Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation

By Emily K Latch, G. Dharmarajan, Jeffrey Glaubitz, OLIN E. RHODES JR. Conservation Genetics, 2006

671 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/dd476859102df5098423592fd5d0a976a79086c2

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In Genetics

Citations in the corpus

Effects of roads on patterns of genetic differentiation in red-backed salamanders, Plethodon cinereus (2008, background): “However, because BAPS often tends to identify relatively large numbers of clusters when genetic differentiation is subtle (Latch et al. 2006), we also examined in detail the optimal two-population clustering for each site.”
Continental‐scale assessment of genetic diversity and population structure in quaking aspen (Populus tremuloides) (2013, methodology): “However, the algorithm implemented in baps is known to result in oversplitting (Latch et al., 2006; Corander et al., 2008a), and hence the finding of K = 5 may not be the most biologically realistic result.”
The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem (2016, methodology): “Such rates were used to obtain levels of genetic differentiation between subpopulations which have been shown to provide reliable estimates of the number of clusters when sampling was even (Latch et al. 2006).”
Phylogeny, phylogeography and genetic diversity of the Pisum genus (2010, methodology): “This is in contrast to STRUCTURE analysis, which partitioned the collection into maximally K ¼ 7 clusters ( Jing et al., 2010).”
Mitochondrial DNA under siege in avian phylogeography (2008, background): “The program structure may be quite useful for detecting units of population management (e.g. Latch et al. 2006), but it cannot be used alone to identify historical entities.”
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).”
Efficiency of markers and methods for detecting hybrids and introgression in stocked populations (2009, methodology): “All individual fish that were more likely to be of hybrid or hatchery origin according to NEWHYBRIDS had moderate or high hatchery ancestry estimations in STRUCTURE and BAPS analyses.”
Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study (2007, methodology): “For the five-island model at levels of genetic differentiation FST ≥ 0.03, Latch et al. (2006) reported that structure correctly inferred K, but that this program could not detect more than one population at an FST = 0.01, and could not discern all five populations at an FST = 0.02.”
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).”
Using spatial Bayesian methods to determine the genetic structure of a continuously distributed population: clusters or isolation by distance? (2009, background): “…for comparisons of structure and the non-spatial algorithm in baps, with the latter having a tendency to overestimate genetic structure (e.g., Latch et al. 2006; Rowe & Beebee 2007). baps is based on identifying populations with different allele frequencies, rather than partitioning…”
Why sampling scheme matters: the effect of sampling scheme on landscape genetic results (2009, methodology): “However , they noted that F ST must be at least 0.05 to reach a 97% assignment accuracy rate (Latch et al. 2006).”
Integrating genetic data into management of marine resources: how can we do it better? (2008, background): “…is not unlimited, and their ability to provide meaningful information when levels of population genetic differentiation are weak (as occurs with many marine species) has not been rigorously studied (Hauser et al. 2006; Latch et al. 2006; Waples and Gaggiotti 2006; Schwartz and McKelvey 2008).”
Genetic diversity and population structure of the Chinese mitten crab Eriocheir sinensis in its native range (2009, background): “However, eight of these clusters where represented by a small number of individuals which appeared to be randomly distributed among clusters indicating that the real number of clusters might be overestimated due to some genotypes which show by chance a higher divergence ( Latch et al. 2006 ).”
Repeatedly out of Beringia: Cassiope tetragona embraces the Arctic (2007, methodology): “These methods have been found successful for inferring number of clusters, also when the clusters are not well defined (Latch et al., 2006).”
Strong maternal fidelity and natal philopatry shape genetic structure in North Pacific humpback whales (2013, positive): “These results are consistent with the known limits of STRUCTURE to detect population structure where differentiation of microsatellite allele frequencies is weak and the number of loci is modest (Latch et al. 2006, Waples & Gaggiotti 2006).”