Genome-scale approaches to resolving incongruence in molecular phylogenies

By Antonis Rokas, B. Williams, N. King, Sean B. Carroll. Nature, 2003

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View Paper: https://www.semanticscholar.org/paper/64d65344e9e549f9c1fa6ebcd89606b32761b671

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Citations in the corpus

Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets (2017, background): “The only difference between concatenation and single-gene tree analyses was the number of sites analyzed, a property that is strongly correlated with phylogenetic signal (Rokas et al. 2003; Shen”
Plastid genome sequencing, comparative genomics, and phylogenomics: Current status and prospects (2010, background): “Recruitment of sequences of more genes, even whole genomes, is expected to avoid or reduce two types of errors inherent in using just one or several genes: the stochastic error (sampling error); and paralogy caused by mechanisms such as gene duplication, horizontal gene transfer or lineage sorting, ”
BioEdit: An important software for molecular biology (2011, background): “The program was used extensively ever since and quoted in many article in high ranking journals and used in many novel and diverse research application (Antonis et al., 2003; Ron et al., 2005; Chen et al., 2006; Aquifer Robert et al., 2003; Klaas et al., 2002).”
The genus Phomopsis: biology, applications, species concepts and names of common phytopathogens (2011, background): “Incongruence of single gene phylogenies is thought to be cause by various analytical and biological factors (Rokas et al. 2003a).”
Genome Rearrangement Distances and Gene Order Phylogeny in γ-Proteobacteria (2005, background): “Genome-scale sequence-based methods help to resolve incongruent 28 phylogenies (Rokas et al. 2003).”
The human phylome (2007, result): “This and other recent findings [85] reinforce the older view [86] that topological differences among phylogenies of proteins are to be expected even in the absence of HGT and underscore the danger of gene-sampling effects when combining the phylogenetic signals of several genes [34].”
Discordant mitochondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation (2010, background): “We also show that phylogenies from single nuclear genes can show striking discordance with the tree from combined nucDNA (e.g. Rokas et al., 2003), even among closely-related species.”
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments (2010, methodology): “This phylogenomic dataset was built by concatenating 106 alignments of DNA sequences gathered from 7 Saccharomyces species and Candida albicans as outgroup (see [77] for more Figure 7 Phylogenetic tree used to simulate the non-stationary evolution of a DNA sequence .”
Inconsistency of phylogenetic estimates from concatenated data under coalescence. (2007, positive): “Recent studies using real data (Chen and Li, 2001; Rokas et al., 2003) have claimed that the procedure of applying standard methods to concatenated multigene data leads to a strongly supported phylogenetic estimate, assumed to be the species tree.”
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees (2018, methodology): “This two-step approach stands in contrast to concatenation [8], where all the data are combined and analyzed in a single analysis.”
L. A. S. JOHNSON REVIEW No. 2 Use of nuclear genes for phylogeny reconstruction in plants (2004, background): “Acquisition of data from multiple independent regions allows an opportunity to determine phylogenetic relationships supported by a majority of the data and can highlight particular genomic regions that may be problematic (Cronn et al. 2002b, 2003; Rokas et al. 2003).”
Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. (2006, background): “…is controversial, and reliability has been examined in a lengthy and intensive debate (Hillis and Bull, 1993; Felsenstein and Kishino, 1993; Sanderson, 1995; Berry and Gascuel, 1996; Suzuki et al., 2002; Wilcox et al., 2002; Alfaro et al., 2003; Cummings et al., 2003; Douady et al., 2003a;…”
Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA (2006, methodology): “For example, in a recent paper, Rokas et al. (2003) used data 556 Simon et al. A nn u.”