(Q30931894)

27 June 2017

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title

Estimating phylogenetic trees from genome-scale data (English)

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27 June 2017

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5

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27 June 2017

Charles Cavender Davis

series ordinal

4

object named as

Charles C Davis

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27 June 2017

Liang Liu

1

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27 June 2017

Zhenxiang Xi

series ordinal

2

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27 June 2017

Shaoyuan Wu

series ordinal

3

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27 June 2017

language of work or name

English

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publication date

14 April 2015

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Annals of the New York Academy of Sciences

27 June 2017

published in

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27 June 2017

volume

1360

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27 June 2017

page(s)

36-53

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Phylogenetic inference using whole genomes

27 June 2017

cites work

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Population Genomics of Human Adaptation

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12747

Species delimitation using genome-wide SNP data

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12747

Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12747

Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12747

A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12747

An HMM-based comparative genomic framework for detecting introgression in eukaryotes

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12747

Is a new and general theory of molecular systematics emerging?

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12747

The inference of gene trees with species trees

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12747

Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes).

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Conserved genes, sampling error, and phylogenomic inference.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12747

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

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12747

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12747

The supermatrix approach to systematics

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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/10.1111%2FNYAS.12747

Land plant origins and coalescence confusion

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Coalescent methods for estimating phylogenetic trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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/10.1111%2FNYAS.12747

High-resolution species trees without concatenation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Concatenation versus coalescence versus "concatalescence".

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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/10.1111%2FNYAS.12747

Phylogenomics and coalescent analyses resolve extant seed plant relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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/10.1111%2FNYAS.12747

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Inconsistency of phylogenetic estimates from concatenated data under coalescence

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Origin of land plants using the multispecies coalescent model

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Applying species-tree analyses to deep phylogenetic histories: challenges and potential suggested from a survey of empirical phylogenetic studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Gene tree rooting methods give distributions that mimic the coalescent process

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Random roots and lineage sorting

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Full modeling versus summarizing gene-tree uncertainty: method choice and species-tree accuracy

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Is recombination a problem for species-tree analyses?

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Gene tree discordance, phylogenetic inference and the multispecies coalescent

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Discordance of species trees with their most likely gene trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Model use in phylogenetics: nine key questions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Estimating species phylogenies using coalescence times among sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Bayesian inference of species trees from multilocus data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Phylotranscriptomic analysis of the origin and early diversification of land plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

The Amborella Genome and the Evolution of Flowering Plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Amborella not a "basal angiosperm"? Not so fast

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Resolution of the early placental mammal radiation using Bayesian phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Using genomic data to unravel the root of the placental mammal phylogeny

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Reanalysis of Murphy et al.'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Calculating bootstrap probabilities of phylogeny using multilocus sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Effects of missing data on species tree estimation under the coalescent

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Prospects for building the tree of life from large sequence databases

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Broad phylogenomic sampling improves resolution of the animal tree of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

The influence of gene flow on species tree estimation: a simulation study

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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/10.1111%2FNYAS.12747

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/10.1111%2FNYAS.12747

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/10.1111%2FNYAS.12747

Phybase: an R package for species tree analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

What is the danger of the anomaly zone for empirical phylogenetics?

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Estimating species trees using approximate Bayesian computation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Incomplete lineage sorting: consistent phylogeny estimation from multiple loci.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

ASTRAL: genome-scale coalescent-based species tree estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Quartet inference from SNP data under the coalescent model

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

A coalescent-based method for population tree inference with haplotypes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Insights into hominid evolution from the gorilla genome sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Phylogenetic analysis of four nuclear protein-encoding genes largely corroborates the traditional classification of Bivalvia (Mollusca).

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Ancestral population genomics: the coalescent hidden Markov model approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Fine-scale phylogenetic discordance across the house mouse genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Maximum likelihood supertrees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Analyzing and synthesizing phylogenies using tree alignment graphs

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Poor fit to the multispecies coalescent is widely detectable in empirical data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

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/10.1111%2FNYAS.12747

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/10.1111%2FNYAS.12747

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Estimating species trees from unrooted gene trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Maximum tree: a consistent estimator of the species tree.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

Concatenation and Species Tree Methods Exhibit Statistically Indistinguishable Accuracy under a Range of Simulated Conditions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12747

21 January 2018

Identifiers

DOI

10.1111/NYAS.12747

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27 June 2017

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