Genealogical trees, coalescent theory and the analysis of genetic polymorphisms

By Noah A. Rosenberg, Magnus Nordborg. Nature reviews genetics, 2002

679 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/d5378a66b31d53a53c3d1807145f987326cdc9b1

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In Genetics

Citations in the corpus

DNA sequence polymorphism analysis using DnaSP. (2009, neutral): “Current population genetics methods, and particularly those based on the coalescent theory, have become the primary framework to analyze DNA polymorphism data (3, 4).”
INVITED REVIEW: Using genome scans of DNA polymorphism to infer adaptive population divergence (2005, background): “Although hitch-hiking is expected to increase correlations in diversity levels among linked loci (Kim & Stephan 2002), correlations in the depths of neutral genealogies are expected even in the absence of selection at linked sites (Rosenberg & Nordborg 2002).”
Sequence-based species delimitation for the DNA taxonomy of undescribed insects. (2006, background): “Branch lengths between species are determined by speciation and extinction rates (macroevolution) (Nee et al., 1994), whereas branch lengths within a species reflect coalescence processes at the level of populations (microevolution) (Hudson, 1991; Rosenberg and Nordborg, 2002; Wakeley, 2006).”
Phylogeographic insights into cryptic glacial refugia. (2008, background): “The application of coalescent theory can better accommodate the stochastic demographic processes associated with postglacial recolonisation, such as population expansion and migration, than ‘classical’ population genetics approaches [50, 51 ].”
DnaSP, DNA polymorphism analyses by the coalescent and other methods (2003, methodology): “In this context, the coalescent theory (see Hudson, 1990; Rosenberg and Nordborg, 2002) has become the primary framework to analyse the data.”
The incomplete natural history of mitochondria (2004, background): “One of the most powerful statistical advances in population genetics over the last few decades has been the introduction of the coalescent (see review by Rosenberg & Nordborg 2002).”
Cancer Evolution: Mathematical Models and Computational Inference (2014, background): “In the diffusion limit, N →∞, two lineages coalesce at rate( j 2 ) , when there are j individuals left (Rosenberg and Nordborg 2002).”
DNA-based species delimitation in algae (2014, background): “…alleles in recently diverging lineages, gene trees will inevitably go through phases where individuals of a species are polyphyletic and paraphyletic before becoming monophyletic as alleles become fixed through time (Avise & Ball, 1990; Klein et al., 1998; Rosenberg & Nordborg, 2002) (Fig.”
Integrating ensemble species distribution modelling and statistical phylogeography to inform projections of climate change impacts on species distributions (2013, background): “The coalescent is a model of population genetics that takes into account the stochasticity of the genetic process when modeling different mechanisms of population history within a species (Rosenberg and Nordborg 2002).”
Computer simulations: tools for population and evolutionary genetics (2012, methodology): “Simulations can also be used to test the power of a particular population-genetics sampling scheme (such as the number of loci and samples needed) to carry out a specific test 68,69 .”
Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets (2013, background): “Sampled genes coalesce to a single common ancestor at a mean rate proportional to the effective population size, N e , in the case of a strict neutral coalescent (Hudson 1990; Rosenberg and Nordborg 2002).”
DnaSP v5: a software for comprehensive analysis of DNA polymorphism data (2009, background): “The analysis of DNA polymorphisms is a powerful approach to understand the evolutionary process and to establish the functional significance of particular genomic regions (Nielsen, 2005; Rosenberg and Nordborg, 2002; Begun et al. , 2007).”