Noise and Incongruence: Interpreting Results of the Incongruence Length Difference Test

2000 ◽  
Vol 17 (3) ◽  
pp. 401-406 ◽  
Author(s):  
Konrad Dolphin ◽  
Robert Belshaw ◽  
C.David L. Orme ◽  
Donald L.J. Quicke
Keyword(s):  
Length Difference ◽  
Difference Test ◽  
Incongruence Length Difference

scholarly journals The Utility of the Incongruence Length Difference Test

2002 ◽  
Vol 51 (4) ◽  
pp. 625-637 ◽  
Author(s):  
F. Keith Barker ◽  
François M. Lutzoni
Keyword(s):  
Length Difference ◽  
Difference Test ◽  
Incongruence Length Difference

scholarly journals Congruence Versus Phylogenetic Accuracy: Revisiting the Incongruence Length Difference Test

2004 ◽  
Vol 53 (1) ◽  
pp. 81-89 ◽  
Author(s):  
Andrew L. Hipp ◽  
Jocelyn C. Hall ◽  
Kenneth J. Sytsma
Keyword(s):  
Length Difference ◽  
Difference Test ◽  
Incongruence Length Difference

Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution

1998 ◽  
Vol 46 (5) ◽  
pp. 419 ◽  
Author(s):  
D. J. Colgan ◽  
A. McLauchlan ◽  
G. D. F. Wilson ◽  
S. P. Livingston ◽  
G. D. Edgecombe ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Histone H3 ◽  
Gc Content ◽  
Length Difference ◽  
Partitioned Data ◽  
Cladistic Analyses ◽  
Group Relationships ◽  
Incongruence Length Difference ◽  
Significant Support ◽  
Basal Position

The range of DNA sequences used to study the interrelationships of the major arthropod groups (chelicerates, myriapods, hexapods and crustaceans) is limited. Here we investigate the value of two genes not previously employed in arthropod phylogenetics. Histone H3 data were collected for 31 species and small nuclear ribonucleic acid U2 data for 29 species. The sequences provided a total of 460 sites and 192 parsimony-informative characters. H3 analyses showed substantial codon usage bias, but had a low consistency index (0.26). Consistency indices were higher for the U2 data (0.49), suggesting that the class of snRNAs may provide several phylogenetically useful genes. The present data are not by themselves sufficient to clarify major arthropod group relationships. Partitioned data for H3 and U2 are incongruent according to Incongruence Length Difference tests. Although the most parsimonious trees, based on combined analyses of all taxa, differ substantially from morphology-based trees, anomalous groupings are weakly supported with only one exception. The trees uphold monophyly of Onychophora, Branchiopoda, and Malacostraca (rather than the rival Phyllopoda). Cladistic analyses constraining the monophyly of morphologically defined classes do not significantly distinguish between the main rival hypotheses of major clade relationships. Combined (‘spliced’) analysis of both genes improves topological congruence with morphological groupings relative to that of either partition. Character congruence between H3, U2, and morphology is increased by downweighting (but not excluding) transitions and third codons. Analyses of four-taxon statements using PHYLTEST found significant support for the basal position of the Crustacea among the euarthropods. This support may be due to the similarity of chelicerates, myriapods and hexapods in percentage GC content.

Phylogeny of Halgerda (Mollusca : Gastropoda) based on combined analysis of mitochondrial CO1 and morphology

2003 ◽  
Vol 17 (5) ◽  
pp. 617 ◽  
Author(s):  
Shireen J. Fahey
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Signal ◽  
Optimality Criteria ◽  
Retention Indices ◽  
Species Level ◽  
Combined Analysis ◽  
Length Difference ◽  
Incongruence Length Difference

A phylogeny of the nudibranch Halgerda Bergh, 1880 is presented based on mitochondrial CO1 and compared with a previously published morphology-based phylogeny. Incongruence length difference (ILD) tests indicated possibly conflicting phylogenetic signals. Both separate and combined analyses resulted in trees that were very similar in topology, both to each other and to the morphology-based tree (albeit with lower consistency and retention indices). Some differences are noted in the topology based on the optimality criteria used: parsimony and maximum likelihood. Results of this study indicate that the CO1 gene contains sufficient phylogenetic signal for inferring species-level phylogeny in the Nudibranchia and also supports many of the clades in the morphological phylogeny. Specifically, the more basal clades of the morphology-based phylogeny are supported with differences noted at the most terminal taxa.

scholarly journals Phylogenetic incongruence and homoplasy in the appendages and bodies of arthropods: why broad character sampling is best

2019 ◽  
Vol 187 (1) ◽  
pp. 100-116 ◽  
Author(s):  
Andrew R Brinkworth ◽  
Robert Sansom ◽  
Matthew A Wills
Keyword(s):  
Morphological Character ◽  
Sequence Data ◽  
Morphological Characters ◽  
Total Evidence ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Length Difference ◽  
Morphological Specialization ◽  
Tree Length ◽  
Incongruence Length Difference

Abstract Notwithstanding the rapidly increasing sampling density of molecular sequence data, morphological characters still make an important contribution to our understanding of the evolutionary relationships of arthropod groups. In many clades, characters relating to the number and morphological specialization of appendages are ascribed particular phylogenetic significance and may be preferentially sampled. However, previous studies have shown that partitions of morphological character matrices often imply significantly different phylogenies. Here, we ask whether a similar incongruence is observed in the appendage and non-appendage characters of arthropods. We apply tree length (incongruence length difference, ILD) and tree distance (incongruence relationship difference, IRD) tests to these partitions in an empirical sample of 53 published neontological datasets for arthropods. We find significant incongruence about one time in five: more often than expected, but markedly less often than in previous partition studies. We also find similar levels of homoplasy in limb and non-limb characters, both in terms of internal consistency and consistency relative to molecular trees. Taken together, these findings imply that sampled limb and non-limb characters are of similar phylogenetic utility and quality, and that a total evidence approach to their analysis is preferable.

Sign in / Sign up

Export Citation Format

Share Document