4.6 Review

Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci

Related references

Note: Only part of the references are listed.
Article Evolutionary Biology

Trees of Trees: An Approach to Comparing Multiple Alternative Phylogenies

Tom M. W. Nye

SYSTEMATIC BIOLOGY (2008)

Article Biology

A new time-scale for ray-finned fish evolution

Imogen A. Hurley et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2007)

Review Ecology

Model use in phylogenetics: nine key questions

Scot A. Kelchner et al.

TRENDS IN ECOLOGY & EVOLUTION (2007)

Article Evolutionary Biology

The importance of data partitioning and the utility of bayes factors in Bayesian phylogenetics

Jeremy M. Brown et al.

SYSTEMATIC BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Lack of resolution in the animal phylogeny: Closely spaced cladogeneses or undetected systematic errors?

Denis Baurain et al.

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Biotechnology & Applied Microbiology

Rooting the eutherian tree: the power and pitfalls of phylogenomics

Hidenori Nishihara et al.

GENOME BIOLOGY (2007)

Article Evolutionary Biology

Inconsistency of phylogenetic estimates from concatenated data under coalescence

Laura Salter Kubatko et al.

SYSTEMATIC BIOLOGY (2007)

Article Biochemistry & Molecular Biology

What is the role of genome duplication in the evolution of complexity and diversity?

KD Crow et al.

MOLECULAR BIOLOGY AND EVOLUTION (2006)

Article Biochemistry & Molecular Biology

Bayesian mixed models and the phylogeny of pitvipers (Viperidae: Serpentes)

TA Castoe et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2006)

Review Evolutionary Biology

Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes

Michelle M. McMahon et al.

SYSTEMATIC BIOLOGY (2006)

Article Multidisciplinary Sciences

Animal evolution and the molecular signature of radiations compressed in time

A Rokas et al.

SCIENCE (2005)

Review Zoology

A review of the lower actinopterygian phylogeny

BG Gardiner et al.

ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY (2005)

Article Biochemistry & Molecular Biology

Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia

H Philippe et al.

MOLECULAR BIOLOGY AND EVOLUTION (2005)

Article Biochemistry & Molecular Biology

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

PJ Waddell

MOLECULAR BIOLOGY AND EVOLUTION (2005)

Article Evolutionary Biology

Bayesian phylogenetic analysis of combined data

JAA Nylander et al.

SYSTEMATIC BIOLOGY (2004)

Article Multidisciplinary Sciences

Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes

RL Mueller et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Review Genetics & Heredity

Novel evolutionary relationship among four fish model systems

WJ Chen et al.

TRENDS IN GENETICS (2004)

Article Zoology

Esociform phylogeny

JA López et al.

COPEIA (2004)

Article Biochemistry & Molecular Biology

A phylogeny of the fish family Sparidae (porgies) inferred from mitochondrial sequence data

TM Orrell et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2004)

Article Biochemistry & Molecular Biology

Coelacanth genome sequence reveals the evolutionary history of vertebrate genes

JP Noonan et al.

GENOME RESEARCH (2004)

Letter Biochemistry & Molecular Biology

Genome-scale phylogeny and the detection of systematic biases

MJ Phillips et al.

MOLECULAR BIOLOGY AND EVOLUTION (2004)

Article Biochemistry & Molecular Biology

Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution

CH Chiu et al.

GENOME RESEARCH (2004)

Article Biochemical Research Methods

MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment

S Kumar et al.

BRIEFINGS IN BIOINFORMATICS (2004)

Article Multidisciplinary Sciences

Genome-scale approaches to resolving incongruence in molecular phylogenies

A Rokas et al.

NATURE (2003)

Article Evolutionary Biology

Performance-based selection of likelihood models for phylogeny estimation

V Minin et al.

SYSTEMATIC BIOLOGY (2003)

Article Evolutionary Biology

Missing data, incomplete taxa, and phylogenetic accuracy

JJ Wiens

SYSTEMATIC BIOLOGY (2003)

Article Evolutionary Biology

Conflicting phylogenetic signals at the base of the metazoan tree

A Rokas et al.

EVOLUTION & DEVELOPMENT (2003)

Article Biochemistry & Molecular Biology

Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the Protacanthopterygii

NB Ishiguro et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2003)

Article Biochemistry & Molecular Biology

Mitochondrial genomics of ostariophysan fishes: Perspectives on phylogeny and biogeography

K Saitoh et al.

JOURNAL OF MOLECULAR EVOLUTION (2003)

Article Biochemistry & Molecular Biology

Genome duplication, a trait shared by 22,000 species of ray-finned fish

JS Taylor et al.

GENOME RESEARCH (2003)

Article Biochemistry & Molecular Biology

Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences

M Miya et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2003)

Article Biochemistry & Molecular Biology

Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the ancient fish

JG Inoue et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2003)

Article Biochemistry & Molecular Biology

Combining multiple data sets in a likelihood analysis: Which models are the best?

T Pupko et al.

MOLECULAR BIOLOGY AND EVOLUTION (2002)

Article Evolutionary Biology

Identifiability of parameters in MCMC Bayesian inference of phylogeny

B Rannala

SYSTEMATIC BIOLOGY (2002)

Article Biochemistry & Molecular Biology

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons

M Remm et al.

JOURNAL OF MOLECULAR BIOLOGY (2001)

Article Multidisciplinary Sciences

Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates

B Venkatesh et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)

Article Biochemistry & Molecular Biology

A mitogenomic perspective on the basal teleostean phylogeny: Resolving higher-level relationships with longer DNA sequences

JG Inoue et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2001)

Article Biochemistry & Molecular Biology

The interrelationships of Acanthomorph fishes: A total evidence approach using molecular and morphological data

EO Wiley et al.

BIOCHEMICAL SYSTEMATICS AND ECOLOGY (2000)