Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study

By Chibiao Chen, Eric Durand, Florence Forbes, Olivier Francois. 2007

740 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/f4945d530f20e07df67a0c37c8d145033205340e

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In Genetics

Citations in the corpus

Clumpak: a program for identifying clustering modes and packaging population structure inferences across K (2015, neutral): “…et al. 2003, 2004, 2008a,b; Falush et al. 2003, 2007; Guillot et al. 2005; Tang et al. 2005; Franc (cid:1) ois et al. 2006; Pella & Masuda 2006; Chen et al. 2007; Gao et al. 2007; Huelsen-beck & Andolfatto 2007; Guillot 2008; Alexander et al. 2009; Durand et al. 2009; Hubisz et al. 2009;…”
Using spatial Bayesian methods to determine the genetic structure of a continuously distributed population: clusters or isolation by distance? (2009, neutral): “One exception is the work by Chen et al. (2007).”
Applications of landscape genetics in conservation biology: concepts and challenges (2010, methodology): “Since admixture may result from processes that are intrinsically spatial, for example following regional migration of populations, recent improvements of Bayesian assignment methods have incorporated geographically explicit prior distributions in their models (see Chen et al. 2007).”
The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem (2016, methodology): “Several methods have been developed to group individual genotypes into clusters (Pritchard et al. 2000; Dawson & Belkhir 2001; Guillot et al. 2005b; Chen et al. 2007; Corander et al. 2008).”
Phylogeography: its development and impact in Australo-Papuan ornithology with special reference to paraphyly in Australian birds (2009, background): “There is now a bewildering array of packages, though only a few stalwarts do much of the published work (see reviews in Excoffier andHeckel 2006; Latch et al. 2006; Chen et al. 2007).”
Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models (2012, background): “Mean squared errors provide additional evidence of relatively poor performances of the linear regression and PC regression estimates when levels of underlying structure increase (Table 1).”
Why sampling scheme matters: the effect of sampling scheme on landscape genetic results (2009, background): “…et al. 2003, 2007), although other approaches and programs exist (e.g., PARTITION, Dawson and Belkhir 2001; BAPS2, Corander et al. 2004; GENELAND, Guillot et al. 2005a, b; 2D LSA in GEN- ALEX, Double et al. 2005, Peakall and Smouse 2006; HMRF models, François et al 2006; TESS Chen et al. 2007).”
Circuit Theory and Model-Based Inference for Landscape Connectivity (2013, positive): “Spatial clustering methods (e.g., Guillot et al. 2005; Chen et al. 2007; Durand et al. 2009) are commonly used to identify genetic boundaries, but are typically based on the assumption of a homogeneous underlying landscape, with any link to the underlying landscape made post hoc (e.g., Wheeler,…”
CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure (2007, methodology): “…employing population-genetic data to assign individuals—and fractions of individuals—to clusters (Anderson and Thompson, 2002; Chen et al. , 2006, 2007; Corander and Marttinen, 2006; Corander et al. , 2003, 2004; Dawson and Belkhir, 2001; Falush et al. , 2003; Franc¸ois et al. , 2006;…”
Identifying future research needs in landscape genetics: where to from here? (2009, background): “At the same time, very few published studies compare the various statistical approaches, or test their reliability under realistic landscape genetic scenarios (Latch et al. 2006; Chen et al. 2007; Balkenhol et al. 2009).”
Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software (2013, background): “Several spatial models for estimating genetic population structure from molecular marker loci have been introduced in the past few years (Wasser et al. 2004; Guillot et al. 2005; Francois et al. 2006; Chen et al. 2007; Corander et al. 2008b).”