Magic bullets and golden rules: data sampling in molecular phylogenetics (Q31025945)

28 June 2017

Magic bullets and golden rules: data sampling in molecular phylogenetics (English)

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28 June 2017

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2

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28 June 2017

Michael P Cummings

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PubMed ID

16351981

28 June 2017

language of work or name

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25 October 2005

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28 June 2017

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28 June 2017

108

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28 June 2017

4

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28 June 2017

329-336

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Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA.

28 June 2017

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Examining Basal Avian Divergences with Mitochondrial Sequences: Model Complexity, Taxon Sampling, and Sequence Length

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Complete mitochondrial genome sequences of the South american and the Australian lungfish: testing of the phylogenetic performance of mitochondrial data sets for phylogenetic problems in tetrapod relationships

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Novel evolutionary relationship among four fish model systems.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Genes and other samples of DNA sequence data for phylogenetic inference

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Phylogenetics and the cohesion of bacterial genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Prospects for building the tree of life from large sequence databases

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Sampling properties of the bootstrap support in molecular phylogeny: influence of nonindependence among sites

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

The Chloroplast Genome of Nymphaea alba: Whole-Genome Analyses and the Problem of Identifying the Most Basal Angiosperm

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

The phylogenetic utility of cytochrome b: lessons from bufonid frogs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Is it better to add taxa or characters to a difficult phylogenetic problem?

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Inferring complex phylogenies.

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Taxonomic sampling, phylogenetic accuracy, and investigator bias

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Is sparse taxon sampling a problem for phylogenetic inference?

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Effect of Nonindependent Substitution on Phylogenetic Accuracy

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Patchiness and correlations in DNA sequences.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Group II introns as phylogenetic tools: structure, function, and evolutionary constraints

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Type I Sts Markers Are More Informative than Cytochrome b in Phylogenetic Reconstruction of the Mustelidae (Mammalia: Carnivora)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Whole chloroplast genome comparison of rice, maize, and wheat: implications for chloroplast gene diversification and phylogeny of cereals

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Shortcomings of the cytochrome b gene as a molecular marker

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

A molecular phylogeny of the New World orioles (Icterus): the importance of dense taxon sampling

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Phylogenomics of eukaryotes: impact of missing data on large alignments

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

The root of the mammalian tree inferred from whole mitochondrial genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Genome-scale phylogeny and the detection of systematic biases

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Evaluation of the strategy of long-branch subdivision to improve the accuracy of phylogenetic methods

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

7 January 2021

Taxon sampling revisited

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https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Assessing an unknown evolutionary process: effect of increasing site-specific knowledge through taxon addition.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Increased taxon sampling is advantageous for phylogenetic inference

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Taxon sampling and the accuracy of large phylogenies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

The ring of life provides evidence for a genome fusion origin of eukaryotes

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Sensitivity of the relative-rate test to taxonomic sampling

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

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

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Genome-scale approaches to resolving incongruence in molecular phylogenies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Incomplete taxon sampling is not a problem for phylogenetic inference

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Taxon sampling, bioinformatics, and phylogenomics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Ancestral state estimation and taxon sampling density

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Patterns of Variation in Levels of Homoplasy

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

The challenge of constructing large phylogenetic trees

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Dynamics and phylogenetic implications of MtDNA control region sequences in New World Jays (Aves: Corvidae).

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

An Updated and Comprehensive rRNA Phylogeny of (Crown) Eukaryotes Based on Rate-Calibrated Evolutionary Distances

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Probabilistic analysis indicates discordant gene trees in chloroplast evolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

The excess of transitions among nucleotide substitutions: new methods of estimating transition bias underscore its significance.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Does adding characters with missing data increase or decrease phylogenetic accuracy?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Missing data, incomplete taxa, and phylogenetic accuracy

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Among-site rate variation and its impact on phylogenetic analyses

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Phylogeny of the Lemuridae: Effects of Character and Taxon Sampling on Resolution of Species Relationships within Eulemur

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

Increased taxon sampling greatly reduces phylogenetic error

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.ZOOL.2005.09.006

10.1016/J.ZOOL.2005.09.006

7 January 2021

Identifiers

DOI

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28 June 2017

1 reference

PubMed ID

16351981