Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards (Q39048580)

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scientific article published on 6 October 2016

Language	Label	Description	Also known as
English	Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards	scientific article published on 6 October 2016

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scholarly article

1 reference

Europe PubMed Central

8 September 2017

Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards (English)

1 reference

Europe PubMed Central

8 September 2017

4

object named as

Craig Moritz

1 reference

Europe PubMed Central

8 September 2017

author name string

Mozes P K Blom

1

1 reference

Europe PubMed Central

8 September 2017

Jason G Bragg

2

1 reference

Europe PubMed Central

8 September 2017

Sally Potter

3

1 reference

Europe PubMed Central

8 September 2017

publication date

6 October 2016

1 reference

Europe PubMed Central

8 September 2017

Systematic Biology

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Europe PubMed Central

8 September 2017

66

1 reference

Europe PubMed Central

8 September 2017

3

1 reference

Europe PubMed Central

8 September 2017

352-366

1 reference

Europe PubMed Central

8 September 2017

Basic local alignment search tool

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Recent trends in molecular phylogenetic analysis: where to next?

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Convergence across a continent: adaptive diversification in a recent radiation of Australian lizards.

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Trimmomatic: a flexible trimmer for Illumina sequence data

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21 January 2018

Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution

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21 January 2018

Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

A comparative study of SVDquartets and other coalescent-based species tree estimation methods

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Gene tree discordance, phylogenetic inference and the multispecies coalescent

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

MUSCLE: multiple sequence alignment with high accuracy and high throughput

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Is a new and general theory of molecular systematics emerging?

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

High-resolution species trees without concatenation

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

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

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Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales

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21 January 2018

Concatenation versus coalescence versus "concatalescence".

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21 January 2018

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

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The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews.

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Bayesian inference of species trees from multilocus data

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21 January 2018

Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods

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CAP3: A DNA sequence assembly program

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A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics

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Phylogenomics: the beginning of incongruence?

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21 January 2018

Targeted capture in evolutionary and ecological genomics.

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes.

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Inconsistency of phylogenetic estimates from concatenated data under coalescence

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Statistics and truth in phylogenomics

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

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

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

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

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

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

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

A hybrid phylogenetic-phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Anchored hybrid enrichment for massively high-throughput phylogenomics

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

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

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Estimating phylogenetic trees from genome-scale data

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

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

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Coalescent methods for estimating phylogenetic trees

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

FLASH: fast length adjustment of short reads to improve genome assemblies

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Applications of next-generation sequencing to phylogeography and phylogenetics

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Illumina sequencing library preparation for highly multiplexed target capture and sequencing

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

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

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

ASTRAL: genome-scale coalescent-based species tree estimation

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Computational approaches to species phylogeny inference and gene tree reconciliation

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

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

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Inferring ancient divergences requires genes with strong phylogenetic signals.

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Novel information theory-based measures for quantifying incongruence among phylogenetic trees

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

De novo transcriptomic analyses for non-model organisms: an evaluation of methods across a multi-species data set.

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21 January 2018

Automated generation of heuristics for biological sequence comparison

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

Inconsistency of Species Tree Methods under Gene Flow.

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW089

21 January 2018

The gene tree delusion

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

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

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21 January 2018

DendroPy: a Python library for phylogenetic computing

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Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae).

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21 January 2018

Profiling phylogenetic informativeness

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The Impact of Missing Data on Species Tree Estimation

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Molecular phylogenetics: principles and practice

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

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

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Deciphering patterns of transoceanic dispersal: the evolutionary origin and biogeography of coastal lizards (Cryptoblepharus) in the Western Indian Ocean region

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Limited overwater dispersal and genetic differentiation of the snake-eyed skink (Cryptoblepharus nigropunctatus) in the Oceanic Ogasawara Islands, Japan

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21 January 2018

Identifiers

10.1093/SYSBIO/SYW089

1 reference

Europe PubMed Central

8 September 2017

1 reference

Europe PubMed Central

8 September 2017

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