Phylogenomics: the beginning of incongruence?

By Olivier Jeffroy, H. Brinkmann, Frédéric Delsuc, Hervé Philippe. Trends in Genetics, 2006

671 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/648973a37beeda83e73519d2e74a8aa581a3dbdd

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Citations in the corpus

Error in Phylogenetic Estimation for Bushes in the Tree of Life (2013, background): “Finally, there are cases where the expected site pattern spectra support a topology that con%icts with the true tree due to factors like long-branch attraction and base compositional convergence [32,35-37].”
The New Tree of Eukaryotes. (2019, background): “on that most of the analysis artefacts known to afflict single-gene phylogenies can also apply to phylogenomics [24].”
Pitfalls in supermatrix phylogenomics (2017, positive): “However, a few discordant voices soon advocated caution (Phillips et al. 2004; Soltis et al. 2004; Jeffroy et al. 2006).”
The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves (2016, background): “At the same time, sampling more genomic loci increases the variance among the gene trees that underlie the species tree, leading to more, not less, phylogenetic discordance (Jeffroy et al. 2006; Philippe et al. 2011; Liu et al. 2015; Hahn & Nakhleh 2016).”
Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes (2011, background): “Moreover, with long sequences and strong systematic bias (due to model violations), any of tested branch support methods will become very confident in supporting wrong bipartitions, as can be seen from phylogenetic analyses of concatenated genes (Jeffroy et al. 2006).”
In search of mitochondrial markers for resolving the phylogeny of cyclophyllidean tapeworms (Platyhelminthes, Cestoda) — a test study with Davaineidae (2008, background): “Clearly, there are limitations in combined evidence phylogenetics (e.g. in phylogenomics; Rokas and Carroll 2005, Jeffroy et al. 2006), but in cestode systematics we are a long way short of saturating phylogenies with molecular data or taxa.”
The influence of rate heterogeneity among sites on the time dependence of molecular rates. (2012, methodology): “To quantify the degree of saturation, a linear regression model with zero intercept was fitted for each plot, the slope representing the degree of saturation (Jeffroy et al. 2006).”
Detecting and overcoming systematic errors in genome-scale phylogenies. (2007, background): “Tree reconstruction artefacts that are invisible in single-gene phylogenies may become dominant in large data sets (Jeffroy et al., 2006).”
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. (2007, methodology): “However, for longer alignments, for example, those used in phylogenomic studies where several genes are concatenated (Delsuc et al., 2005; Jeffroy et al, 2006), there is enough total information so that selecting the best pieces with Gblocks using the stringent conditions allows to get closer to…”
Plastid genome sequencing, comparative genomics, and phylogenomics: Current status and prospects (2010, background): “Chloroplast phylogenomics can overcome the limitations of single-gene phylogenies by combining many genes and ultimately complete plastid genomes (Jeffroy et al., 2006).”
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model (2007, positive): “In some cases, in particular under poor taxon sampling [3-6], highly resolved trees have been proposed, which have nevertheless been followed by subsequent critical re-analyses, claiming that, however strongly supported, the trees obtained were probably wrong [7-9].”
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough (2011, methodology): “The level of saturation was estimated for each dataset by computing the slope of the regression line of patristic distances (y-axis) versus uncorrected distances (x-axis), as previously described [12].”
The human phylome (2007, neutral): “However, it has been claimed that these trees are representative of only a small fraction of the genes encoded in a given genome, and that gene-sampling effects might lead to biased results supporting a specific species phylogeny [33,34].”