Computing the Internode Certainty and Related Measures from Partial Gene Trees

Kobert, Kassian; Salichos, Leonidas; Rokas, Antonis; Stamatakis, Alexandros

doi:10.1093/molbev/msw040

Cited by 75 publications

(39 citation statements)

References 16 publications

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“…To quantify incongruence between the 1233 orthologous groups across the 93 internodes of the yeast phylogeny, we used the 1233 individual ML gene trees to calculate IC values (Salichos and Rokas 2013; Salichos et al 2014; Kobert et al 2016). Our results showed that most of the internodes in concatenation- and coalescence-based phylogenies inferred from AA and C12 data matrices had IC values >0 (Figure 3, Figure 4, Figure S6, and Figure S7), suggesting that those relationships were recovered by the majority of 1233 genes.…”

Section: Resultsmentioning

confidence: 99%

“…Finally, we used internode certainty (IC) to quantify the incongruence by considering all most prevalent conflicting bipartitions for each individual internode among individual gene trees (Salichos and Rokas 2013; Salichos et al 2014; Kobert et al 2016). The (partial) IC values were calculated from the set of the 1233 ML gene trees (Kobert et al 2016), as implemented in RA×ML, version 8.2.3.…”

Section: Methodsmentioning

confidence: 99%

“…The (partial) IC values were calculated from the set of the 1233 ML gene trees (Kobert et al 2016), as implemented in RA×ML, version 8.2.3. We found that the mean IC values of our 93 internal branches in both the concatenation- and coalescence-based phylogenies inferred from the AA data matrix were slightly higher than those of 93 internal branches in both the concatenation- and coalescence-based phylogenies inferred from the C12 data matrix (mean IC values in the concatenation- and coalescence-based phylogenies from the AA data matrix are 0.404 and 0.399, respectively, whereas mean IC values in the concatenation- and coalescence-based phylogenies from the C12 data matrix were 0.368 and 0.367, respectively).…”

Section: Methodsmentioning

confidence: 99%

“…Since the AA data matrix showed lower levels of incongruence than the C12 data matrix (see above result), we examined the phylogenetic signal of individual genes using only the gene alignments of the AA data matrix. To quantify support for individual gene trees, we used two common phylogenetic measures on the AA data matrix: (1) the average bootstrap support (ABS), which was calculated using a custom Perl script, and corresponds to the average of bootstrap support values across the ML tree of a given gene; (2) the relative tree certainty (RTC), which was calculated in RA×ML, and corresponds to the average of all IC values across the ML tree of a given gene (Salichos et al 2014; Kobert et al 2016). IC values on each ML tree were calculated by examining the bipartitions present in the topologies generated by the 100 rapid bootstrap replicates.…”

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Shen

Zhou

Kominek

et al. 2016

G3 Genes|Genomes|Genetics

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193

159

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Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Shen

Zhou

Kominek

et al. 2016

G3 Genes|Genomes|Genetics

Self Cite

193

159

View full text Add to dashboard Cite

show abstract

“…The probabilistic and observed adjustment schemes were applied, because the gene trees contained both comprehensive and partial trees (Kobert et al 2016). An IC or ICA value close to 1 means absence of conflicting bipartitions for a given internode, while a value close to zero suggests that incongruent bipartitions equally exist, and a value close to −1 indicates the lack of support for a given internode (Salichos et al 2014).…”

Section: Methodsmentioning

confidence: 99%

Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants

Torre

Sterck

et al. 2017

Genome Biology and Evolution

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Phylogenetic relationships among seed plant taxa, especially within the gymnosperms, remain contested. In contrast to angiosperms, for which several genomic, transcriptomic and phylogenetic resources are available, there are few, if any, molecular markers that allow broad comparisons among gymnosperm species. With few gymnosperm genomes available, recently obtained transcriptomes in gymnosperms are a great addition to identifying single-copy gene families as molecular markers for phylogenomic analysis in seed plants. Taking advantage of an increasing number of available genomes and transcriptomes, we identified single-copy genes in a broad collection of seed plants and used these to infer phylogenetic relationships between major seed plant taxa. This study aims at extending the current phylogenetic toolkit for seed plants, assessing its ability for resolving seed plant phylogeny, and discussing potential factors affecting phylogenetic reconstruction. In total, we identified 3,072 single-copy genes in 31 gymnosperms and 2,156 single-copy genes in 34 angiosperms. All studied seed plants shared 1,469 single-copy genes, which are generally involved in functions like DNA metabolism, cell cycle, and photosynthesis. A selected set of 106 single-copy genes provided good resolution for the seed plant phylogeny except for gnetophytes. Although some of our analyses support a sister relationship between gnetophytes and other gymnosperms, phylogenetic trees from concatenated alignments without 3rd codon positions and amino acid alignments under the CAT + GTR model, support gnetophytes as a sister group to Pinaceae. Our phylogenomic analyses demonstrate that, in general, single-copy genes can uncover both recent and deep divergences of seed plant phylogeny.

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Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

Pease

Brown

Walker

et al. 2018

American J of Botany

203

244

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PREMISE OF THE STUDY : Phylogenetic support has been difficult to evaluate within the green plant tree of life partly due to a lack of specificity between conflicted versus poorly informed branches. As data sets continue to expand in both breadth and depth, new support measures are needed that are more efficient and informative. METHODS:We describe the Quartet Sampling (QS) method, a quartet-based evaluation system that synthesizes several phylogenetic and genomic analytical approaches. QS characterizes discordance in large-sparse and genome-wide data sets, overcoming issues of alignment sparsity and distinguishing strong conflict from weak support. We tested QS with simulations and recent plant phylogenies inferred from variously sized data sets.KEY RESULTS: QS scores demonstrated convergence with increasing replicates and were not strongly affected by branch depth. Patterns of QS support from different phylogenies led to a coherent understanding of ancestral branches defining key disagreements, including the relationships of Ginkgo to cycads, magnoliids to monocots and eudicots, and mosses to liverworts. The relationships of ANA-grade angiosperms (Amborella, Nymphaeales, Austrobaileyales), major monocot groups, bryophytes, and fern families are likely highly discordant in their evolutionary histories, rather than poorly informed. QS can also detect discordance due to introgression in phylogenomic data. CONCLUSIONS:Quartet Sampling is an efficient synthesis of phylogenetic tests that offers more comprehensive and specific information on branch support than conventional measures. The QS method corroborates growing evidence that phylogenomic investigations that incorporate discordance testing are warranted when reconstructing complex evolutionary histories, in particular those surrounding ANA-grade, monocots, and nonvascular plants.

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Computing the Internode Certainty and Related Measures from Partial Gene Trees

Cited by 75 publications

References 16 publications

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants

Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

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