(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

1

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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

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

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Naive binning improves phylogenomic analyses

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The age and diversification of the angiosperms re-revisited

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

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

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

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

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7 January 2021

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

7 January 2021

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

7 January 2021

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THE RETENTION INDEX AND THE RESCALED CONSISTENCY INDEX

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Confidence Limits on Phylogenies: an Approach using the Bootstrap

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

7 January 2021

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

7 January 2021

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Resolution of a supertree/supermatrix paradox

7 January 2021

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

7 January 2021

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

7 January 2021

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Bias in tree searches and its consequences for measuring group supports

7 January 2021

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

7 January 2021

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Automated removal of noisy data in phylogenomic analyses.

7 January 2021

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The evolutionary root of flowering plants

7 January 2021

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

7 January 2021

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

7 January 2021

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

7 January 2021

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

7 January 2021

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Inferring complex phylogenies.

7 January 2021

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Taxonomic sampling, phylogenetic accuracy, and investigator bias

7 January 2021

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

7 January 2021

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

7 January 2021

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Ancestral polyploidy in seed plants and angiosperms

7 January 2021

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

7 January 2021

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Quantitative Phyletics and the Evolution of Anurans

7 January 2021

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Inconsistency of phylogenetic estimates from concatenated data under coalescence

7 January 2021

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

7 January 2021

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

7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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The Root of Angiosperm Phylogeny Inferred from Duplicate Phytochrome Genes

7 January 2021

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

7 January 2021

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Shortcomings of the cytochrome b gene as a molecular marker

7 January 2021

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ASTRAL: genome-scale coalescent-based species tree estimation

7 January 2021

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

7 January 2021

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

7 January 2021

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A Reevaluation of Seed Plant Phylogeny

7 January 2021

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Resolving difficult phylogenetic questions: why more sequences are not enough

7 January 2021

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Increased taxon sampling is advantageous for phylogenetic inference

7 January 2021

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7 January 2021

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7 January 2021

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Angiosperm phylogeny inferred from sequences of four mitochondrial genes

7 January 2021

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Phylogenetic inference based on matrix representation of trees

7 January 2021

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Random roots and lineage sorting

7 January 2021

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

7 January 2021

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Inferring ancient divergences requires genes with strong phylogenetic signals.

7 January 2021

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Patterns of Variation in Levels of Homoplasy

7 January 2021

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Phylogenetic supertrees: Assembling the trees of life

7 January 2021

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Phylogenomic interrogation of arachnida reveals systemic conflicts in phylogenetic signal

7 January 2021

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The problem of rooting rapid radiations.

7 January 2021

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7 January 2021

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Independence of alignment and tree search.

7 January 2021

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Spurious 99% bootstrap and jackknife support for unsupported clades.

7 January 2021

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

7 January 2021

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

7 January 2021

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Divergent maximum-likelihood-branch-support values for polytomies

7 January 2021

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Disparate parametric branch-support values from ambiguous characters

7 January 2021

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7 January 2021

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

7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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

7 January 2021

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TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

7 January 2021

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

7 January 2021

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Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics

7 January 2021

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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

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Signal sequences. The limits of variation

7 January 2021

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Phylotranscriptomic analysis of the origin and early diversification of land plants

7 January 2021

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Alignment uncertainty and genomic analysis

7 January 2021

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Phylogenomics and coalescent analyses resolve extant seed plant relationships

7 January 2021

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

7 January 2021

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Origin of land plants using the multispecies coalescent model

7 January 2021

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

7 January 2021

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7 January 2021

Identifiers

DOI

1 reference

24 September 2017

1 reference