(Q36332268)

13 August 2017

title

Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling (English)

1 reference

13 August 2017

1 reference

0 references

Sarah Kingston

10

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Peter A. Hosner

Peter A Hosner

4

0 references

Christopher C. Witt

Christopher C Witt

15

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Edward L. Braun

Edward L Braun

17

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Rebecca Kimball

Rebecca T Kimball

2

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Sushma Reddy

Sushma Reddy

1

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author name string

Akanksha Pandey

3

1 reference

13 August 2017

Michael J Braun

5

1 reference

13 August 2017

Shannon J Hackett

6

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13 August 2017

Kin-Lan Han

7

1 reference

13 August 2017

John Harshman

8

1 reference

13 August 2017

Christopher J Huddleston

9

1 reference

13 August 2017

Ben D Marks

11

1 reference

13 August 2017

Kathleen J Miglia

12

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13 August 2017

William S Moore

13

1 reference

13 August 2017

Frederick H Sheldon

14

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13 August 2017

Tamaki Yuri

16

1 reference

13 August 2017

publication date

27 March 2017

1 reference

13 August 2017

1 reference

ExaBayes: massively parallel bayesian tree inference for the whole-genome era.

13 August 2017

cites work

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Combining Trees as a Way of Combining Data Sets for Phylogenetic Inference, and the Desirability of Combining Gene Trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Homoplastic microinversions and the avian tree of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Model misspecification and probabilistic tests of topology: evidence from empirical data sets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Building the avian tree of life using a large-scale, sparse supermatrix

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Selection on protein structure, interaction, and sequence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Choosing the best genes for the job: the case for stationary genes in genome-scale phylogenetics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

The Hill-Robertson effect: evolutionary consequences of weak selection and linkage in finite populations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Clann: investigating phylogenetic information through supertree analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Phylogenomics and the reconstruction of the tree of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Can We Identify Genes with Increased Phylogenetic Reliability?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Causes of evolutionary rate variation among protein sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Is a new and general theory of molecular systematics emerging?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Diversification of Neoaves: integration of molecular sequence data and fossils

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Parallel radiations in the primary clades of birds

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

The phylogenetic likelihood library.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Modeling compositional heterogeneity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

A phylogenomic study of birds reveals their evolutionary history

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Irrational exuberance for resolved species trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Are transposable element insertions homoplasy free?: an examination using the avian tree of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Phylogenomic evidence for multiple losses of flight in ratite birds

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Inferring complex phylogenies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Is sparse taxon sampling a problem for phylogenetic inference?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Low-parameter phylogenetic inference under the general markov model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Whole-genome analyses resolve early branches in the tree of life of modern birds

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Phylogenomics: the beginning of incongruence?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

The global diversity of birds in space and time

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

From reptilian phylogenomics to reptilian genomes: analyses of c-Jun and DJ-1 proto-oncogenes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Human genome ultraconserved elements are ultraselected

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Identifying localized biases in large datasets: a case study using the avian tree of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Inconsistency of phylogenetic estimates from concatenated data under coalescence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Divergence across Australia's Carpentarian barrier: statistical phylogeography of the red-backed fairy wren (Malurus melanocephalus).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Polytomies and Bayesian phylogenetic inference

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Phylogenetic mixtures on a single tree can mimic a tree of another topology.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Translational control by the 3'-UTR: the ends specify the means.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Incongruence among different mitochondrial regions: a case study using complete mitogenomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Ultrafast approximation for phylogenetic bootstrap

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

ASTRAL: genome-scale coalescent-based species tree estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Phylogenomics resolves the timing and pattern of insect evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Phylogeny and Biogeography of the Core Babblers (Aves: Timaliidae)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Deep metazoan phylogeny: when different genes tell different stories.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Birds in a bush: five genes indicate explosive evolution of avian orders

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Increased taxon sampling is advantageous for phylogenetic inference

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Assessing parameter identifiability in phylogenetic models using data cloning

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

How Meaningful Are Bayesian Support Values?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Ratite nonmonophyly: independent evidence from 40 novel Loci

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

21 January 2018

The gene tree delusion

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

A rapid bootstrap algorithm for the RAxML Web servers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Should phylogenetic models be trying to "fit an elephant"?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

The Bayesian "star paradox" persists for long finite sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

The Status of Avian Systematics and Its Unsolved Problems

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

DendroPy: a Python library for phylogenetic computing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

On the distributions of bootstrap support and posterior distributions for a star tree

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Testing hypotheses about the sister group of the passeriformes using an independent 30-locus data set.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

nhmmer: DNA homology search with profile HMMs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Error, signal, and the placement of Ctenophora sister to all other animals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

The genetic code can cause systematic bias in simple phylogenetic models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Phylotranscriptomic analysis of the origin and early diversification of land plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Branch-length prior influences Bayesian posterior probability of phylogeny.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Comparative genomics reveals insights into avian genome evolution and adaptation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Increased taxon sampling greatly reduces phylogenetic error

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Comparative molecular evolution and phylogenetic utility of 3′-UTRs and introns in Galliformes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

POLYTOMIES, THE POWER OF PHYLOGENETIC INFERENCE, AND THE STOCHASTIC NATURE OF MOLECULAR EVOLUTION: A COMMENT ON WALSH ET AL. (1999)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Examining Basal Avian Divergences with Mitochondrial Sequences: Model Complexity, Taxon Sampling, and Sequence Length

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

A well-tested set of primers to amplify regions spread across the avian genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Phylogenetic inference based on matrix representation of trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Ancestral range reconstruction of Galliformes: the effects of topology and taxon sampling

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

Hydrophobicity and phylogeny

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

21 January 2018

Taxon sampling revisited

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX041

21 January 2018

Identifiers

DOI

10.1093/SYSBIO/SYX041

1 reference

13 August 2017

1 reference