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

https://doi.org/10.1007/bf00173421
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What this work says

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

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Relative Efficiencies of the Maximum Likelihood, Maximum Parsimony, and Neighbor-Joining Methods for Estimating Protein Phylogeny
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Toward a Phylogenetic Classification of the Mammalia
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Inference of Evolutionary Trees from DNA and Protein Sequence Data
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Man's place in hominoidea revealed by mitochondrial DNA genealogy
inferredcites →https://doi.org/10.1007/bf00160463openalex-snapshot
The complete mitochondrial DNA sequence of the harbor seal, Phoca vitulina
inferredcites →https://doi.org/10.1007/bf00160483openalex-snapshot
Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: Rapid evolution in warm-blooded vertebrates
inferredcites →https://doi.org/10.1007/bf00160484openalex-snapshot
The giant panda is closer to a bear, judged by ?- and ?-hemoglobin sequences
inferredcites →https://doi.org/10.1007/bf00170463openalex-snapshot
Close phylogenetic relationship between vestimentifera (tube worms) and annelida revealed by the amino acid sequence of elongation factor-l?
inferredcites →https://doi.org/10.1007/bf00182185openalex-snapshot
Early branchings in the evolution of eukaryotes: Ancient divergence of entamoeba that lacks mitochondria revealed by protein sequence data
inferredcites →https://doi.org/10.1007/bf01734101openalex-snapshot
Mitochondrial DNA sequences of primates: Tempo and mode of evolution
inferredcites →https://doi.org/10.1007/bf02099932openalex-snapshot
Robustness of maximum likelihood tree estimation against different patterns of base substitutions
inferredcites →https://doi.org/10.1007/bf02100115openalex-snapshot
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea
inferredcites →https://doi.org/10.1007/bf02101694openalex-snapshot
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
inferredcites →https://doi.org/10.1007/bf02102808openalex-snapshot
The complete nucleotide sequence of the mitochondrial DNA of the fin whale,Balaenoptera physalus
inferredcites →https://doi.org/10.1007/bf02109483openalex-snapshot
Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
inferredcites →https://doi.org/10.1007/bf02602930openalex-snapshot
The complete nucleotide sequence of theRattus norvegicus mitochondrial genome: Cryptic signals revealed by comparative analysis between vertebrates
inferredcites →https://doi.org/10.1016/0022-2836(82)90137-1openalex-snapshot
Complete sequence of bovine mitochondrial DNA conserved features of the mammalian mitochondrial genome
inferredcites →https://doi.org/10.1016/0022-2836(90)90225-bopenalex-snapshot
Sequence and gene organization of the chicken mitochondrial genome
inferredcites →https://doi.org/10.1016/0092-8674(81)90300-7openalex-snapshot
Sequence and gene organization of mouse mitochondrial DNA
inferredcites →https://doi.org/10.1016/0169-5347(93)90027-mopenalex-snapshot
Molecular phylogeny and the higher classification of eutherian mammals
inferredcites →https://doi.org/10.1016/s0021-9258(17)39303-1openalex-snapshot
The complete nucleotide sequence of the Xenopus laevis mitochondrial genome.
inferredcites →https://doi.org/10.1038/290457a0openalex-snapshot
Sequence and organization of the human mitochondrial genome
inferredcites →https://doi.org/10.1038/330401a0openalex-snapshot
Adaptive evolution in the stomach lysozymes of foregut fermenters
inferredcites →https://doi.org/10.1038/355595a0openalex-snapshot
Rodent polyphyly?
inferredcites →https://doi.org/10.1038/355595b0openalex-snapshot
Biased DNA repair
inferredcites →https://doi.org/10.1038/356121a0openalex-snapshot
Mammalian phytogeny: shaking the tree
inferredcites →https://doi.org/10.1073/pnas.87.17.6703openalex-snapshot
Molecular phylogeny of Rodentia, Lagomorpha, Primates, Artiodactyla, and Carnivora and molecular clocks.
inferredcites →https://doi.org/10.1073/pnas.88.14.5974openalex-snapshot
Synonymous nucleotide substitution rates in mammalian genes: implications for the molecular clock and the relationship of mammalian orders.
inferredcites →https://doi.org/10.1093/bioinformatics/8.3.275openalex-snapshot
The rapid generation of mutation data matrices from protein sequences
inferredcites →https://doi.org/10.1093/genetics/124.1.165openalex-snapshot
The pattern of mammalian evolution and the relative rate of molecular evolution.
inferredcites →https://doi.org/10.1093/genetics/137.1.243openalex-snapshot
The marsupial mitochondrial genome and the evolution of placental mammals.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040093openalex-snapshot
Protein phylogeny gives a robust estimation for early divergences of eukaryotes: phylogenetic place of a mitochondria-lacking protozoan, Giardia lamblia.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040097openalex-snapshot
Accuracies of the Simple Methods for Estimating the Bootstrap Probability of a Maximum-Likelihood Tree
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040435openalex-snapshot
Amino acid sequence versus morphological data and the interordinal relationships of mammals.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040454openalex-snapshot
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
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A new look at the statistical model identification
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CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
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Amino acid substitution of proteins coded for in mitochondrial DNA during mammalian evolution.
inferredcites →https://doi.org/10.2307/1268842openalex-snapshot
Akaike Information Criterion Statistics
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Akaike Information Criterion Statistics.
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The principles of classification and a classification of mammals

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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The Complete Mitochondrial Genome of Rhea americana and Early Avian Divergences
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Gene Duplication and the Evolution of Hemoglobin Isoform Differentiation in Birds
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The complete mitochondrial genome of the Chinese Sika deer (Cervus nipponTemminck, 1838), and phylogenetic analysis among Cervidae, Moschidae and Bovidae
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Evolutionary relationships in Aspergillus section Fumigati inferred from partial β-tubulin and hydrophobin DNA sequences
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Comparative analysis of the complete mitochondrial genomes of three geographical topmouth culter (Culter alburnus) groups and implications for their phylogenetics
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inferred← citeshttps://doi.org/10.1080/10635150590945278openalex-snapshot
Mitogenomic Perspectives on the Origin and Phylogeny of Living Amphibians
inferred← citeshttps://doi.org/10.1080/10635150590945368openalex-snapshot
Hidden Likelihood Support in Genomic Data: Can Forty-Five Wrongs Make a Right?
inferred← citeshttps://doi.org/10.1080/10635150802158670openalex-snapshot
Synonymous Substitutions Substantially Improve Evolutionary Inference from Highly Diverged Proteins
inferred← citeshttps://doi.org/10.1080/106351599260445openalex-snapshot
Additional Support for Afrotheria and Paenungulata, the Performance of Mitochondrial versus Nuclear Genes, and the Impact of Data Partitions with Heterogeneous Base Composition
inferred← citeshttps://doi.org/10.1080/10635159950127367openalex-snapshot
c-Myc Gene Sequences and the Phylogeny of Bats and Other Eutherian Mammals
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.001.0001openalex-snapshot
Computational Molecular Evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.002.0004openalex-snapshot
Copyright Page
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.002.0005openalex-snapshot
Dedication
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.002.0006openalex-snapshot
Preface
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0001openalex-snapshot
Models of nucleotide substitution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0002openalex-snapshot
Models of amino acid and codon substitution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0003openalex-snapshot
Phylogeny reconstruction: overview
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0004openalex-snapshot
Maximum likelihood methods
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0005openalex-snapshot
Bayesian methods
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0006openalex-snapshot
Comparison of methods and tests on trees
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0007openalex-snapshot
Molecular clock and estimation of species divergence times
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0008openalex-snapshot
Neutral and adaptive protein evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0009openalex-snapshot
Simulating molecular evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0010openalex-snapshot
Perspectives
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.005.0001openalex-snapshot
Appendices
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.001.0001openalex-snapshot
Molecular Evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.002.0003openalex-snapshot
Copyright Page
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.002.0004openalex-snapshot
Foreword
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.002.0005openalex-snapshot
Preface
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0001openalex-snapshot
Models of nucleotide substitution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0002openalex-snapshot
Models of amino acid and codon substitution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0003openalex-snapshot
Phylogeny reconstruction: overview
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0004openalex-snapshot
Maximum likelihood methods
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0005openalex-snapshot
Comparison of phylogenetic methods and tests on trees
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0006openalex-snapshot
Bayesian theory
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0007openalex-snapshot
Bayesian computation (MCMC)
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0008openalex-snapshot
Bayesian phylogenetics
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0009openalex-snapshot
Coalescent theory and species trees
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0010openalex-snapshot
Molecular clock and estimation of species divergence times
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0011openalex-snapshot
Neutral and adaptive protein evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0012openalex-snapshot
Simulating molecular evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0013openalex-snapshot
Appendices
inferred← citeshttps://doi.org/10.1093/auk/121.3.682openalex-snapshot
VICARIANT SPECIATION OF CURASSOWS (AVES, CRACIDAE): A HYPOTHESIS BASED ON MITOCHONDRIAL DNA PHYLOGENY
inferred← citeshttps://doi.org/10.1093/bib/bbm052openalex-snapshot
Correlated substitution analysis and the prediction of amino acid structural contacts
inferred← citeshttps://doi.org/10.1093/bioinformatics/bti263openalex-snapshot
ProtTest: selection of best-fit models of protein evolution
inferred← citeshttps://doi.org/10.1093/condor/107.3.514openalex-snapshot
MULTIPLE GENE EVIDENCE FOR PARALLEL EVOLUTION AND RETENTION OF ANCESTRAL MORPHOLOGICAL STATES IN THE SHANKS (CHARADRIIFORMES: SCOLOPACIDAE)
inferred← citeshttps://doi.org/10.1093/gbe/evx168openalex-snapshot
Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements
inferred← citeshttps://doi.org/10.1093/genetics/142.3.915openalex-snapshot
Details of Retropositional Genome Dynamics That Provide a Rationale for a Generic Division: The Distinct Branching of All the Pacific Salmon and Trout (Oncorhynchus) From the Atlantic Salmon and Trout (Salmo)
inferred← citeshttps://doi.org/10.1093/genetics/144.3.1165openalex-snapshot
The Complete Mitochondrial DNA Sequence of the Bichir (Polypterus ornatipinnis), a Basal Ray-Finned Fish: Ancient Establishment of the Consensus Vertebrate Gene Order
inferred← citeshttps://doi.org/10.1093/genetics/149.1.445openalex-snapshot
Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution
inferred← citeshttps://doi.org/10.1093/molbev/msab026openalex-snapshot
Genome-Scale Profiling Reveals Noncoding Loci Carry Higher Proportions of Concordant Data
inferred← citeshttps://doi.org/10.1093/molbev/msi005openalex-snapshot
Different Versions of the Dayhoff Rate Matrix
inferred← citeshttps://doi.org/10.1093/molbev/msi075openalex-snapshot
Sister Group Relationship of Turtles to the Bird-Crocodilian Clade Revealed by Nuclear DNA–Coded Proteins
inferred← citeshttps://doi.org/10.1093/molbev/msl136openalex-snapshot
MtArt: A New Model of Amino Acid Replacement for Arthropoda
inferred← citeshttps://doi.org/10.1093/molbev/msm064openalex-snapshot
An Empirical Codon Model for Protein Sequence Evolution
inferred← citeshttps://doi.org/10.1093/molbev/msm097openalex-snapshot
Quantifying the Impact of Protein Tertiary Structure on Molecular Evolution
inferred← citeshttps://doi.org/10.1093/molbev/msn215openalex-snapshot
Origins and Evolution of the Formin Multigene Family That Is Involved in the Formation of Actin Filaments
inferred← citeshttps://doi.org/10.1093/molbev/msu044openalex-snapshot
An Amino Acid Substitution-Selection Model Adjusts Residue Fitness to Improve Phylogenetic Estimation
inferred← citeshttps://doi.org/10.1093/oxfordjournals.jbchem.a021527openalex-snapshot
Complete Nucleotide Sequences of the Genes Encoding Translation Elongation Factors 1 and 2 from a microsporidian parasite, Glugea plecoglossi: Implications for the Deepest Branching of Eukaryotes
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a003787openalex-snapshot
Mitochondrial Versus Nuclear Gene Sequences in Deep-Level Mammalian Phylogeny Reconstruction
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a003851openalex-snapshot
A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a003863openalex-snapshot
A New Theory of Phylogeny Inference Through Construction of Multidimensional Vector Space
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a004007openalex-snapshot
A Novel Use of Equilibrium Frequencies in Models of Sequence Evolution
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a004090openalex-snapshot
Conserved Primers for Rapid Sequencing of the Complete Mitochondrial Genome from Carnivores, Applied to Three Species of Bears
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025580openalex-snapshot
Molecular evolutionary dynamics of cytochrome b in strepsirrhine primates: the phylogenetic significance of third-position transversions
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025599openalex-snapshot
Cytochrome b nucleotide sequences and the identification of five primary lineages of extant cetaceans
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025613openalex-snapshot
Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025632openalex-snapshot
Phylogenetic position of cetaceans relative to artiodactyls: reanalysis of mitochondrial and nuclear sequences
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025647openalex-snapshot
Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025661openalex-snapshot
Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025736openalex-snapshot
The complete mitochondrial genome of Alligator mississippiensis and the separation between recent archosauria (birds and crocodiles)
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025789openalex-snapshot
Detection of convergent and parallel evolution at the amino acid sequence level
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025792openalex-snapshot
Phylogenetic relationships of artiodactyls and cetaceans as deduced from the comparison of cytochrome b and 12S rRNA mitochondrial sequences
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025800openalex-snapshot
Color vision of ancestral organisms of higher primates
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025815openalex-snapshot
The mtDNA sequence of the ostrich and the divergence between paleognathous and neognathous birds
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025816openalex-snapshot
Phylogenetic analyses of mitochondrial DNA suggest a sister group relationship between Xenarthra (Edentata) and Ferungulates
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025845openalex-snapshot
Molecular systematics and paleobiogeography of the South American sigmodontine rodents [published erratum appears in Mol Biol Evol 1998 Feb;15(2):224]
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025862openalex-snapshot
The correlation of protein structure and evolution of a protein-coding gene: phylogenetic inference using cytochrome oxidase III
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025888openalex-snapshot
Models of amino acid substitution and applications to mitochondrial protein evolution
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025891openalex-snapshot
The complete mitochondrial DNA sequence of the shark Mustelus manazo: evaluating rooting contradictions to living bony vertebrates
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025930openalex-snapshot
The rate heterogeneity of nonsynonymous substitutions in mammalian mitochondrial genes
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025950openalex-snapshot
Searching for the Closest Living Relative(s) of Tetrapods Through Evolutionary Analysis of Mitochondrial and Nuclear Data
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025956openalex-snapshot
The "five-sites" rule and the evolution of red and green color vision in mammals
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026220openalex-snapshot
Phylogenetic relationships of the enigmatic hoatzin (Opisthocomus hoazin) resolved using mitochondrial and nuclear gene sequences Process Citation]
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026238openalex-snapshot
The Phylogenetic Position of the Talpidae Within Eutheria Based on Analysis of Complete Mitochondrial Sequences
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026278openalex-snapshot
A Case for Evolutionary Genomics and the Comprehensive Examination of Sequence Biodiversity
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026302openalex-snapshot
Mitochondrial Genes and Mammalian Phylogenies: Increasing the Reliability of Branch Length Estimation
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a040187openalex-snapshot
Phylogeny of whales: dependence of the inference on species sampling.
inferred← citeshttps://doi.org/10.1093/sysbio/syp015openalex-snapshot
Statistical Comparison of Nucleotide, Amino Acid, and Codon Substitution Models for Evolutionary Analysis of Protein-Coding Sequences
inferred← citeshttps://doi.org/10.1094/phyto.1999.89.10.884openalex-snapshot
Genetic Analysis ofEutypaStrains from California Supports the Presence of Two Pathogenic Species
inferred← citeshttps://doi.org/10.1098/rspb.1996.0060openalex-snapshot
Excessive homoplasy in an evolutionarily constrained protein
inferred← citeshttps://doi.org/10.1098/rspb.1998.0567openalex-snapshot
Analyses of mitochondrial genomes strongly support a hippopotamus-whale clade
inferred← citeshttps://doi.org/10.1098/rspb.1999.0638openalex-snapshot
Analyses of mitochondrial DNA nest ratite birds within the Neognathae: supporting a neotenous origin of ratite morphological characters
inferred← citeshttps://doi.org/10.1098/rspb.1999.0643openalex-snapshot
The mitochondrial DNA molecule of the aardvark, Orycteropus afer, and the position of the Tubulidentata in the eutherian tree
inferred← citeshttps://doi.org/10.1098/rspb.2000.1402openalex-snapshot
The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): implications for amniote phylogeny
inferred← citeshttps://doi.org/10.1098/rspb.2001.1587openalex-snapshot
Complete mitochondrial DNA geonome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis
inferred← citeshttps://doi.org/10.1098/rspb.2002.1961openalex-snapshot
Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds
inferred← citeshttps://doi.org/10.1098/rspb.2004.2895openalex-snapshot
Nuclear markers confirm taxonomic status and relationships among highly endangered and closely related right whale species
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