Do we still need supertrees?

Haeseler, Arndt von

doi:10.1186/1741-7007-10-13

Cited by 29 publications

(22 citation statements)

References 11 publications

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“…When such data are missing, both supertree and supermatrix strategies can lack statistical support and ignore uncertainties in the subtrees/matrices [66], [68], which sometimes can lead to a misinterpretation of the phylogenetic relationship among species. In fact, the lack of data due to the incomplete presence of genes for all of the species analyzed can yield irregular matrices.…”

Section: Discussionmentioning

confidence: 99%

Desmophyllum dianthus (Esper, 1794) in the Scleractinian Phylogeny and Its Intraspecific Diversity

Addamo

Reimer²,

Taviani³

et al. 2012

PLoS ONE

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The cosmopolitan solitary deep-water scleractinian coral Desmophyllum dianthus (Esper, 1794) was selected as a representative model species of the polyphyletic Caryophylliidae family to (1) examine phylogenetic relationships with respect to the principal Scleractinia taxa, (2) check population structure, (3) test the widespread connectivity hypothesis and (4) assess the utility of different nuclear and mitochondrial markers currently in use. To carry out these goals, DNA sequence data from nuclear (ITS and 28S) and mitochondrial (16S and COI) markers were analyzed for several coral species and for Mediterranean populations of D. dianthus. Three phylogenetic methodologies (ML, MP and BI), based on data from the four molecular markers, all supported D. dianthus as clearly belonging to the “robust” clade, in which the species Lophelia pertusa and D. dianthus not only grouped together, but also shared haplotypes for some DNA markers. Molecular results also showed shared haplotypes among D. dianthus populations distributed in regions separated by several thousands of kilometers and by clear geographic barriers. These results could reflect limited molecular and morphological taxonomic resolution rather than real widespread connectivity. Additional studies are needed in order to find molecular markers and morphological features able to disentangle the complex phylogenetic relationship in the Order Scleractinia and to differentiate isolated populations, thus avoiding the homoplasy found in some morphological characters that are still considered in the literature.

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Section: Discussionmentioning

confidence: 99%

Desmophyllum dianthus (Esper, 1794) in the Scleractinian Phylogeny and Its Intraspecific Diversity

Addamo

Reimer²,

Taviani³

et al. 2012

PLoS ONE

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“…Both supertree methods supported similar topology, but there are few differences in blue group -in phylogenetic position of pre-WGD and post-WGD species. Supertree methodology has been considered a robust approach to analyze broad phylogenies (Daubin et al, 2001;Qian and Zhang, 2016), but the difficulty to carry statistical analysis is considered challenging in supertree methodology (von Haeseler, 2012). Therefore, the phylogenetic approach based on Bayesian trees could compensate this disadvantage in supertree methodology.…”

Section: Resultsmentioning

confidence: 99%

Evolution of pathogenic and nonpathogenic yeasts mitochondrial genomes inferred by supertrees and supermatrices with divergence estimates based on relaxed molecular clocks

Lopes

Ferreira

Antoneli

et al. 2018

Preprint

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The evolution of mitochondrial genomes is essential for the adaptation of yeasts to the variation of environmental levels of oxygen. Although Saccharomyces cerevisiae mitochondrial DNA lacks all complex I genes, respiration is possible because alternative NADH dehydrogenases are encoded by NDE1 and NDI1 nuclear genes. The proposed whole genome duplication (WGD) in the yeast ancestor at 150-100 million years ago caused nuclear gene duplications and secondary losses, although its relation to the loss of complex I mitocondrial is unknown. Here we present phylogenomic supertrees and supermatrix tree of 46 mitochondrial genomes showing that the loss of complex I predates WGD and occurred independently in the S. cerevisiae group and the fission yeast Schizosaccharomyces pombe. We also show that the branching patterns do not differ dramatically in supertrees and supermatrix phylogenies. Our inferences indicated consistent relations between conserved mitochondrial chromosomal gene order (synteny) in closely related yeasts. Correlation of mitochondrial molecular clock estimates and atmospheric oxygen variation in the Phanerozoic suggests that the Saccharomyces lineage might have lost the complex I during hypoxic periods near Perminian-Triassic or Triassic-Jurassic mass extinction events, while the Schizosaccharomyces lineage possibly lost the complex I during hypoxic environment periods during Middle Cambrian until Lower Devonian. The loss of mitochondrial complex I during low oxygen might not affect yeast metabolism due to fermentative switch. The return to increased oxygen periods might have favored adaptations to aerobic metabolism. Additionally, we also showed that NDE1 and NDI1 phylogenies indicate evolutionary convergence in yeasts where mitochondrial complex I is absent.

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“…Supertree methods are used to combine a set of phylogenetic trees with non-identical but overlapping taxon sets, into a larger supertree that contains all the taxa of every input tree. Many supertree methods have been established over the years, see for example (Bininda-Emonds, 2004;Ross and Rodrigo, 2004;Chen et al, 2006;Holland et al, 2007;Scornavacca et al, 2008;Ranwez et al, 2010;Bansal et al, 2010;Snir and Rao, 2010;Swenson et al, 2012;Brinkmeyer et al, 2013;Berry et al, 2013;Gysel et al, 2013;Whidden et al, 2014); these methods complement supermatrix methods which combine the "raw" sequence data rather than the trees (von Haeseler, 2012).…”

Section: Introductionmentioning

confidence: 99%

Peer Review #2 of "Collecting reliable clades using the Greedy Strict Consensus Merger (v0.2)"

Swenson¹

2016

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Supertree methods combine a set of phylogenetic trees into a single supertree. Similar to supermatrix methods, these methods provide a way to reconstruct larger parts of the Tree of Life, potentially evading the computational complexity of phylogenetic inference methods such as maximum likelihood. The supertree problem can be formalized in different ways, to cope with contradictory information in the input. Many supertree methods have been developed. Some of them solve NP-hard optimization problems like the well known Matrix Representation with Parsimony, others have polynomial worst-case running time but work in a greedy fashion (FlipCut). Both can profit from a set of clades that are already known to be part of the supertree. The Superfine approach shows how the Greedy Strict Consensus Merger (GSCM) can be used as preprocessing to find these clades. We introduce different scoring functions for the GSCM, a randomization, as well as a combination thereof to improve the GSCM to find more clades. This helps, in turn, to improve the resolution of the GSCM supertree. We find this modifications to increase the number of true positive clades by 18 % compared to the currently used Overlap scoring.

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Do we still need supertrees?

Cited by 29 publications

References 11 publications

Desmophyllum dianthus (Esper, 1794) in the Scleractinian Phylogeny and Its Intraspecific Diversity

Desmophyllum dianthus (Esper, 1794) in the Scleractinian Phylogeny and Its Intraspecific Diversity

Evolution of pathogenic and nonpathogenic yeasts mitochondrial genomes inferred by supertrees and supermatrices with divergence estimates based on relaxed molecular clocks

Peer Review #2 of "Collecting reliable clades using the Greedy Strict Consensus Merger (v0.2)"

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