ArticleMolecular ecology2014
ABC inference of multi-population divergence with admixture from unphased population genomic data.
Article in Molecular ecology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 62 citations in OpenAlex.
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- Summary statistics and approximate bayesian computation are comparable to convolutional neural networks for inferring times to fixation.bioRxiv : the preprint server for biology · 2026Article
- Genetic signatures of lineage fusion closely resemble population decline.Ecology and evolution · 2023Article
- The combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability.Nature communications · 2022Article
- The Evolution of Comparative Phylogeography: Putting the Geography (and More) into Comparative Population Genomics.Genome biology and evolution · 2022Review
- Genomic insights into historical population dynamics, local adaptation, and climate change vulnerability of the East Asian Tertiary relictEvolutionary applications · 2020Article
- Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Ecology and evolution · 2020Article
- Twin introductions by independent invader mussel lineages are both associated with recent admixture with a native congener in Australia.Evolutionary applications · 2020Article
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- Coalescent models characterize sources and demographic history of recent round goby colonization of Great Lakes and inland waters.Evolutionary applications · 2019Article
- The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.PLoS genetics · 2018Article
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- Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies.Current zoology · 2016Article
- A genomic perspective on hybridization and speciation.Molecular ecology · 2016Review
- The aggregate site frequency spectrum for comparative population genomic inference.Molecular ecology · 2015Article
- Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data.Systematic biology · 2015Article
- Reconstructing Past Admixture Processes from Local Genomic Ancestry Using Wavelet Transformation.Genetics · 2015Article
- Population genomics reveals seahorses (Hippocampus erectus) of the western mid-Atlantic coast to be residents rather than vagrants.PloS one · 2015Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rapidly developing sequencing technologies and declining costs have made it possible to collect genome-scale data from population-level samples in nonmodel systems. Inferential tools for historical demography given these data sets are, at present, underdeveloped. In particular, approximate Bayesian computation (ABC) has yet to be widely embraced by researchers generating these data. Here, we demonstrate the promise of ABC for analysis of the large data sets that are now attainable from nonmodel taxa through current genomic sequencing technologies. We develop and test an ABC framework for model selection and parameter estimation, given histories of three-population divergence with admixture. We then explore different sampling regimes to illustrate how sampling more loci, longer loci or more individuals affects the quality of model selection and parameter estimation in this ABC framework. Our results show that inferences improved substantially with increases in the number and/or length of sequenced loci, while less benefit was gained by sampling large numbers of individuals. Optimal sampling strategies given our inferential models included at least 2000 loci, each approximately 2 kb in length, sampled from five diploid individuals per population, although specific strategies are model and question dependent. We tested our ABC approach through simulation-based cross-validations and illustrate its application using previously analysed data from the oak gall wasp, Biorhiza pallida.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.