Assessing Congruence Among Ultrametric Distance Matrices

Campbell, Véronique; Legendre, Pierre; Lapointe, François‐Joseph

doi:10.1007/s00357-009-9028-x

Cited by 17 publications

(12 citation statements)

References 18 publications

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“…Sequences of H3 have been deposited in Genbank (MT733538-MT733543). In order to determine if the three genes could be concatenated for phylogenetic analyses, we tested the congruence among the three distance matrices genes using the congruence among distance matrices approach (CADM) developed by [ 97 , 98 ] available in ape R-package [ 99 ]. Briefly, the CADM tests for the presence of incongruency among all the distance matrices.…”

Section: Methodsmentioning

confidence: 99%

Extensive gene rearrangements in the mitogenomes of congeneric annelid species and insights on the evolutionary history of the genus Ophryotrocha

et al. 2020

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Background Annelids are one the most speciose and ecologically diverse groups of metazoans. Although a significant effort has been recently invested in sequencing genomes of a wide array of metazoans, many orders and families within the phylum Annelida are still represented by a single specimen of a single species. The genus of interstitial annelids Ophryotrocha (Dorvilleidae, Errantia, Annelida) is among these neglected groups, despite its extensive use as model organism in numerous studies on the evolution of life history, physiological and ecological traits. To compensate for the paucity of genomic information in this genus, we here obtained novel complete mitochondrial genomes of six Ophryotrocha species using next generation sequencing. In addition, we investigated the evolution of the reproductive mode in the Ophryotrocha genus using a phylogeny based on two mitochondrial markers (COXI and 16S rDNA) and one nuclear fragment (Histone H3). Results Surprisingly, gene order was not conserved among the six Ophryotrocha species investigated, and varied greatly as compared to those found in other annelid species within the class Errantia. The mitogenome phylogeny for the six Ophryotrocha species displayed a separation of gonochoric and hermaphroditic species. However, this separation was not observed in the phylogeny based on the COX1, 16S rDNA, and H3 genes. Parsimony and Bayesian ancestral trait reconstruction indicated that gonochorism was the most parsimonious ancestral reproductive mode in Ophryotrocha spp. Conclusions Our results highlight the remarkably high level of gene order variation among congeneric species, even in annelids. This encourages the need for additional mitogenome sequencing of annelid taxa in order to properly understand its mtDNA evolution, high biodiversity and phylogenetic relationships.

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Section: Methodsmentioning

confidence: 99%

Extensive gene rearrangements in the mitogenomes of congeneric annelid species and insights on the evolutionary history of the genus Ophryotrocha

et al. 2020

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“…Nexus files of the data matrices are available in the Supplementary Data section of the online version of this article. Congruence Assessment among ultrametric Distance Matrices (CADM) was done to test incongruence of data partitions (Legendre & Lapointe, 2004;Campbell & al., 2009). Thirty-seven species (including representatives of all tribes in Polygonoideae [except Fagopyreae] and representatives of Eriogonoideae) were tested with CADM to allow for the comparison of each gene region against all others.…”

Section: Methodsmentioning

confidence: 99%

Phylogeny of Polygoneae (Polygonaceae: Polygonoideae)

Schuster

Reveal

Kron

2011

TAXON

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Genera included in Polygoneae such as Atraphaxis, Duma, Fallopia, Muehlenbeckia, Polygonella, Polygonum, Oxygonum, and Reynoutria are investigated using a molecular framework. Previous morphological studies had indicated that Polygonum is composed of sections Duravia, Polygonum, and Pseudomollia with the genus Polygonella included as a subsection of Polygonum sect. Duravia. One nuclear (nrITS) and three chloroplast (matK, ndhF, trnL–trnF) regions were analyzed with Maximum Parsimony and Maximum Likelihood methods to address evolutionary relationships within the tribe. The results show that Polygoneae is composed of three main clades: Knorringia as sister to all other taxa within Polygoneae, a clade of Reynoutria and Fallopia+Muehlenbeckia, and their sister clade of Atraphaxis, Duma, and Polygonum. The currently accepted sections within Polygonum are recovered and Polygonum sect. Duravia is sister to sections Polygonum and Pseudomollia. With Polygonella included in Polygonum, the appropriate new combinations and names are proposed. In addition, a few species of Polygonum are transferred to Atraphaxis. Oxygonum is not supported as a member of Polygoneae and its exact position awaits additional data.

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“…Identical results were obtained in simulations involving ultrametric distance matrices [56]. CADM has also been successfully used to detect congruence among phylogenetic trees obtained from different gene sequences [57].…”

Section: Introductionmentioning

confidence: 85%

The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis

2011

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BackgroundCADM is a statistical test used to estimate the level of Congruence Among Distance Matrices. It has been shown in previous studies to have a correct rate of type I error and good power when applied to dissimilarity matrices and to ultrametric distance matrices. Contrary to most other tests of incongruence used in phylogenetic analysis, the null hypothesis of the CADM test assumes complete incongruence of the phylogenetic trees instead of congruence. In this study, we performed computer simulations to assess the type I error rate and power of the test. It was applied to additive distance matrices representing phylogenies and to genetic distance matrices obtained from nucleotide sequences of different lengths that were simulated on randomly generated trees of varying sizes, and under different evolutionary conditions.ResultsOur results showed that the test has an accurate type I error rate and good power. As expected, power increased with the number of objects (i.e., taxa), the number of partially or completely congruent matrices and the level of congruence among distance matrices.ConclusionsBased on our results, we suggest that CADM is an excellent candidate to test for congruence and, when present, to estimate its level in phylogenomic studies where numerous genes are analysed simultaneously.

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Assessing Congruence Among Ultrametric Distance Matrices

Abstract: Incongruence, Power, Statistical test, Simulation, Type I error rate,

Cited by 17 publications

References 18 publications

Extensive gene rearrangements in the mitogenomes of congeneric annelid species and insights on the evolutionary history of the genus Ophryotrocha

Extensive gene rearrangements in the mitogenomes of congeneric annelid species and insights on the evolutionary history of the genus Ophryotrocha

Phylogeny of Polygoneae (Polygonaceae: Polygonoideae)

The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis

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