Missing data, incomplete taxa, and phylogenetic accuracy.

By John J. Wiens. Systematic Biology, 2003

661 citations recorded by the source corpus.

Subfields: Geometry and Topology, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/8256ecfbea3d05d93df7054b4344dd19ef4c3b46

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In Geometry and Topology

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Citations in the corpus

Missing data and the accuracy of Bayesian phylogenetics (2008, methodology): “Asymmetric trees are expected to be more common when all topologies are considered to be equally likely (e.g., Huelsenbeck & Kirkpatrick, 1996), and previous studies suggest that tree shape will have little impact on the results ( Wiens, 2003 ).”
Molecular Evolution of Zika Virus during Its Emergence in the 20th Century (2014, methodology): “This is in line with the use of Maximum Likelihood approaches, which is fairly robust to the introduction of gaps [64,65].”
Increased gene sampling yields robust support for higher‐level clades within Bombycoidea (Lepidoptera) (2011, background): “…that higher-level groups are still multiply sampled, and that no previous data are excluded, but the resulting data matrix will thereby have blocks of missing data, which may (Lemmon et al., 2009) or may not (Wiens, 2003, 2006) compromise phylogenetic accuracy by introducing a nonphylogenetic bias.”
TRY – a global database of plant traits (2011, background): “On the other hand, simulation work in phylogenetics has shown that missing data are not by themselves proble- matic for phylogenetic reconstruction (Wiens, 2003, 2005).”
Disintegrating Portulacaceae: a new familial classification of the suborder Portulacineae (Caryophyllales) based on molecular and morphological data (2010, background): “Furthermore, the issue of missing data is no longer regarded as a major problem when dealing with incompletely coded taxa (Kearny, 2002) if “there are sufficient characters in one broadly sampled dataset to allow the position of these taxa to be resolved” (Wiens, 2003: 536).”
An osteology‐based appraisal of the phylogeny and evolution of kangaroos and wallabies (Macropodidae: Marsupialia) (2010, neutral): “Wiens JJ. 2003.”
Phylogenomics and the reconstruction of the tree of life (2005, background): “20,36 studies have shown that this proportion can be surprisingly high without losing too much accuracy.”
Taxon sampling and the accuracy of phylogenetic analyses (2008, background): “Incomplete fossil data are not always beneficial, as they may reduce support for some nodes (Wiens, 2003; Wiens, 2005; Cobbett et al., 2007).”
Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices (2016, neutral): “It has been comprehensively shown that incompletely coded characters can provide a strong signal (Wiens 2003b), and that characters with high levels of missing data can still improve phylogenetic accuracy under many conditions (Wiens 1998, 2003a, 2006; Edgecombe 2010; Wiens & Morrill 2011), while…”
Missing data and the design of phylogenetic analyses (2006, background): “Simulation results [40] strongly support the second hypothesis (Fig.”
A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. (2011, background): “Simulations suggest that this sampling design can be critically important for allowing the accurate placement of taxa with extensive missing data, as opposed to having all genes be randomly sampled across species with limited overlap (Wiens, 2003).”
Discordant mitochondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation (2010, methodology): “Emydid turtles consist of 12 genera (following Stephens & Wiens, 2003a) and approximately 41–47 currently recognized species (Turtle Taxonomy Working Group, 2007; Uetz, 2008).”
Floral Developmental Morphology of Amborella trichopoda (Amborellaceae) (2004, background): “Another reason may be the sometimes ambiguous coding of taxa, in that no characters were coded as ordered or continuous (Wiens 2003a, 2003b; Zanis et al. 2003).”
A new phylogeny of ichthyosaurs (Reptilia: Diapsida) (2019, methodology): “Although this is the simplest method, it does not always prove the best in resolving relationships (Wiens 2003).”