ArticleMolecular ecology2010
In defence of model-based inference in phylogeography.
Article in Molecular ecology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- The Evolution of Comparative Phylogeography: Putting the Geography (and More) into Comparative Population Genomics.Genome biology and evolution · 2022Review
- Distribution of genetic diversity reveals colonization patterns and philopatry of the loggerhead sea turtles across geographic scales.Scientific reports · 2020Article
- A Likelihood Approach for Uncovering Selective Sweep Signatures from Haplotype Data.Molecular biology and evolution · 2020Article
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- Glacial survival of trophically linked boreal species in northern Europe.Proceedings. Biological sciences · 2017Article
- Origin and spread of human mitochondrial DNA haplogroup U7.Scientific reports · 2017Article
- Phylogeographic model selection leads to insight into the evolutionary history of four-eyed frogs.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Historical Biogeography Using Species Geographical Ranges.Systematic biology · 2015Article
- Relaxed Observance of Traditional Marriage Rules Allows Social Connectivity without Loss of Genetic Diversity.Molecular biology and evolution · 2015Article
- New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation.PLoS genetics · 2015Article
- The impact of whole-genome sequencing on the reconstruction of human population history.Nature reviews. Genetics · 2014Review
- Article
- Article
- Hierarchical and spatially explicit clustering of DNA sequences with BAPS software.Molecular biology and evolution · 2013Article
- Approximation Bayesian Computation.OA genetics · 2013Article
- Reconstructing past changes in locus-specific recombination rates.BMC genetics · 2013Article
- The phylogeographic history of the new world screwworm fly, inferred by approximate bayesian computation analysis.PloS one · 2013Article
- Approximate Bayesian computation.PLoS computational biology · 2013Article
- Female and male perspectives on the neolithic transition in Europe: clues from ancient and modern genetic data.PloS one · 2013Article
Corrections and comments
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Authors and funding
22 authors.
Funding
Abstract
Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model-based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model-based inference in population genetics.
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