Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting (Q29037546)

27 March 2017

0 references

4

Michael B. Eisen

1 reference

27 March 2017

author name string

Daniel A. Pollard

series ordinal

1

1 reference

27 March 2017

Venky N. Iyer

series ordinal

2

1 reference

27 March 2017

Alan M. Moses

series ordinal

3

1 reference

27 March 2017

publication date

2006

1 reference

27 March 2017

1 reference

27 March 2017

volume

2

1 reference

27 March 2017

page(s)

e173

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27 March 2017

issue

10

1 reference

Creative Commons CC0 License

27 March 2017

copyright license

start time

27 October 2006

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

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cites work

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6 April 2017

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6 April 2017

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Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees

6 April 2017

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The population genetics of the origin and divergence of the Drosophila simulans complex species

6 April 2017

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6 April 2017

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The new animal phylogeny: reliability and implications

6 April 2017

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6 April 2017

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6 April 2017

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6 April 2017

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Evolutionary trees from DNA sequences: A maximum likelihood approach

6 April 2017

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Rates and patterns of scnDNA and mtDNA divergence within the Drosophila melanogaster subgroup

6 April 2017

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Inferences of species phylogeny in relation to segregation of ancient polymorphisms

6 April 2017

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Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis

6 April 2017

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Aligning multiple genomic sequences with the threaded blockset aligner

7 April 2017

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Genome-scale approaches to resolving incongruence in molecular phylogenies

7 April 2017

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Approximate Bayesian computation in population genetics

7 April 2017

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Evolutionary relationship of DNA sequences in finite populations

7 April 2017

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Inferring phylogeny despite incomplete lineage sorting

7 April 2017

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Performance of a divergence time estimation method under a probabilistic model of rate evolution

7 April 2017

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Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies

7 April 2017

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Rare genomic changes as a tool for phylogenetics

7 April 2017

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Relationships between gene trees and species trees

7 April 2017

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Balancing selection and its effects on sequences in nearby genome regions

7 April 2017

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Population size does not influence mitochondrial genetic diversity in animals

3 June 2018

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Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts

3 June 2018

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Molecular evolution in the Drosophila melanogaster species subgroup: frequent parameter fluctuations on the timescale of molecular divergence

3 June 2018

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The concordance of gene trees and species trees at two linked loci

3 June 2018

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Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster

3 June 2018

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An empirical examination of the utility of codon-substitution models in phylogeny reconstruction

3 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

The phylogeny of the subgroups within the melanogaster species group: likelihood tests on COI and COII sequences and a Bayesian estimate of phylogeny

3 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Hidden likelihood support in genomic data: can forty-five wrongs make a right?

3 June 2018

1 reference

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DNA sequence polymorphism and divergence at the erect wing and suppressor of sable loci of Drosophila melanogaster and D. simulans

3 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Lateral gene transfer in eukaryotes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Inferring the mode of speciation from genomic data: a study of the great apes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

The Bayesian revolution in genetics

3 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Nucleotide variation and recombination along the fourth chromosome in Drosophila simulans

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Selective constraints on intron evolution in Drosophila

3 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Comment on "Hexapod origins: monophyletic or paraphyletic?".

3 June 2018

1 reference

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The root of the mammalian tree inferred from whole mitochondrial genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Statistical phylogeography

3 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Increased taxon sampling is advantageous for phylogenetic inference

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Phylogeny of Drosophilinae (Diptera: Drosophilidae), with comments on combined analysis and character support

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Stability of cladistic relationships between Cetacea and higher-level artiodactyl taxa

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Genealogical trees, coalescent theory and the analysis of genetic polymorphisms

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Phylogeny of the subgenus sophophora (Diptera: drosophilidae) based on combined analysis of nuclear and mitochondrial sequences

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Interactions between natural selection, recombination and gene density in the genes of Drosophila.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Linkage disequilibria and the site frequency spectra in the su(s) and su(w(a)) regions of the Drosophila melanogaster X chromosome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Molecular evolution of the histone 3 multigene family in the Drosophila melanogaster species subgroup.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Maximum likelihood estimation of population divergence times and population phylogenies under the infinite sites model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Can three incongruence tests predict when data should be combined?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Differences in crossover frequency and distribution among three sibling species of Drosophila.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Molecular evolution of the duplicated Amy locus in the Drosophila melanogaster species subgroup: concerted evolution only in the coding region and an excess of nonsynonymous substitutions in speciation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

On the detection of nonrandom associations between DNA polymorphisms in natural populations of Drosophila

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

The molecular evolution of the alcohol dehydrogenase and alcohol dehydrogenase-related genes in the Drosophila melanogaster species subgroup

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Inferring phylogenies from DNA sequences of unequal base compositions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Mitochondrial DNA differentiation during the speciation process in Peromyscus

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Linkage disequilibrium between two segregating nucleotide sites under the steady flux of mutations in a finite population

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Mitochondrial DNA evolution in the melanogaster species subgroup of Drosophila.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Gene genealogy in three related populations: consistency probability between gene and population trees

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Population genetics and evolution of species related to Drosophila melanogaster

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

On the rate of DNA sequence evolution in Drosophila.

3 June 2018

1 reference

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Mitochondrial DNA sequence divergence in the Melanogaster and oriental species subgroups of Drosophila.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Gene trees, species trees and the segregation of ancestral alleles

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Rates of synonymous substitution and base composition of nuclear genes in Drosophila

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Population genetics of polymorphism and divergence

3 June 2018

1 reference

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The distribution of satellite and main-band DNA components in the melanogaster species subgroup of Drosophila. I. Fractionation of DNA in actinomycin D and distamycin A density gradients

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Relationships within the melanogaster species subgroup of the genus Drosophila ( Sophophora ) - II. Phylogenetic relationships between six species based upon polytene chromosome banding sequences

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Evolution. Is the "Big Bang" in animal evolution real?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci?

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogeny

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Phylogenetic MCMC algorithms are misleading on mixtures of trees.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Gene tree distributions under the coalescent process

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic Accuracy

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Detecting putative orthologs.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree

26 November 2018

1 reference

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The probability and chromosomal extent of trans-specific polymorphism

26 November 2018

1 reference

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Convergence among cave catfishes: long-branch attraction and a Bayesian relative rates test.

26 November 2018

1 reference

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Molecular phylogeny of the Drosophila melanogaster species subgroup

26 November 2018

1 reference

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The dog genome: survey sequencing and comparative analysis.

26 November 2018

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The shapes of neutral gene genealogies in two species: probabilities of monophyly, paraphyly, and polyphyly in a coalescent model.

26 November 2018

1 reference

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Functional constraints of the Cu,Zn superoxide dismutase in species of the Drosophila melanogaster subgroup and phylogenetic analysis.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

The probability of topological concordance of gene trees and species trees

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Local changes in GC/AT substitution biases and in crossover frequencies on Drosophila chromosomes

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

A phylogeny of the Drosophilidae using the sex-behaviour gene fruitless

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Paleo-demography of the Drosophila melanogaster subgroup: application of the maximum likelihood method.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Comparative evolutionary analysis of rDNA ITS regions in Drosophila.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Molecular phylogeny and divergence times of drosophilid species.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1626107

Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated?

26 November 2018

1 reference

12 December 2020

Phylogeny of the Oriental Drosophila melanogaster species group: a multilocus reconstruction

1 reference

12 December 2020

Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny

1 reference

12 December 2020

Animal evolution and the molecular signature of radiations compressed in time

1 reference

12 December 2020

Confidence Limits on Phylogenies: an Approach using the Bootstrap

1 reference

12 December 2020

GENETIC DIFFERENTIATION WITHIN THE MELANOGASTER SPECIES GROUP OF THE GENUS DROSOPHILA (SOPHOPHORA)

1 reference

12 December 2020

Stochastic errors in DNA evolution and molecular phylogeny

1 reference

12 December 2020

How often do wrong models produce better phylogenies?

1 reference

12 December 2020

10.1371/JOURNAL.PGEN.0020173

Identifiers

DOI

2 references

27 March 2017

4539248

4539248

1 reference

1 reference

1 reference