The Multispecies Coalescent Model Outperforms Concatenation across Diverse Phylogenomic Data Sets (Q89502978)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:32011711%20AND%20SRC:MED&resulttype=core&format=json

5 April 2020

title

The Multispecies Coalescent Model Outperforms Concatenation across Diverse Phylogenomic Data Sets (English)

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:32011711%20AND%20SRC:MED&resulttype=core&format=json

5 April 2020

author name string

Xiaodong Jiang

series ordinal

1

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:32011711%20AND%20SRC:MED&resulttype=core&format=json

5 April 2020

Scott V Edwards

series ordinal

2

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:32011711%20AND%20SRC:MED&resulttype=core&format=json

5 April 2020

Liang Liu

series ordinal

3

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:32011711%20AND%20SRC:MED&resulttype=core&format=json

5 April 2020

language of work or name

English

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publication date

3 February 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:32011711%20AND%20SRC:MED&resulttype=core&format=json

5 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:32011711%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution-NonCommercial 4.0 International

5 April 2020

volume

69

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page(s)

795-812

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issue

4

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copyright license

start time

3 February 2020

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA

1 reference

12 December 2020

Statistical tests of models of DNA substitution.

1 reference

12 December 2020

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods

1 reference

12 December 2020

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

1 reference

12 December 2020

GeneTree: comparing gene and species phylogenies using reconciled trees.

1 reference

12 December 2020

An approximately unbiased test of phylogenetic tree selection

1 reference

12 December 2020

Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci

1 reference

12 December 2020

Measuring the fit of sequence data to phylogenetic model: allowing for missing data

1 reference

12 December 2020

Phylogenetic networks: modeling, reconstructibility, and accuracy

1 reference

12 December 2020

Inconsistency of phylogenetic estimates from concatenated data under coalescence

1 reference

12 December 2020

High-resolution species trees without concatenation

1 reference

12 December 2020

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

1 reference

12 December 2020

Phylogenetic inference using whole genomes

1 reference

12 December 2020

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

1 reference

12 December 2020

Is a new and general theory of molecular systematics emerging?

1 reference

12 December 2020

Measuring fit of sequence data to phylogenetic model: gain of power using marginal tests

1 reference

12 December 2020

Bayesian inference of species trees from multilocus data

1 reference

12 December 2020

Isolation with migration models for more than two populations

1 reference

12 December 2020

Phybase: an R package for species tree analysis.

1 reference

12 December 2020

Identifying hybridization events in the presence of coalescence via model selection

1 reference

12 December 2020

Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus)

1 reference

12 December 2020

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

1 reference

12 December 2020

Estimating species trees from unrooted gene trees.

1 reference

12 December 2020

Speciation in the White-breasted Nuthatch (Sitta carolinensis): a multilocus perspective

1 reference

12 December 2020

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

1 reference

12 December 2020

Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals

1 reference

12 December 2020

Assessing the Goodness of Fit of Phylogenetic Comparative Methods: A Meta-Analysis and Simulation Study

1 reference

12 December 2020

Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes.

1 reference

12 December 2020

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

1 reference

12 December 2020

Posterior predictive Bayesian phylogenetic model selection

1 reference

12 December 2020

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

1 reference

12 December 2020

Investigating the performance of AIC in selecting phylogenetic models.

1 reference

12 December 2020

A new method for modeling coalescent processes with recombination

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Error, signal, and the placement of Ctenophora sister to all other animals

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

The gene tree delusion

1 reference

12 December 2020

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

1 reference

12 December 2020

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

1 reference

12 December 2020

The Impact of Missing Data on Species Tree Estimation

1 reference

12 December 2020

Replicated divergence in cichlid radiations mirrors a major vertebrate innovation

1 reference

12 December 2020

The effects of subsampling gene trees on coalescent methods applied to ancient divergences

1 reference

12 December 2020

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

1 reference

12 December 2020

Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent

1 reference

12 December 2020

Rapid and recent diversification of curassows, guans, and chachalacas (Galliformes: Cracidae) out of Mesoamerica: Phylogeny inferred from mitochondrial, intron, and ultraconserved element sequences

1 reference

12 December 2020

Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses

1 reference

12 December 2020

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

1 reference

12 December 2020

Incomplete Lineage Sorting in Mammalian Phylogenomics

1 reference

12 December 2020

PHRAPL: Phylogeographic Inference Using Approximate Likelihoods

1 reference

12 December 2020

Analytical Biases Associated with GC-Content in Molecular Evolution

1 reference

12 December 2020

A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals

1 reference

12 December 2020

Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary

1 reference

12 December 2020

Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life.

1 reference

12 December 2020

Contentious relationships in phylogenomic studies can be driven by a handful of genes.

1 reference

12 December 2020

Phylogenomic data yield new and robust insights into the phylogeny and evolution of weevils.

1 reference

12 December 2020

A Comprehensive and Dated Phylogenomic Analysis of Butterflies.

1 reference

12 December 2020

Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?

1 reference

12 December 2020

The Biogeography of Deep Time Phylogenetic Reticulation.

1 reference

12 December 2020

Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations

1 reference

12 December 2020

The performance of coalescent-based species tree estimation methods under models of missing data.

1 reference

12 December 2020

Phylogenomic analysis of Apoidea sheds new light on the sister group of bees.

1 reference

12 December 2020

Genome-scale DNA sequence data and the evolutionary history of placental mammals.

1 reference

12 December 2020

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10.

1 reference

12 December 2020

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

1 reference

12 December 2020

Multiple origins of sexual dichromatism and aposematism within large carpenter bees

1 reference

12 December 2020

Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex

1 reference

12 December 2020

Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini)

1 reference

12 December 2020

Phylogenomics, life history and morphological evolution of ophiocomid brittlestars

1 reference

12 December 2020

Validity of the Diplostomoidea and Diplostomida (Digenea, Platyhelminthes) upheld in phylogenomic analysis

1 reference

12 December 2020

A phylogenomic approach to reconstruct interrelationships of main clupeocephalan lineages with a critical discussion of morphological apomorphies

1 reference

12 December 2020

Phylogenomic Signatures of Ancient Introgression in a Rogue Lineage of Darters (Teleostei: Percidae)

1 reference

12 December 2020

Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes

1 reference

12 December 2020

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

1 reference

12 December 2020

Model selection may not be a mandatory step for phylogeny reconstruction

1 reference

12 December 2020

Testing adequacy for DNA substitution models

1 reference

12 December 2020

Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts

1 reference

12 December 2020

Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data

1 reference

12 December 2020