An Assessment of Accuracy, Error, and Conflict with Support Values from Genome-Scale Phylogenetic Data

Taylor, Derek J.; Piel, William H.

doi:10.1093/molbev/msh156

Cited by 94 publications

(83 citation statements)

References 15 publications

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“…Even with this reduced threshold, only 4.0% and 2.8% of the bipartitions are different, strongly arguing for the absence of statistically significant incongruence among the 106 genes when analyzed with the same method. These results are in line with a similar analysis based on the same 106 genes, although with only eight species [16]. In addition, single gene phylogenies are not significantly incongruent with concatenation-based trees.…”

Section: Congruence Among Phylogenetic Markerssupporting

confidence: 89%

Phylogenomics: the beginning of incongruence?

et al. 2006

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International audienceUntil recently, molecular phylogenies based on a single or few orthologous genes often yielded contradictory results. Using multiple genes in a large concatenation was proposed to end these incongruences. Here we show that single-gene phylogenies often produce incongruences, albeit ones lacking statistically significant support. By contrast, the use of different tree reconstruction methods on different partitions of the concatenated supergene leads to well-resolved, but real (i.e. statistically significant) incongruences. Gathering a large amount of data is not sufficient to produce reliable trees, given the current limitation of tree reconstruction methods, especially when the quality of data is poor. We propose that selecting only data that contain minimal nonphylogenetic signals takes full advantage of phylogenomics and markedly reduces incongruence

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Section: Congruence Among Phylogenetic Markerssupporting

confidence: 89%

Phylogenomics: the beginning of incongruence?

et al. 2006

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“…Here, we compare the results of maximum parsimony (MP; Swofford 2002), neighbor-joining (NJ; Saitou and Nei 1987), and BI analyses (Huelsenbeck and Ronquist 2001). We follow a growing number of studies that contrast BI with other methods of phylogenetic inference (Suzuki et al 2002;Wilcox et al 2002;Alfaro et al 2003;Douady et al 2003;Taylor and Piel 2004), with explicit comparisons among methods.…”

Section: Introductionmentioning

confidence: 99%

Phylogeny of the Grasses (Poaceae) Revisited

Duvall¹,

Davis²,

Clark³

et al. 2007

aliso

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The most robust previously published phylogeny for the overall structure of the grass family (Poaceae) shows three early diverging lineages and two major derived clades, the BEP clade and the PACCAD clade (Grass Phylogeny Working Group 2001). A few key taxa were incompletely sampled, however, and support for the BEP clade was moderate at best and relationships among the major lineages within the PACCAD clade remained unresolved. In addition, recent studies indicated that the sister group to Poaceae may be Joinvilleaceae and/or Ecdeiocoleaceae, the latter of which were not previously sampled. In this study, missing structural data were determined and analyzed as well as sequence data for ndhF and rbcL, the two most complete plastid sequence data sets. Sampling was increased with a particular focus on key taxa such as Danthoniopsis, Eriachne, Micraira, and Streptogyna and a representative of the outgroup, Ecdeiocoleaceae. A total of 61 ingroup and two outgroup taxa were analyzed using maximum parsimony for total data, and maximum parsimony, Bayesian inference, and neighbor joining for the molecular data. A strongly supported clade of ((Eriachneae, Isachne) Micraira) was recovered as a sister subfamily to Arundinoideae and excluded from Panicoideae. Arundinaria was strongly united with Bambusoideae. The position of Streptogyna was weakly supported among Ehrhartoideae, and is still unresolved. An outgroup effect on ingroup topology was observed demonstrating that highly divergent outgroups may unpredictably alter ingroup relationships.

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“…and to provide an overestimate of accuracy in a phylogenomic dataset 172 . In fact, the posterior probability of a tree represents the probability that the tree is correct, assuming that the model is correct 173 .…”

mentioning

confidence: 99%

Phylogenomics and the reconstruction of the tree of life

2005

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Correspondence to H.P. email: herve.philippe@umontreal.ca -2 - PrefaceAs more complete genomes are sequenced, phylogenetic analysis is entering a new era -that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms based on the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to a number of fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life may prove difficult, if not impossible, to resolve with confidence. Introductory paragraphUnderstanding phylogenetic relationships between organisms is a prerequisite of almost any evolutionary study, as contemporary species all share a common history through their ancestry. The notion of phylogeny follows directly from the theory of evolution presented by Charles Darwin in "The Origin of Species" 1 : the only illustration in his famous book is the first representation of evolutionary relationships among species, in the form of a phylogenetic tree. The subsequent enthusiasm of biologists for the phylogenetic concept is illustrated by the publication of Ernst Haeckel's famous "trees" as early as 1866 2 .Today, phylogenetics -the reconstruction of evolutionary history -relies on using mathematical methods to infer the past from features of contemporary species, with only the fossil record to provide a window on the evolutionary past of life on our planet. This reconstruction involves the identification of HOMOLOGOUS CHARACTERS that are shared among different organisms, and the inference of phylogenetic trees from the comparison of these characters using reconstruction methods (BOX 1). The accuracy of -3 -the inference is therefore heavily dependent upon the quality of models for the evolution of such characters. Because the underlying mechanisms are not yet well understood, reconstructing the evolutionary history of life on Earth based solely on the information provided by living organisms has turned out to be difficult.Until the 1970s, which brought the dawn of molecular techniques for sequencing proteins and DNA, phylogenetic reconstruction was essentially based on the analysis of morphological or ultrastructural characters. The comparative anatomy of fossils and extant species has proved powerful in some respects; for example, the main groups of animals and plants have been delineated fairly easily using these methods. However, this approach is hampered by the limited number of reliable homologous characters available; these are almost non-existent in micro-organisms 3 and are rare even in complex organisms.The introduction of the use of molecular data in phylogenetics 4 led to a revolution.In the late 1980s, access to DNA sequences increased the number of homologous characters that could be compared from less than 100 to more than 1,000, ...

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An Assessment of Accuracy, Error, and Conflict with Support Values from Genome-Scale Phylogenetic Data

Cited by 94 publications

References 15 publications

Phylogenomics: the beginning of incongruence?

Phylogenomics: the beginning of incongruence?

Phylogeny of the Grasses (Poaceae) Revisited

Phylogenomics and the reconstruction of the tree of life

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