scientific reports · 2024Article
- Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations.eLife · 2023Article
- Article
- Developing an evolutionary baseline model for humans: jointly inferring purifying selection with population history.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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3 authors.
Funding
Abstract
Inference of demographic history from genetic data is a primary goal of population genetics of model and nonmodel organisms. Whole genome-based approaches such as the pairwise/multiple sequentially Markovian coalescent methods use genomic data from one to four individuals to infer the demographic history of an entire population, while site frequency spectrum (SFS)-based methods use the distribution of allele frequencies in a sample to reconstruct the same historical events. Although both methods are extensively used in empirical studies and perform well on data simulated under simple models, there have been only limited comparisons of them in more complex and realistic settings. Here we use published demographic models based on data from three human populations (Yoruba, descendants of northwest-Europeans, and Han Chinese) as an empirical test case to study the behavior of both inference procedures. We find that several of the demographic histories inferred by the whole genome-based methods do not predict the genome-wide distribution of heterozygosity, nor do they predict the empirical SFS. However, using simulated data, we also find that the whole genome methods can reconstruct the complex demographic models inferred by SFS-based methods, suggesting that the discordant patterns of genetic variation are not attributable to a lack of statistical power, but may reflect unmodeled complexities in the underlying demography. More generally, our findings indicate that demographic inference from a small number of genomes, routine in genomic studies of nonmodel organisms, should be interpreted cautiously, as these models cannot recapitulate other summaries of the data.
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