Inconsistency of phylogenetic estimates from concatenated data under coalescence.

By Laura Salter Kubatko, James H. Degnan. Systematic Biology, 2007

1,006 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/5ab6d37d1cdc03a29d8382b31ecb5b2cd0113589

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Citations in the corpus

StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates (2016, background): “In the so-called “anomaly zone” of short branch lengths, the most probable gene tree topology will be different from the species tree, and estimated tree topologies will likely differ from the true species tree topologies (Degnan and Rosenberg, 2006; Kubatko and Degnan, 2007).”
Evolutionary history of the Paradoxurus palm civets – a new model for Asian biogeography (2010, background): “Mitochondrial and nuclear datasets were analysed separately given their potentially conflicting phylogenetic signals (see Knowles & Carstens, 2007; Kubatko & Degnan, 2007).”
Error in Phylogenetic Estimation for Bushes in the Tree of Life (2013, background): “However, recent studies argue that concatenation can result in inaccurate estimates of relationships, sometimes with deceptively high support, when there is incongruence among gene trees [30,40,68,69].”
Integrative taxonomy, or iterative taxonomy? (2011, background): “…and concatenation would be expected to perform poorly in these situations (Carstens & Knowles, 2007; Edwards et al., 2007; © 2010 CSIRO Systematic Entomology © 2010 The Royal Entomological Society, Systematic Entomology, 36, 209–217 Kubatko & Degnan, 2007; reviewed in Degnan & Rosenberg, 2009).”
Development of COS genes as universally amplifiable markers for phylogenetic reconstructions of closely related plant species (2008, background): “A broader choice of universally amplifiable markers with equally high polymorphism level could, on the one hand, contribute to avoid the overweighing of topologies provided by more informative markers, at the risk of positively misleading the phylogeny (Bull et al., 1993; Kubatko and Degnan, 2007).”
Multi‐gene phylogenetic analysis of south‐east Asian pest members of the Bactrocera dorsalis species complex (Diptera: Tephritidae) does not support current taxonomy (2014, methodology): “We recognize the caveats of using concatenated DNA sequence data to generate a species-tree hypothesis (Degnan and Salter 2005; Kubatko and Degnan 2007; Kubatko et al. 2011); however, as J. Appl.”
Delimiting species without monophyletic gene trees. (2007, background): “Studies have shown that when the gene trees of loci are discordant (as expected with recent species divergence) concatenation of the nucleotide data across loci can result in positively misleading inferences about the history of divergence (Kubatko and Degnan, 2007).”
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis (2010, background): “Concatenation of all loci is known to be powerful in some cases, but also known to report inflated support values or to be misleading in other cases (Kubatko and Degnan, 2007).”
STEM: species tree estimation using maximum likelihood for gene trees under coalescence (2009, background): “, 2003), others have highlighted situations in which such procedures fail (Carstens and Knowles, 2007; Kolaczkowski and Thornton, 2004; Kubatko and Degnan, 2007; Mossel and Vigoda, 2005).”
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes (2015, background): “However, concatenation-based analyses can be statistically inconsistent under the multi-species coalescent (Roch and Steel, 2014) and can result in incorrect trees with high support (Kubatko and Degnan, 2007).”
ASTRAL: genome-scale coalescent-based species tree estimation (2014, background): “For example, the standard approach, concatenation (which concatenates the multiple sequence alignments for different genes together into one superalignment, and then estimates a tree on the super-alignment) can return incorrect trees with high confidence (Kubatko and Degnan, 2007).”