An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. (Q52994145)

10 May 2018

review article

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title

An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. (English)

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10 May 2018

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2

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10 May 2018

Hervé Philippe

5

object named as

Hervé Philippe

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10 May 2018

author name string

Henner Brinkmann

1

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10 May 2018

Yan Zhou

3

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10 May 2018

Gaëtan Poncelin de Raucourt

4

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10 May 2018

publication date

1 October 2005

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10 May 2018

published in

Systematic Biology

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10 May 2018

volume

54

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10 May 2018

page(s)

743-757

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10 May 2018

issue

5

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10 May 2018

Instability of quartet analyses of molecular sequence data by the maximum likelihood method: the Cetacea/Artiodactyla relationships

cites work

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Evidence for a clade of nematodes, arthropods and other moulting animals

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

A kingdom-level phylogeny of eukaryotes based on combined protein data

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

The evolutionary position of nematodes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

The power of relative rates tests depends on the data

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Evolution of monoblepharidalean fungi based on complete mitochondrial genome sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Systematics of primary osmotrophic euglenids: a molecular approach to the phylogeny of Distigma and Astasia (Euglenozoa)

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Membrane heredity and early chloroplast evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Analyses of RNA Polymerase II genes from free-living protists: phylogeny, long branch attraction, and the eukaryotic big bang

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Oxymonads are closely related to the excavate taxon Trimastix.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Phylogenomics and the reconstruction of the tree of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

The highly reduced genome of an enslaved algal nucleus

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Hydrogenosomes, mitochondria and early eukaryotic evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Where is the root of the universal tree of life?

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Maximum-likelihood phylogenetic analysis under a covarion-like model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Critical analysis of the topology and rooting of the parabasalian 16S rRNA tree.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Relative efficiencies of the maximum likelihood, maximum parsimony, and neighbor-joining methods for estimating protein phylogeny.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Is sparse taxon sampling a problem for phylogenetic inference?

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Is the Felsenstein zone a fly trap?

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Congruent evidence from alpha-tubulin and beta-tubulin gene phylogenies for a zygomycete origin of microsporidia.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Microsporidia: Biology and Evolution of Highly Reduced Intracellular Parasites

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Evolution of key cell signaling and adhesion protein families predates animal origins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Was the nucleus the first endosymbiont?

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

The Closest Unicellular Relatives of Animals

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Species sampling has a major impact on phylogenetic inference

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Metabolic symbiosis at the origin of eukaryotes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Parallel adaptive radiations in two major clades of placental mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

The hydrogen hypothesis for the first eukaryote

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Resolution of the early placental mammal radiation using Bayesian phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

The Opisthokonta and the Ecdysozoa may not be clades: stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

The new phylogeny of eukaryotes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Phylogenomics of eukaryotes: impact of missing data on large alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Genome-scale phylogeny and the detection of systematic biases

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Identifying and removing fast-evolving sites using compatibility analysis: an example from the Arthropoda

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Early evolution: prokaryotes, the new kids on the block

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Was the ANITA rooting of the angiosperm phylogeny affected by long-branch attraction? Amborella, Nymphaeales, Illiciales, Trimeniaceae, and Austrobaileya

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes.

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Genome-scale approaches to resolving incongruence in molecular phylogenies

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

CONSEL: for assessing the confidence of phylogenetic tree selection

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Evolutionary history of "early-diverging" eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia.

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Anaerobic fungi and their cellulolytic and xylanolytic enzymes.

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

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1 reference

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Can Incomplete Taxa Rescue Phylogenetic Analyses from Long-Branch Attraction?

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis

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1 reference

https://api.crossref.org/works/10.1080%2F10635150500234609

Cloning and expression of multiple cellulase cDNAs from the anaerobic rumen fungus Neocallimastix patriciarum in Escherichia coli

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1 reference

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1 reference

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1 reference

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Identifiers

DOI

10.1080/10635150500234609

1 reference

10 May 2018

PubMed ID

16243762

1 reference

10 May 2018