Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms (Q40909237)

24 September 2017

title

Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms (English)

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24 September 2017

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Mark P Simmons

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24 September 2017

John Gatesy

series ordinal

2

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24 September 2017

language of work or name

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19 May 2015

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Molecular Phylogenetics and Evolution

24 September 2017

number of pages

25

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based on heuristic

inferred from page(s)

published in

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24 September 2017

volume

91

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24 September 2017

page(s)

98-122

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ProtTest: selection of best-fit models of protein evolution

24 September 2017

cites work

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

A new look at the statistical model identification

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Naive binning improves phylogenomic analyses

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

The age and diversification of the angiosperms re-revisited

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes).

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Phylogenetics of Seed Plants: An Analysis of Nucleotide Sequences from the Plastid Gene rbcL

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Discordance of species trees with their most likely gene trees.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

The Irrelevance of Allele Tree Topologies for Species Delimitation, and a Non-Topological Alternative

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Another look at the root of the angiosperms reveals a familiar tale

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

MUSCLE: multiple sequence alignment with high accuracy and high throughput

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Mitochondrial resolution of a deep branch in the genealogical tree for perching birds

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

THE RETENTION INDEX AND THE RESCALED CONSISTENCY INDEX

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Confidence Limits on Phylogenies: an Approach using the Bootstrap

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Hidden likelihood support in genomic data: can forty-five wrongs make a right?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Resolution of a supertree/supermatrix paradox

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruence

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Bias in tree searches and its consequences for measuring group supports

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

TNT, a free program for phylogenetic analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Analysis of the Amborella trichopoda chloroplast genome sequence suggests that amborella is not a basal angiosperm.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Automated removal of noisy data in phylogenomic analyses.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

The evolutionary root of flowering plants

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Is it better to add taxa or characters to a difficult phylogenetic problem?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Phylogenetic and coalescent strategies of species delimitation in snubnose darters (Percidae: Etheostoma).

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

The Supertree Toolkit 2: a new and improved software package with a Graphical User Interface for supertree construction

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Inferring complex phylogenies.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Taxonomic sampling, phylogenetic accuracy, and investigator bias

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Outgroup misplacement and phylogenetic inaccuracy under a molecular clock--a simulation study.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Ancestral polyploidy in seed plants and angiosperms

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

A Concern for Evidence and a Phylogenetic Hypothesis of Relationships Among Epicrates (Boidae, Serpentes)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Quantitative Phyletics and the Evolution of Anurans

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Inconsistency of phylogenetic estimates from concatenated data under coalescence

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Applying species-tree analyses to deep phylogenetic histories: challenges and potential suggested from a survey of empirical phylogenetic studies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Identifying the Basal Angiosperm Node in Chloroplast Genome Phylogenies: Sampling One's Way Out of the Felsenstein Zone

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Estimating species phylogenies using coalescence times among sequences.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

CLADISTICS OF THE MAGNOLIIDAE

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Gene Trees in Species Trees

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Land plant evolutionary timeline: gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

The Root of Angiosperm Phylogeny Inferred from Duplicate Phytochrome Genes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Shortcomings of the cytochrome b gene as a molecular marker

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

ASTRAL: genome-scale coalescent-based species tree estimation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Increasing the efficiency of searches for the maximum likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

A Reevaluation of Seed Plant Phylogeny

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Resolving difficult phylogenetic questions: why more sequences are not enough

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Increased taxon sampling is advantageous for phylogenetic inference

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

jModelTest: phylogenetic model averaging

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Phylogenetic Analyses of Basal Angiosperms Based on Nine Plastid, Mitochondrial, and Nuclear Genes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Angiosperm phylogeny inferred from sequences of four mitochondrial genes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Phylogenetic inference based on matrix representation of trees

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Random roots and lineage sorting

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Inferring ancient divergences requires genes with strong phylogenetic signals.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Patterns of Variation in Levels of Homoplasy

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Phylogenetic supertrees: Assembling the trees of life

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Phylogenomic interrogation of arachnida reveals systemic conflicts in phylogenetic signal

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

The problem of rooting rapid radiations.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

STRAW: Species TRee Analysis Web server

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Independence of alignment and tree search.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Spurious 99% bootstrap and jackknife support for unsupported clades.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

An artifact caused by undersampling optimal trees in supermatrix analyses of locally sampled characters.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Dubious resolution and support from published sparse supermatrices: the importance of thorough tree searches

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Divergent maximum-likelihood-branch-support values for polytomies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Disparate parametric branch-support values from ambiguous characters

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

How can third codon positions outperform first and second codon positions in phylogenetic inference? An empirical example from the seed plants

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Phyutility: a phyloinformatics tool for trees, alignments and molecular data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Angiosperm phylogeny: 17 genes, 640 taxa

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Land plant origins and coalescence confusion

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Biases in phylogenetic estimation can be caused by random sequence segments.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Signal sequences. The limits of variation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Phylotranscriptomic analysis of the origin and early diversification of land plants

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Alignment uncertainty and genomic analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Phylogenomics and coalescent analyses resolve extant seed plant relationships

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

Origin of land plants using the multispecies coalescent model

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

The multispecies coalescent model and land plant origins: a reply to Springer and Gatesy

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.05.011

10.1016/J.YMPEV.2015.05.011

7 January 2021

Identifiers

DOI

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24 September 2017

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