INCOMPLETE TAXA, INCOMPLETE CHARACTERS, AND PHYLOGENETIC ACCURACY: IS THERE A MISSING DATA PROBLEM?

By John J. Wiens. 2003

167 citations recorded by the source corpus.

Subfields: Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/67eb491a6717bbab67517bd58c77e1023fd92123

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. P. Stephens
2. M. Friedman
3. J. Conrad
4. Phillip Barden
5. Jerald D. Harris
6. Jun Liu
7. P. Olsen
8. D. Ksepka

In Paleontology

1. D. Ksepka
2. J. Clarke
3. P. Stephens
4. Jerald D. Harris
5. J. Conrad
6. M. Friedman
7. Phillip Barden
8. Jun Liu

Citations in the corpus

• The Basal Penguin (Aves: Sphenisciformes) Perudyptes devriesi and a Phylogenetic Evaluation of the Penguin Fossil Record (2010, background): “Rather than improving accuracy or resolution, exclusion of characters with missing data is likely to reduce accuracy (e.g., Wiens, 1998).”
• The significance of Suuwassea emilieae (Dinosauria: Sauropoda) for flagellicaudatan intrarelationships and evolution (2006, background): “This does not mean that these characters were poor or should not have been added; only that further characters whose states may be determined in ANS 21122 have not yet been identified (Wiens 2003).”
• Ecological diversification and phylogeny of emydid turtles (2003, background): “These taxa were included in some analyses, despite the large amount of missing data, because previous studies suggest that limited taxon sampling may be more problematic than the inclusion of missing data cells in incomplete taxa (Wiens & Reeder, 1995; Wiens, 1998a, 2003a,b).”
• Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities (2005, background): “Thus, we have an extreme instance of the missing data problem, which has been extensively discussed in the phylogenetics literature [63,64].”
• The phylogeny of the living and fossil Sphenisciformes (penguins) (2006, background): “Numerous theoretical and empirical studies have pointed out that a high percentage of missing data does not necessarily lead to lack of resolution in phylogenetic analysis (see Kearney and Clark, 2003; Wiens, 2003).”
• The early evolution of ray‐finned fishes (2015, background): “…by a similar reinvigoration of systematic efforts; even the most extensive analyses of early actinopterygian interrelationships are of limited scope in terms of character coverage and taxonomic sampling, two factors with established relationships to phylogenetic accuracy (Wiens 2003, 2005).”
• Phylogeny And Systematics Of Squamata (Reptilia) Based On Morphology (2008, background): “Similarly, soft tissue (or molecular) characters remain important in analyses including large numbers of fossils if taxa and characters are well sampled overall (Kearney and Clark, 2003; Wiens, 2003).”
• A phylogenetic perspective on 160 years of troubled taxonomy of Niphargus (Crustacea: Amphipoda) (2008, background): “Incomplete data sets have been systematically investigated by Wiens (1998, 2003, 2005, 2006), who suggests that missing data does not per se hamper phylogenetic reconstructions.”
• Fossil ants (Hymenoptera: Formicidae): ancient diversity and the rise of modern lineages (2017, background): “In both treatments, the formiciine terminal was represented by a majority of missing characters, which can be problematic in phylogenetic reconstruction if the "wrong" characters are missing a d there are few morphological characters overall (WIENS 2003).”
• Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices (2016, unknown): “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…”
• Morphological and molecular evidence for phylogeny and classification of South American pitvipers, genera Bothrops, Bothriopsis, and Bothrocophias (Serpentes: Viperidae) (2009, background): “…with morphological data only, is our preferred hypothesis for delineating species groups as it had the highest support values overall and was based on the largest data set, while avoiding the possible complications of adding taxa with 90% or more missing data to the analysis (Wiens, 2003, 2006).”
• The Phylogenetic Relationships of Eucynodontia (Amniota: Synapsida) (2010, result): “This agrees with the simulations of Wiens (2003), which also shows that the inclusion of highly incomplete taxa tends to have little impact on the recovered pattern of relationships among more complete ones.”