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Evaluating the Phylogenetic Utility of Genes: A Search for Genes Informative About Deep Divergences among Vertebrates

https://doi.org/10.1093/sysbio/43.2.174

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Character-State Weighting for Restriction Site Data in Phylogenetic Reconstruction, with an Example from Chloroplast DNA

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The Mitochondrial Genome of Animals

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Structure and evolution of opossum, guinea pig, and porcupine cytochrome b genes

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DNA cloning and amino acid sequence determination of a major constituent protein of mammalian nucleoli

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Rates of molecular evolution and the fraction of nucleotide positions free to vary

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Phylogeny of the major tetrapod groups: Morphological data and divergence dates

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Amino acid composition and the evolutionary rates of protein-coding genes

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Evolution of the cytochromeb gene of mammals

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An evaluation of the molecular clock hypothesis using mammalian DNA sequences

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Progressive sequence alignment as a prerequisitetto correct phylogenetic trees

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Evidence suggesting a non-random character to nucleotide replacements in naturally occurring mutations

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Fundamentals of molecular evolution

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Structure and evolution of the Xenopus laevis albumin genes

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Plasma and cytoplasmic gelsolins are encoded by a single gene and contain a duplicated actin-binding domain

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Conservation of structural and functional domains in complement component C3 of Xenopus and mammals.

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Genomic organization and biosynthesis of secreted and cytoplasmic forms of gelsolin

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The neighbor-joining method: a new method for reconstructing phylogenetic trees.

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Mitochondrial DNA-like sequence in the nuclear genome of an akodontine rodent.

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Comparative structural analysis of the transcriptionally active proopiomelanocortin genes A and B of Xenopus laevis.

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Testing phylogenetic approaches with empirical data, as illustrated with the parsimony method.

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Evolutionary Relationships Within the Ensatina Eschscholtzii Complex Confirm the Ring Species Interpretation

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For Consensus (Sometimes)

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The estimate of total nucleotide substitutions from pairwise differences is biased

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Structural analysis of the entire proopiomelanocortin gene ofXenopus laevis

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Ability of the c- mos Product to Associate with and Phosphorylate Tubulin

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Structure and expression of canary myc family genes.

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RATES OF MOLECULAR EVOLUTION

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EVOLUTION OF ANIMAL MITOCHONDRIAL DNA: RELEVANCE FOR POPULATION BIOLOGY AND SYSTEMATICS

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DNA Systematics and Evolution of Primates

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THE myc ONCOGENE: ITS ROLE IN TRANSFORMATION AND DIFFERENTIATION

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Homage to Clio, or, Toward an Historical Philosophy for Evolutionary Biology

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Vertebrate Paleontology and Evolution

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MacClade 4.0: analysis of phylogeny and character evolution

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A phylogenetic analysis of Myriapoda (Arthropoda) using two nuclear protein-encoding genes

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Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion

inferred← citeshttps://doi.org/10.1111/j.1365-2583.2006.00689.xopenalex-snapshot

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements

inferred← citeshttps://doi.org/10.1111/j.1365-294x.2006.02813.xopenalex-snapshot

Extensive intraspecific polymorphism detected by SSCP at the nuclear C‐mos gene in the endemic Iberian lizard Lacerta schreiberi

inferred← citeshttps://doi.org/10.1111/j.1463-6409.2005.00182.xopenalex-snapshot

Phylogenetics of the common raven complex (Corvus: Corvidae) and the utility of ND4, COI and intron 7 of the β‐fibrinogen gene in avian molecular systematics

inferred← citeshttps://doi.org/10.1111/j.1558-5646.1997.tb01486.xopenalex-snapshot

EXAMINING TWO STANDARD ASSUMPTIONS OF ANCESTRAL RECONSTRUCTIONS: REPEATED LOSS OF DICHROMATISM IN DABBLING DUCKS (ANATINI)

inferred← citeshttps://doi.org/10.1111/j.1755-0998.2012.03143.xopenalex-snapshot

Utility of the DNA barcoding gene fragment for parasitic wasp phylogeny (Hymenoptera: Ichneumonoidea): data release and new measure of taxonomic congruence

inferred← citeshttps://doi.org/10.1111/j.2041-210x.2010.00052.xopenalex-snapshot

Selecting ribosomal protein genes for invertebrate phylogenetic inferences: how many genes to resolve the Mollusca?

inferred← citeshttps://doi.org/10.1111/zoj.12044openalex-snapshot

Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea:Lysmata,Exhippolysmata, andMerguia)

inferred← citeshttps://doi.org/10.1126/science.1077795openalex-snapshot

Dating the Tree of Life

inferred← citeshttps://doi.org/10.1126/science.1151532openalex-snapshot

Alignment Uncertainty and Genomic Analysis

inferred← citeshttps://doi.org/10.1146/annurev.ento.45.1.1openalex-snapshot

The Current State Of Insect Molecular Systematics: A Thriving Tower of Babel

inferred← citeshttps://doi.org/10.1155/2013/621604openalex-snapshot

Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets

inferred← citeshttps://doi.org/10.1163/18759866-07001002openalex-snapshot

Hierarchical analysis of mtDNA variation and the use of mtDNA for isopod (Crustacea: Peracarida: Isopoda) systematics

inferred← citeshttps://doi.org/10.1186/1471-2164-7-202openalex-snapshot

Comparative evolutionary genomics of the HADH2 gene encoding Aβ-binding alcohol dehydrogenase/17β-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10)

inferred← citeshttps://doi.org/10.1186/s12862-014-0169-0openalex-snapshot

Phylogenetic informativeness reconciles ray-finned fish molecular divergence times

inferred← citeshttps://doi.org/10.1186/s40168-022-01295-yopenalex-snapshot

Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies

inferred← citeshttps://doi.org/10.1186/s40246-022-00429-5openalex-snapshot

Placing human gene families into their evolutionary context

inferred← citeshttps://doi.org/10.13110/humanbiology.89.3.05openalex-snapshot

Mitochondrial-DNA Phylogenetic Information and the Reconstruction of Human Population History: The South American Case

inferred← citeshttps://doi.org/10.1371/journal.pone.0018803openalex-snapshot

Finding Single Copy Genes Out of Sequenced Genomes for Multilocus Phylogenetics in Non-Model Fungi

inferred← citeshttps://doi.org/10.1371/journal.pone.0060615openalex-snapshot

Phylogenetic Analysis and Molecular Dating Suggest That Hemidactylus anamallensis Is Not a Member of the Hemidactylus Radiation and Has an Ancient Late Cretaceous Origin

inferred← citeshttps://doi.org/10.1371/journal.pone.0084080openalex-snapshot

Performance of Single and Concatenated Sets of Mitochondrial Genes at Inferring Metazoan Relationships Relative to Full Mitogenome Data

inferred← citeshttps://doi.org/10.1371/journal.pone.0099725openalex-snapshot

Impact of Gene Molecular Evolution on Phylogenetic Reconstruction: A Case Study in the Rosids (Superorder Rosanae, Angiosperms)

inferred← citeshttps://doi.org/10.1371/journal.pone.0107709openalex-snapshot

Strepsiptera, Phylogenomics and the Long Branch Attraction Problem

inferred← citeshttps://doi.org/10.1642/0004-8038(2001)118[0248:akiann]2.0.co;2openalex-snapshot

Adenylate Kinase Intron 5: A New Nuclear Locus for Avian Systematics

inferred← citeshttps://doi.org/10.17129/botsci.1510openalex-snapshot

Codificación de las inserciones-deleciones en el análisis filogenético de secuencias génicas

inferred← citeshttps://doi.org/10.2144/btn-2018-0096openalex-snapshot

DNA Barcodes from Snake Venom: a Broadly Applicable Method for Extraction of DNA from Snake Venoms

inferred← citeshttps://doi.org/10.2307/2656759openalex-snapshot

Phylogenetic relationships of land plants using mitochondrial small‐subunit rDNA sequences

inferred← citeshttps://doi.org/10.23860/diss-ada-eren-2023openalex-snapshot

Utilization of Large-Scale Genomic Data and Phylogenetic Methods in Studying Evolutionary Radiations

inferred← citeshttps://doi.org/10.3389/fevo.2014.00011openalex-snapshot

The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise

inferred← citeshttps://doi.org/10.3389/fevo.2024.1243221openalex-snapshot

Incomplete lineage sorting and long-branch attraction confound phylogenomic inference of Pancrustacea

inferred← citeshttps://doi.org/10.3390/d16110674openalex-snapshot

Integrated Genetic and Statolith Shape Analysis Reveals the Population Structure of Loliolus (Nipponololigo) uyii (Cephalopoda: Loliginidae) in the Coastal Waters of China

inferred← citeshttps://doi.org/10.3724/sp.j.1002.2008.08016openalex-snapshot

Taxon sampling and the accuracy of phylogenetic analyses

inferred← citeshttps://doi.org/10.3897/zookeys.775.24258openalex-snapshot

Genetic structure of Octopus minor around Chinese waters as indicated by nuclear DNA variations (Mollusca, Cephalopoda)

inferred← citeshttps://doi.org/10.4137/ebo.s8486openalex-snapshot

Interkingdom Gene Transfer May Contribute to the Evolution of Phytopathogenicity in Botrytis Cinerea

inferred← citeshttps://doi.org/10.4314/gjpas.v23i2.2openalex-snapshot

Sequence analysis of Maturase K (matK): A chloroplast-encoding gene in some selected pulses

inferred← citeshttps://doi.org/10.5962/bhl.title.4053openalex-snapshot

Phylogenetic Relationships and Classification of the Major Lineages of Apoidea (Hymenoptera): With Emphasis on the Crabronid Wasps

inferred← citeshttps://doi.org/10.6084/m9.figshare.20267413openalex-snapshot

Additional file 1 of Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies

inferred← citeshttps://doi.org/10.7717/peerj.361openalex-snapshot

Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix

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