Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny (Q46214761)

20 December 2017

title

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

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20 December 2017

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Meng-Yun Chen

1

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20 December 2017

Dan Liang

series ordinal

2

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20 December 2017

Peng Zhang

series ordinal

3

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20 December 2017

publication date

13 August 2015

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20 December 2017

published in

Systematic Biology

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20 December 2017

volume

64

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20 December 2017

page(s)

1104-1120

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20 December 2017

issue

6

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20 December 2017

The African coelacanth genome provides insights into tetrapod evolution

cites work

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

A transcriptomic approach to ribbon worm systematics (nemertea): resolving the pilidiophora problem.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

The tree of life and a new classification of bony fishes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Conserved genes, sampling error, and phylogenomic inference.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

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%2FSYV059

Gene tree discordance, phylogenetic inference and the multispecies coalescent

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Phylogenomics and the reconstruction of the tree of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Broad phylogenomic sampling improves resolution of the animal tree of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Is a new and general theory of molecular systematics emerging?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Diversification of Neoaves: integration of molecular sequence data and fossils

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

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%2FSYV059

Evaluating topological conflict in centipede phylogeny using transcriptomic data sets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

CD-HIT: accelerated for clustering the next-generation sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Field guide to next-generation DNA sequencers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Full-length transcriptome assembly from RNA-Seq data without a reference genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

A phylogenomic study of birds reveals their evolutionary history

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Mammalian evolution may not be strictly bifurcating

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationships with longer DNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

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%2FSYV059

Phylogenomics: the beginning of incongruence?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

The global diversity of birds in space and time

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Resolving an ancient, rapid radiation in Saxifragales

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

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%2FSYV059

Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

An improved general amino acid replacement matrix

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

A 28S rRNA-based phylogeny of the gnathostomes: first steps in the analysis of conflict and congruence with morphologically based cladograms.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

One thousand two hundred ninety nuclear genes from a genome-wide survey support lungfishes as the sister group of tetrapods.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

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%2FSYV059

Estimating species phylogenies using coalescence times among sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

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%2FSYV059

A phylogenomic approach to resolve the arthropod tree of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Heterogeneous models place the root of the placental mammal phylogeny

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Resolution of ray-finned fish phylogeny and timing of diversification

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Mitochondrial molecular clocks and the origin of the major Otocephalan clades (Pisces: Teleostei): A new insight.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Phylogenomics of eukaryotes: impact of missing data on large alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Resolving difficult phylogenetic questions: why more sequences are not enough

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Phylogenomics revives traditional views on deep animal relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Difficult phylogenetic questions: more data, maybe; better methods, certainly

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Global patterns of diversification in the history of modern amphibians

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Genome-scale approaches to resolving incongruence in molecular phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

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%2FSYV059

Impact of missing data on phylogenies inferred from empirical phylogenomic data sets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Inferring ancient divergences requires genes with strong phylogenetic signals.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Missing data and influential sites: choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on the position of turtles.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Resolving the evolutionary relationships of molluscs with phylogenomic tools

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

A rapid bootstrap algorithm for the RAxML Web servers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

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%2FSYV059

Rapid progress on the vertebrate tree of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Phylogenetic signal and noise: predicting the power of a data set to resolve phylogeny

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Phylogenomic analyses elucidate the evolutionary relationships of bats

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Missing data in phylogenetic analysis: reconciling results from simulations and empirical data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

Mitogenomic perspectives on the origin and phylogeny of living amphibians

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV059

21 January 2018

Identifiers

DOI

10.1093/SYSBIO/SYV059

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20 December 2017

PubMed ID

26276158

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20 December 2017