Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting (Q45198031)

10 December 2017

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

1 reference

10 December 2017

Charles Cavender Davis

series ordinal

3

object named as

Charles C Davis

1 reference

10 December 2017

Liang Liu

1

1 reference

PubMed ID

25431481

10 December 2017

Zhenxiang Xi

series ordinal

2

1 reference

10 December 2017

26 November 2014

1 reference

Molecular Biology and Evolution

10 December 2017

1 reference

10 December 2017

32

1 reference

10 December 2017

3

1 reference

10 December 2017

791-805

1 reference

Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA.

10 December 2017

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

A review of long-branch attraction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina buntings

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Explosive radiation of Malpighiales supports a mid-cretaceous origin of modern tropical rain forests

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

The supermatrix approach to systematics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Discordance of species trees with their most likely gene trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Gene tree discordance, phylogenetic inference and the multispecies coalescent

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Broad phylogenomic sampling improves resolution of the animal tree of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Is a new and general theory of molecular systematics emerging?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Cases in which Parsimony or Compatibility Methods will be Positively Misleading

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Multigene phylogeny of the green lineage reveals the origin and diversification of land plants.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

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/10.1093%2FMOLBEV%2FMSU331

Assessing the root of bilaterian animals with scalable phylogenomic methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Bayesian inference of species trees from multilocus data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Application and accuracy of molecular phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Long-branch attraction bias and inconsistency in Bayesian phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Inconsistency of phylogenetic estimates from concatenated data under coalescence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Watching the clock: studying variation in rates of molecular evolution between species

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

A functional phylogenomic view of the seed plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Phybase: an R package for species tree analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Estimating species trees from unrooted gene trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

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%2FMOLBEV%2FMSU331

Coalescent methods for estimating phylogenetic trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Estimating species phylogenies using coalescence times among sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Escaping from the Felsenstein zone by detecting long branches in phylogenetic data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

ASTRAL: genome-scale coalescent-based species tree estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Acoelomorph flatworms are deuterostomes related to Xenoturbella

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Resolving difficult phylogenetic questions: why more sequences are not enough

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Inferring ancient divergences requires genes with strong phylogenetic signals.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Calculating bootstrap probabilities of phylogeny using multilocus sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

21 January 2018

Long-Branch Abstractions

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Rates of molecular evolution are linked to life history in flowering plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Resolving the evolutionary relationships of molluscs with phylogenomic tools

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

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%2FMOLBEV%2FMSU331

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%2FMOLBEV%2FMSU331

Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Broad phylogenomic sampling and the sister lineage of land plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Phylogenomic analyses elucidate the evolutionary relationships of bats

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Incomplete lineage sorting is common in extant gibbon genera

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Ancient rapid radiations of insects: challenges for phylogenetic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Deciphering ancient rapid radiations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Can Incomplete Taxa Rescue Phylogenetic Analyses from Long-Branch Attraction?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Origin of land plants: do conjugating green algae hold the key?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

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/10.1093%2FMOLBEV%2FMSU331

Malpighiales phylogenetics: Gaining ground on one of the most recalcitrant clades in the angiosperm tree of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Phylogenomics and coalescent analyses resolve extant seed plant relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Origin of land plants using the multispecies coalescent model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the laurasiatherian mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU331

21 January 2018

Identifiers

DOI

10.1093/MOLBEV/MSU331

1 reference

10 December 2017

1 reference

PubMed ID

25431481