(Q35920327)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26865273%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

title

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

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26865273%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

1 reference

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26865273%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

Edward L. Braun

series ordinal

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26865273%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

Kelly Ann Meiklejohn

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26865273%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

Rebecca Kimball

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26865273%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

3

Travis C Glenn

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26865273%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

publication date

10 February 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26865273%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26865273%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

volume

65

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26865273%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

issue

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26865273%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

page(s)

612-627

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26865273%20AND%20SRC:MED&resulttype=core&format=json

Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes

7 March 2020

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The phylogenetic position and speciation dynamics of the genus Perdix (Phasianidae, Galliformes)

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

21 January 2018

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Ultraconserved Elements in the Human Genome

21 January 2018

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Conserved genes, sampling error, and phylogenomic inference.

21 January 2018

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

21 January 2018

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

21 January 2018

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

21 January 2018

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Phylogenetic relationships of the phasianidae reveals possible non-pheasant taxa

21 January 2018

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Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites

21 January 2018

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

21 January 2018

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PHYLOGENETIC POSITION OF THE NEW WORLD QUAIL (ODONTOPHORIDAE): EIGHT NUCLEAR LOCI AND THREE MITOCHONDRIAL REGIONS CONTRADICT MORPHOLOGY AND THE SIBLEY-AHLQUIST TAPESTRY

21 January 2018

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More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

21 January 2018

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A phylogenomic analysis of turtles

21 January 2018

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Clann: investigating phylogenetic information through supertree analyses

21 January 2018

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Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves: Galliformes): effects of character exclusion, data partitioning and missing data

21 January 2018

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Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis

21 January 2018

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Fast and consistent estimation of species trees using supermatrix rooted triples

21 January 2018

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An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines

21 January 2018

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Discordance of species trees with their most likely gene trees.

21 January 2018

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Is a new and general theory of molecular systematics emerging?

21 January 2018

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

21 January 2018

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Rooted triple consensus and anomalous gene trees

21 January 2018

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Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Cases in which Parsimony or Compatibility Methods will be Positively Misleading

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Turtle phylogeny: insights from a novel nuclear intron

21 January 2018

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Concatenation versus coalescence versus "concatalescence".

21 January 2018

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

21 January 2018

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Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

21 January 2018

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

21 January 2018

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A phylogenomic study of birds reveals their evolutionary history

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Phylogenomic evidence for multiple losses of flight in ratite birds

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Targeted enrichment: maximizing orthologous gene comparisons across deep evolutionary time

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Bayesian inference of species trees from multilocus data

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

21 January 2018

1 reference

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

21 January 2018

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A justification for reporting the majority-rule consensus tree in Bayesian phylogenetics.

21 January 2018

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Using supernetworks to distinguish hybridization from lineage-sorting

21 January 2018

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

21 January 2018

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Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo.

21 January 2018

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MRBAYES: Bayesian inference of phylogenetic trees

21 January 2018

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Regression and time series model selection in small samples

21 January 2018

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

21 January 2018

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Phylogenomics: the beginning of incongruence?

21 January 2018

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The global diversity of birds in space and time

21 January 2018

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

21 January 2018

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Slicing hyperdimensional oranges: the geometry of phylogenetic estimation.

21 January 2018

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Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix

21 January 2018

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

21 January 2018

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A molecular phylogeny of the pheasants and partridges suggests that these lineages are not monophyletic

21 January 2018

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A macroevolutionary perspective on multiple sexual traits in the phasianidae (galliformes)

21 January 2018

1 reference

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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%2FSYW014

Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

STEM: species tree estimation using maximum likelihood for gene trees under coalescence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Inconsistency of phylogenetic estimates from concatenated data under coalescence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

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%2FSYW014

Selecting optimal partitioning schemes for phylogenomic datasets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

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

21 January 2018

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Is recombination a problem for species-tree analyses?

21 January 2018

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Anchored hybrid enrichment for massively high-throughput phylogenomics

21 January 2018

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Capturing protein-coding genes across highly divergent species

21 January 2018

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BEST: Bayesian estimation of species trees under the coalescent model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Indel evolution of mammalian introns and the utility of non-coding nuclear markers in eutherian phylogenetics

21 January 2018

1 reference

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

21 January 2018

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

21 January 2018

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

21 January 2018

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Statistical binning enables an accurate coalescent-based estimation of the avian tree

21 January 2018

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Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting

21 January 2018

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ASTRAL: genome-scale coalescent-based species tree estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Evolution of an avian pigmentation gene correlates with a measure of sexual selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Error in Phylogenetic Estimation for Bushes in the Tree of Life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Genetic evidence for complex speciation of humans and chimpanzees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Resolving difficult phylogenetic questions: why more sequences are not enough

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

MODELTEST: testing the model of DNA substitution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Phylogenetic inference based on matrix representation of trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Bushes in the tree of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Genome-scale approaches to resolving incongruence in molecular phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

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%2FSYW014

Inferring ancient divergences requires genes with strong phylogenetic signals.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Parametric phylogenetics?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Estimating the Dimension of a Model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Subdivision in an ancestral species creates asymmetry in gene trees

21 January 2018

1 reference

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21 January 2018

1 reference

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Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales

21 January 2018

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Ratite nonmonophyly: independent evidence from 40 novel Loci

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

21 January 2018

The gene tree delusion

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

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%2FSYW014

A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Assessing phylogenetic relationships among galliformes: a multigene phylogeny with expanded taxon sampling in Phasianidae

21 January 2018

1 reference

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Deciphering ancient rapid radiations

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

Primers for a PCR-Based Approach to Mitochondrial Genome Sequencing in Birds and Other Vertebrates

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW014

21 January 2018

Identifiers

DOI

10.1093/SYSBIO/SYW014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26865273%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

1 reference