Detecting and overcoming systematic errors in genome-scale phylogenies.

By N. Rodríguez‐Ezpeleta, H. Brinkmann, Béatrice Roure, Nicolas Lartillot, B. Franz Lang, Hervé Philippe. Systematic Biology, 2007

295 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/716cdc82a2649739dd3213d6cee7d9292cf73ac4

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Citations in the corpus

Taxon sampling and the accuracy of phylogenetic analyses (2008, background): “it has been suggested that either eliminating fast-evolving sites from the analysis (Delsuc et al., 2002; Delsuc et al., 2005; Rodriguez-Ezpeleta et al., 2007) or coding all the data to represent only less”
Evolution of lacewings and allied orders using anchored phylogenomics (Neuroptera, Megaloptera, Raphidioptera) (2018, background): “Phylogeny estimation can potentially be biased by a number of factors, including model mis-specification, heterotachy, compositional heterogeneity and across-site rate variation, among others (Rodríguez-Ezpeleta et al., 2007).”
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough (2011, background): “, heterogeneity of rate over time), had limited effects on phylogenetic reconstruction [69]; heterogeneity of rates across genes, handled by separate models [50], also has limited impact ([70], but see [71]).”
High-Throughput Genomic Data in Systematics and Phylogenetics (2013, background): “Although systematic error may have the greatest effect when phylogenetic information is weak (e.g., Lemmon et al. 2009), some types of systematic error can overwhelm substantial phylogenetic information (Rodriguez-Ezpeleta et al. 2007, Philippe et al. 2011).”
New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data (2014, methodology): “Convergence of the runs and stability of parameters were assessed using Tracer v.1.5 (Rambaut and Drummond, 2007).”