Phylogenetic incongruence in the Drosophila melanogaster species group (Q36091948)

12 August 2017

Phylogenetic incongruence in the Drosophila melanogaster species group (English)

1 reference

12 August 2017

Drosophila melanogaster

0 references

1 reference

John E Pool

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Jeffrey D Jensen

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Alex Wong

1 reference

PMC publication ID

2041876

12 August 2017

Charles F Aquadro

series ordinal

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12 August 2017

9 September 2006

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Molecular Phylogenetics and Evolution

12 August 2017

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inferred from page(s)

published in

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12 August 2017

1 reference

12 August 2017

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12 August 2017

1138-1150

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Combining data in phylogenetic analysis.

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Discordance of species trees with their most likely gene trees.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Basal relationships in the Drosophila melanogaster species group

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Estimating diversifying selection and functional constraint in the presence of recombination

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Positive selection of Iris, a retroviral envelope-derived host gene in Drosophila melanogaster

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Evolutionary expressed sequence tag analysis of Drosophila female reproductive tracts identifies genes subjected to positive selection

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Multiple data sets, high homoplasy, and the phylogeny of softshell turtles (Testudines: Trionychidae).

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Birds in a bush: five genes indicate explosive evolution of avian orders

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

MAVID: constrained ancestral alignment of multiple sequences

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Genome-scale approaches to resolving incongruence in molecular phylogenies

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

MrBayes 3: Bayesian phylogenetic inference under mixed models

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

The utility of the incongruence length difference test.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

MRBAYES: Bayesian inference of phylogenetic trees

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Codon-substitution models for heterogeneous selection pressure at amino acid sites

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

The phylogeny of closely related species as revealed by the genealogy of a speciation gene, Odysseus

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

DNA archives and our nearest relative: the trichotomy problem revisited

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Molecular phylogeny of the hominoids: inferences from multiple independent DNA sequence data sets

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Evolutionary trees from DNA sequences: A maximum likelihood approach

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Relationships between gene trees and species trees

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Inferences of species phylogeny in relation to segregation of ancient polymorphisms

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Adaptive protein evolution at the Adh locus in Drosophila

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Molecular phylogeny of the subgenus Sophophora of Drosophila derived from large subunit of ribosomal RNA sequences

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Phylogenetic MCMC algorithms are misleading on mixtures of trees.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Gene tree distributions under the coalescent process

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Molecular phylogeny of the Drosophila melanogaster species subgroup

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Phylogenetic relationships of Drosophila melanogaster species group deduced from spacer regions of histone gene H2A-H2B.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Macroevolutionary relationships of species of Drosophila melanogaster group based on mtDNA sequences

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Detecting recombination in 4-taxa DNA sequence alignments with Bayesian hidden Markov models and Markov chain Monte Carlo.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Evolution of male sexual characters in the oriental Drosophila melanogaster species group.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Reciprocal functions of the Drosophila yellow and ebony proteins in the development and evolution of pigment patterns

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Comparative evolutionary analysis of rDNA ITS regions in Drosophila

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Molecular phylogeny and divergence times of drosophilid species

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2041876

Biochemical phylogeny of the eight species in the Drosophila melanogaster subgroup, including D. sechellia and D. orena

21 October 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2006.09.002

When does the incongruence length difference test fail?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2006.09.002

GENE TREE DISTRIBUTIONS UNDER THE COALESCENT PROCESS

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2006.09.002

Noise and Incongruence: Interpreting Results of the Incongruence Length Difference Test

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2006.09.002

Testing Significance of Incongruence

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2006.09.002

A Likelihood Ratio Test to Detect Conflicting Phylogenetic Signal

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2006.09.002

A Concern for Evidence and a Phylogenetic Hypothesis of Relationships Among Epicrates (Boidae, Serpentes)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2006.09.002

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2006.09.002

Rapid evaluation of the phylogenetic congruence of sequence data using likelihood ratio tests

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2006.09.002

10.1016/J.YMPEV.2006.09.002

7 January 2021

Identifiers

DOI

1 reference

12 August 2017

1 reference

PMC publication ID

2041876

12 August 2017

PubMed publication ID

17071113

1 reference

PMC publication ID

2041876