Inferring ancient divergences requires genes with strong phylogenetic signals

By Leonidas Salichos, Antonis Rokas. Nature, 2013

618 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/88aa4bf08b28c4ade553f8080ebc39283a49004d

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Citations in the corpus

ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference (2020, methodology): “reference topology among gene trees [17].”
HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment (2016, background): “The utility of phylogenomic approaches is maximized when the resolution at individual loci is sufficient for the phylogenetic depth of the analysis (Salichos and Rokas, 2013).”
UFBoot2: Improving the Ultrafast Bootstrap Approximation (2017, methodology): “To investigate the impact of the three resampling strategies, we reanalyzed the metazoan data with 21 species, 225 genes, and a total of 171,077 amino-acid sites (Salichos and Rokas 2013).”
Phylogenomic analyses of species relationships in the genus Sabal (Arecaceae) using targeted sequence capture (2016, background): “Binning increases the phylogenetic signal for each set of five concatenated gene alignments, resulting in better phylogenetic estimation (Salichos & Rokas, 2013).”
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies (2014, methodology): “Beyond this, it implements a method for identifying the so-called rogue taxa (Pattengale et al. , 2011), and I recently implemented options for calculating the TC (Tree Certainty) and IC (Internode Certainty) measures as introduced by Salichos and Rokas (2013).”
The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves (2016, background): “Salichos & Rokas (2013) foresaw this problem a few years ago when they stated that ‘[. . .] relying on bootstrap to analyse phylogenomic data sets is misleading, [. . .] because its application will, even in the presence of notable conflict or systematic error, almost always result in 100% values’.”
Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life (2016, methodology): “In the present study, we used TC, one of the new measures proposed for quantifying incongruence among phylogenies based on information theory (Salichos & Rokas, 2013), as a way to judge the performance of the five different ranking criteria in selecting sets of genes supporting congruent topologies.”
Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies (2015, background): “…by concatenated RAD loci given that concatenation of multilocus data almost always returns high statistical support (Rokas and Carroll 2006; Salichos and Rokas 2013; Simmons and Goloboff 2014) instead of reflecting the true levels of support or incongruence inherent to the data (Seo 2008;…”
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies (2016, background): “Despite the long-standing debate about correct interpretations of various measures of support (e.g., Felsenstein and Kishino 1993; Hillis and Bull 1993; Susko, 2009; Salichos and Rokas 2013), biologists typically use support to judge branch reliability.”
Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics (2014, methodology): “Finally, despite the recognition that the bootstrap method may provide a poor measurement of confidence in genomewide data sets (Salichos and Rokas 2013), we carried out 200 rapid bootstrap replicates for the HYM and MIL data sets to compare to their respective original analyses.”
STAG: Species Tree Inference from All Genes (2018, background): “However, doubts have been raised about CMSA, with problems ranging from high bootstrap support for contentious branches (Salichos and Rokas 2013), to its statistical inconsistency under the multi-species coalescent model of incomplete lineage sorting (Roch and Steel 2015).”