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14 results for “Phylogenetic Incongruence”
Data from: Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence
Incongruence, or topological conflict, is prevalent in genome-scale data sets. Internode Certainty (IC) and related measures were recently introduced to explicitly quantify the level of incongruence of a given internal branch among a set of phylogenetic trees and complement regular branch support measures (e.g., bootstrap, posterior probability) that instead assess the statistical confidence of inference. Since most phylogenomic studies contain data partitions (e.g., genes) with missing taxa and IC scores stem from the frequencies of bipartitions (or splits) on a set of trees, IC score calculation typically requires adjusting the frequencies of bipartitions from these partial gene trees. However, when the proportion of missing taxa is high, the scores yielded by current approaches that adjust bipartition frequencies in partial gene trees differ substantially from each other and tend to be overestimates. To overcome these issues, we developed three new IC measures based on the frequencies of quartets, which naturally apply to both complete and partial trees. Comparison of our new quartet-based measures to previous bipartition-based measures on simulated data shows that: 1) on complete data sets, both quartet-based and bipartition-based measures yield very similar IC scores; 2) IC scores of quartet-based measures on a given data set with and without missing taxa are more similar than the scores of bipartition-based measures; and 3) quartet-based measures are more robust to the absence of phylogenetic signal and errors in phylogenetic inference than bipartition-based measures. Additionally, the analysis of an empirical mammalian phylogenomic data set using our quartet-based measures reveals the presence of substantial levels of incongruence for numerous internal branches. An efficient open-source implementation of these quartet-based measures is freely available in the program QuartetScores (https://github.com/lutteropp/QuartetScores).
Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence
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Figure 7 in Root causes of phylogenetic incongruence observed within basal sauropodomorph interrelationships
Figure 7. Phylogenetic trees obtained after new analyses were performed. They are based on a compilation of data sets and three scorings by different authors. Out-groups are indicated in grey. The shared part, not shared previously, is shaded in grey. A, strict consensus tree of the four most-parsimonious trees found using the scoring in Upchurch et al. (2007a) (tree length, TL: 1078 steps). The matrix includes 469 characters. B, strict consensus tree of the six most-parsimonious trees found using the scoring in Yates et al. (2010) (TL: 1118 steps). The matrix includes 450 characters. C, strict consensus tree of the three most-parsimonious trees found using the scoring in Pol et al. (2011) (TL: 996 steps). The matrix includes 450 characters.
Figure 6 in Root causes of phylogenetic incongruence observed within basal sauropodomorph interrelationships
Figure 6. Adams consensus trees (except for Yates et al., 2010) found after a reduction of the taxonomic scope (21 ingroups). Out-groups are not represented. A, Adams consensus tree of the 252 most-parsimonious trees obtained running the data set from Upchurch et al. (2007a) (tree length, TL: 680 steps). B, most-parsimonious tree obtained running the data set from Yates et al. (2010) (TL: 896 steps). C, Adams consensus tree of the 88 most-parsimonious trees obtained running the data set of Pol et al. (2011) (TL: 546 steps). D, strict consensus of trees A, B, and C. Branches in grey illustrate the common parts in the three analyses.
Figure 5 in Root causes of phylogenetic incongruence observed within basal sauropodomorph interrelationships
Figure 5. Strict consensus trees (except for Yates et al., 2010) found after a reduction of the taxonomic scope (21 ingroups). Out-groups are not represented. A, strict consensus tree of the 252 most-parsimonious trees obtained running the data set from Upchurch et al. (2007a) (tree length, TL: 680 steps). B, most-parsimonious tree obtained running the data set from Yates et al. (2010) (TL: 896 steps). C, strict consensus tree of the 88 most-parsimonious trees obtained running the data set from Pol et al. (2011) (TL: 546 steps). D, strict consensus of the trees A, B, and C. Branches in grey indicate areas in common among the three analyses.
Figure 1 in Root causes of phylogenetic incongruence observed within basal sauropodomorph interrelationships
Figure 1. Original phylogenetic tree and character distribution map from the analysis presented by Upchurch et al. (2007a). A, strict consensus tree, where Blikanasaurus was removed a posteriori. Out-group taxa branches are in grey; in-group taxa branches are in black. B, character distribution map where the x-axis represents the percentage of total characters in each major subdivision (e.g. cranial, axial, and appendicular), and the y-axis represents the percentage of characters within a region (for instance skull roof, braincase, etc., in the cranial region). The percentage written in the rectangle formed by each minor subdivision represents its contribution to the total number of characters.
Figure 2 in Root causes of phylogenetic incongruence observed within basal sauropodomorph interrelationships
Figure 2. Original phylogenetic tree and character distribution map from the analysis presented by Yates et al. (2010). A, strict consensus tree, where authors removed Blikanasaurus, Camelotia, and Isanosaurus a priori. Out-group taxa branches are in grey; in-group taxa branches are in black; Plateosaurus e, Plateosaurus engelhardti; Plateosaurus g, Plateosaurus gracilis. B, character distribution map where the x-axis represents the percentage of total characters in each major subdivision (e.g. cranial, axial, and appendicular), and the y-axis represents the percentage of characters within a region (for instance skull roof, braincase, etc., in the cranial region). The percentage written in the rectangle formed by each minor subdivision represents its contribution to the total number of characters.
Figure 3 in Root causes of phylogenetic incongruence observed within basal sauropodomorph interrelationships
Figure 3. Original phylogenetic tree and character distribution map from the analysis presented by Pol et al. (2011). A, strict consensus tree, where Jingshanosaurus, Blikanasaurus, Camelotia, and Ferganasaurus were removed a posteriori. Out-group taxa branches are in grey; in-group taxa branches are in black; Azendhosaurus m, Azendhosaurus madagascar; Azendhosaurus l, Azendhosaurus laroussi. B, character distribution map, where the x-axis represents the percentage of total characters in each major subdivision (e.g. cranial, axial, and appendicular), and the y-axis represents the percentage of characters within a region (for instance skull roof, braincase, etc., in the cranial region). The percentage written in the rectangle formed by each minor subdivision represents its contribution to the total number of characters.
Data from: Phylogenetics of New World ‘justicioids’ (Justicieae: Acanthaceae): major lineages, morphological patterns and widespread incongruence with classification
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Data from: Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences
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Data from: Deep phylogenetic incongruence in the angiosperm clade Rosidae
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Data from: Taxon Influence Index: assessing taxon-induced incongruities in phylogenetic inference
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Data from: Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test
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Figure 4 in Root causes of phylogenetic incongruence observed within basal sauropodomorph interrelationships
Figure 4. Pie charts illustrating different features of the characters shared by at least two of the three analyses: P, Pol et al. (2011); U, Upchurch et al. (2007a); Y, Yates et al. (2010). A, distribution of the characters common to the three analyses or shared by two matrices. B, location of the characters. C, character types. D, complexity of characters in Yates et al. (2010) and Pol et al. (2011).
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