Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum (Q44161169)

30 November 2017

title

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

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30 November 2017

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Mark S Springer

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30 November 2017

John Gatesy

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30 November 2017

publication date

22 August 2014

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Molecular Phylogenetics and Evolution

30 November 2017

published in

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30 November 2017

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30 November 2017

page(s)

231-266

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Conventional simulation of biological sequences leads to a biased assessment of multi-Loci phylogenetic analysis

30 November 2017

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Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals

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Hidden morphological support for the phylogenetic placement of Pseudoryx nghetinhensis with bovine bovids: a combined analysis of gross anatomical evidence and DNA sequences from five genes

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Combined support for wholesale taxic atavism in gavialine crocodylians

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7 January 2021

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7 January 2021

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Sources of Error Inherent in Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing among Different Methods

7 January 2021

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7 January 2021

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Coalescent-based genome analyses resolve the early branches of the euarchontoglires.

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How low can you go? The effects of mutation rate on the accuracy of species-tree estimation

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The accuracy of species tree estimation under simulation: a comparison of methods

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Partitioned likelihood support and the evaluation of data set conflict

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Multiple instances of ancient balancing selection shared between humans and chimpanzees

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The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference

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Heterogeneous models place the root of the placental mammal phylogeny

7 January 2021

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Early history of mammals is elucidated with the ENCODE multiple species sequencing data

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Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions

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Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals

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Bayesian phylogenetic analysis of combined data

7 January 2021

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A time-calibrated species tree of Crocodylia reveals a recent radiation of the true crocodiles

7 January 2021

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The promise of comparative genomics in mammals

7 January 2021

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Impact of increased character sampling on the phylogeny of Cetartiodactyla (Mammalia): combined analysis including fossils

7 January 2021

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The placental mammal ancestor and the post-K-Pg radiation of placentals

7 January 2021

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Microevolutionary processes generate phylogenomic discordance at ancient divergences

7 January 2021

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Error in Phylogenetic Estimation for Bushes in the Tree of Life

7 January 2021

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Major radiations in the evolution of Caviid rodents: reconciling fossils, ghost lineages, and relaxed molecular clocks

7 January 2021

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The evolutionary ecology of the major histocompatibility complex

7 January 2021

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Matrix representation with parsimony, taxonomic congruence, and total evidence

7 January 2021

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Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting

7 January 2021

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OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics

7 January 2021

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An empirical examination of the utility of codon-substitution models in phylogeny reconstruction

7 January 2021

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A Comment on Baum's Method for Combining Phylogenetic Trees

7 January 2021

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Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals

7 January 2021

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A total-evidence approach to dating with fossils, applied to the early radiation of the hymenoptera

7 January 2021

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Discordance of species trees with their most likely gene trees: a unifying principle.

7 January 2021

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Discordance of species trees with their most likely gene trees: the case of five taxa.

7 January 2021

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Random roots and lineage sorting

7 January 2021

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Inferring ancient divergences requires genes with strong phylogenetic signals.

7 January 2021

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STRAW: Species TRee Analysis Web server

7 January 2021

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Misleading results of likelihood-based phylogenetic analyses in the presence of missing data

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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Quantification and relative severity of inflated branch-support values generated by alternative methods: an empirical example

7 January 2021

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How should species phylogenies be inferred from sequence data?

7 January 2021

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Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

7 January 2021

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Relationships of Cetacea (Artiodactyla) among mammals: increased taxon sampling alters interpretations of key fossils and character evolution

7 January 2021

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Phylogenetics. Which mammalian supertree to bark up?

7 January 2021

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Land plant origins and coalescence confusion

7 January 2021

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Placental mammal diversification and the Cretaceous-Tertiary boundary

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.08.013

Molecules consolidate the placental mammal tree

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.08.013

Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix

7 January 2021

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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.08.013

Phylogeny of Eunicida (Annelida) and exploring data congruence using a partition addition bootstrap alteration (PABA) approach

7 January 2021

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Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods

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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Phylogenomic analyses elucidate the evolutionary relationships of bats

7 January 2021

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Use of y chromosome and mitochondrial DNA population structure in tracing human migrations

7 January 2021

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Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers

7 January 2021

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Genomics, biogeography, and the diversification of placental mammals

7 January 2021

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Reply to Gatesy and Springer: the multispecies coalescent model can effectively handle recombination and gene tree heterogeneity

7 January 2021

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Phylogenomics and coalescent analyses resolve extant seed plant relationships

7 January 2021

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Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles

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

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.08.013

Increased taxon sampling greatly reduces phylogenetic error

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2014.08.013

10.1016/J.YMPEV.2014.08.013

7 January 2021

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DOI

1 reference

30 November 2017

1 reference