Phylogenomics of eukaryotes: impact of missing data on large alignments.

By Hervé Philippe, Elizabeth A. Snell, Éric Bapteste, Philippe Lopez, Peter W. H. Holland, D. Casane. Molecular biology and evolution, 2004

417 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/808b39ba3a8bb7f30fc16b88eaf424026a96231c

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Citations in the corpus

Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly (2010, methodology): “Unfortunately, studies show that the amount of missing data is not a good predictor for wildcard taxa and a numerical technique for their detection is needed (Novacek, 1992; Anderson, 2001; Kearney, 2002; Philippe et al., 2004; Goloboff et al., 2008; Pol & Escapa, 2009).”
Relaxed Phylogenetics and Dating with Confidence (2006, background): “The metazoan alignment was a subset of a larger dataset comprising 123 genes from 36 eukaryotes [40].”
Discordant mitochondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation (2010, background): “Recent studies based on simulations (Wiens, 2003; Philippe et al., 2004; Wiens & Moen, 2008) and empirical data (Driskell et al.”
Missing data and the design of phylogenetic analyses (2006, background): “These results have recently been supported by another set of simulations, this time modeled after a data set of 30,399 characters (129 protein-coding genes) for 36 diverse eukaryote taxa [41].”
A new subfamilial and tribal classification of the pantropical flowering plant family Annonaceae informed by molecular phylogenetics (2012, positive): “We adopted a sampling strategy that addressed both issues at once, specifically by following a supermatrix approach in which missing data are tolerated (Philippe et al., 2004; Wiens, 2005, 2006; Pirie et al., 2008).”
The human phylome (2007, background): “Evidence supporting this group comes from phylogenies based on concatenated alignments of up to 149 genes [39] as well as from morphological data.”
Higher-level metazoan relationships: recent progress and remaining questions (2011, background): “…2004; Dellaporta et al. 2006; Delsuc et al. 2006; Dopazo and Dopazo 2005; Dunn et al. 2008; Hejnol et al. 2009; Lartillot and Philippe 2008; Marlétaz et al. 2006; Matus et al. 2006; Philippe et al. 2004, 2005, 2007; Roeding et al. 2007; Schierwater et al. 2009; Siddall 2009; Webster et al. 2006).”
The New Tree of Eukaryotes. (2019, background): “The introduction of phylogenomics offered the promise of overcoming the limited information afforded by single genes, which were mostly inadequate to resolve deep divergences within the eToL [23].”
The evolution of cell types in animals: emerging principles from molecular studies (2008, background): “The multifunctionality of ancient cell types is even more obvious if we consider the first metazoan cell type, which most probably resembled a choanoflagellat”
Pitfalls in supermatrix phylogenomics (2017, positive): “…of the incompleteness is deleterious and sparse supermatrices must be avoided (Huelsenbeck 1991; Lemmon et al. 2009) and (2) missing data are not problematic per se as long as a suffi cient number of characters are known for each taxon (Wiens 2003; Philippe et al. 2004; Wiens & Morrill 2011).”
The influence of rate heterogeneity among sites on the time dependence of molecular rates. (2012, methodology): “…derived by accounting for the change of variables between y and f and between z and r. Saturation Analysis Mutational saturation in the simulated sequences was assessed for the different root ages by plotting observed (uncorrected pairwise) against inferred genetic distances (Philippe et al. 2004).”
Inferring Phylogenies from RAD Sequence Data (2012, background): “Our success at accurately inferring phylogenies from data matrices with vast amounts of missing data suggests that missing data per se is not problematic for reconstructing phylogenies; rather, inaccuracy may arise more from phylogenetically misleading data and lack of informative data [33,37–40].”