Assessing Congruence: Empirical Examples from Molecular Data

Johnson, Leigh A.; Soltis, Douglas E.

doi:10.1007/978-1-4615-5419-6_11

Cited by 134 publications

(102 citation statements)

References 83 publications

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“…However, in the analysis of tribe Vandeae, ycf 1 yielded more PICs and a longer tree than ITS and mat K. Minor incongruence exists among data sets in our genus--level (Carlsward et al 2006 ) and species--level (Sobralia and Elleanthus ) analyses, but lack strong bootstrap support. Incongruence is common when comparing multiple datasets and can be caused by many different biological, experimental, or analytical reasons (Johnson and Soltis 1998 ;Buckley et al 2001 ).…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

et al. 2008

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Section: Resultsmentioning

confidence: 99%

Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

et al. 2008

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“…Lavin et al 2005) before carrying out any combined analysis, just as individual datasets are examined for differing phylogenetic signals before combination in phylogenetic analysis (e.g. Johnson & Soltis 1998).…”

Section: Methodological Issuesmentioning

confidence: 99%

Introduction and synthesis: plant phylogeny and the origin of major biomes

Pennington

Cronk

Richardson³

2004

Phil. Trans. R. Soc. Lond. B

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Phylogenetic trees based upon DNA sequence data, when calibrated with a dimension of time, allow inference of: (i) the pattern of accumulation of lineages through time; (ii) the time of origin of monophyletic groups; (iii) when lineages arrived in different geographical areas; (iv) the time of origin of biome-specific morphologies. This gives a powerful new view of the history of biomes that in many cases is not provided by the incomplete plant fossil record. Dated plant phylogenies for angiosperm families such as Leguminosae (Fabaceae), Melastomataceae sensu stricto, Annonaceae and Rhamnaceae indicate that long-distance, transoceanic dispersal has played an important role in shaping their distributions, and that this can obscure any effect of tectonic history, previously assumed to have been the major cause of their biogeographic patterns. Dispersal from other continents has also been i mportant in the assembly of the Amazonian rainforest flora and the Australian flora. Comparison of dated biogeographic patterns of plants and animals suggests that recent long-distance dispersal might be more prevalent in plants, which has major implications for community assembly and coevolution. Dated plant phylogenies also reveal the role of past environmental changes on the evolution of lineages in species-rich biomes, and show that recent Plio-Pleistocene diversification has contributed substantially to their current species richness. Because of the critical role of fossils and morphological characters in assigning ages to nodes in phylogenetic trees, future studies must include careful morphological consideration of fossils and their extant relatives in a phylogenetic context. Ideal study systems will be based upon DNA sequence data from multiple loci and multiple fossil calibrations. This allows cross-validation both of age estimates from different loci, and from different fossil calibrations. For a more complete view of biome history, future studies should emphasize full taxon sampling in ecologically important groups, and should focus on geographical areas for which few species-level phylogenies are available, such as tropical Africa and Asia. These studies are urgent because understanding the history of biomes can both inform conservation decisions, and help predict the effects of future environmental changes at a time when biodiversity is being impacted on an unprecedented scale.

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“…Several indices that assess the degree of congruence between data sets for the same organisms were also calculated (Johnson and Soltis, 1998). We computed two topological congruence indices.…”

Section: Congruence Among Data Setsmentioning

confidence: 99%

“…The incongruence metric of Mickevich and Farris (I MF ) (Mickevich and Farris, 1981) is similar but instead of mapping each data set on the other data set, it uses the number of homoplastic steps required by each individual data set to explain the shortest tree recovered from the combined matrix. Both indices were computed with the length and fit measures given by PAUP and following the indications by Johnson and Soltis (1998).…”

Section: Congruence Among Data Setsmentioning

confidence: 99%

“…Other authors maintain that data from different sources should not be combined but should be independently analyzed (Miyamoto and Fitch, 1995), the latter representing the consensus approach (taxonomic congruence, partitioned analysis). A third, intermediate approach advocates merging the data into a single matrix only if there is evidence that the various matrices do not contain serious incongruence, i.e., that they do not represent different branching histories or that they have not been affected by different evolutionary mechanisms (Bull et al, 1993;Johnson and Soltis, 1998).…”

Section: Introductionmentioning

confidence: 99%

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A Phylogenetic Analysis of Doronicum (Asteraceae, Senecioneae) Based on Morphological, Nuclear Ribosomal (ITS), and Chloroplast (trnL-F) Evidence

Álvarez

Aguilar

Panero

et al. 2001

Molecular Phylogenetics and Evolution

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A phylogenetic analysis of the Old World genus Doronicum (26 species, 4 subspecies) based on sequence data of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA, the chloroplast spacer trnL-F, and morphology is presented. Congruence among the three data sets was explored by the computing of several indices, all of which suggest homogeneity between only the two molecular matrices. We argue that the morphological data set contains poor phylogenetic signal and advocate simultaneous analysis of the three data sets (total evidence approach) so that morphological characters are tested for homology by congruence with molecular data. The resulting phylogenetic hypothesis allows several well-supported conclusions including the placement of a Corsican endemic (D. corsicum), sister to the remainder of the genus, and the inference that an early southern European or Mediterranean diversification took place in the genus. Shifts in morphological characters (e.g., homocarpy to heterocarpy) are confirmed to have evolved several times. Results from comparative studies of sequence data of the chloroplast gene ndhF support inclusion of Doronicum in tribe Senecioneae.

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Assessing Congruence: Empirical Examples from Molecular Data

Cited by 134 publications

References 83 publications

Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

Introduction and synthesis: plant phylogeny and the origin of major biomes

A Phylogenetic Analysis of Doronicum (Asteraceae, Senecioneae) Based on Morphological, Nuclear Ribosomal (ITS), and Chloroplast (trnL-F) Evidence

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