Reference health
Accurate Branch Length Estimation in Partitioned Bayesian Analyses Requires Accommodation of Among-Partition Rate Variation and Attention to Branch Length Priors
2 of 63 checkable references need attention · checked 2026-07-22
At the dated check, the references listed below either did not resolve in Crossref or DataCite, or carried a retraction notice. Each one is shown with the registry record that put it there.
7 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
References needing attention
does not resolve to a known work10.1080/10635150116786
does not resolve to a known work10.1093/sysbio/44.1.64
The 61 checked references that resolve
resolves10.1146/annurev.ecolsys.33.010802.150500
Estimating Divergence Times from Molecular Data on Phylogenetic and Population Genetic Timescales
resolves10.1080/10635150590946808
Partitioned Bayesian Analyses, Partition Choice, and the Phylogenetic Relationships of Scincid Lizards
resolves10.1073/pnas.91.14.6491
Rapid morphological radiation and convergence among races of the butterfly Heliconius erato inferred from patterns of mitochondrial DNA evolution.
resolves10.1080/106351502753475844
Combined Data, Bayesian Phylogenetics, and the Origin of the New Zealand Cicada Genera
resolves10.1093/oxfordjournals.molbev.a004094
The Effects of Nucleotide Substitution Model Assumptions on Estimates of Nonparametric Bootstrap Support
resolves10.1080/10635150490445797
Data Partitions and Complex Models in Bayesian Analysis: The Phylogeny of Gymnophthalmid Lizards
resolves10.1093/oxfordjournals.molbev.a025813
Can three incongruence tests predict when data should be combined?
resolves10.1111/j.1558-5646.1998.tb01827.x
BEST‐FIT MAXIMUM‐LIKELIHOOD MODELS FOR PHYLOGENETIC INFERENCE: EMPIRICAL TESTS WITH KNOWN PHYLOGENIES
resolves10.1126/science.271.5248.470
Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock
resolves10.1080/106351502753475853
Increased Congruence Does Not Necessarily Indicate Increased Phylogenetic Accuracy—The Behavior of the Incongruence Length Difference Test in Mixed-Model Analyses
resolves10.1098/rstb.1986.0010
The estimate of total nucleotide substitutions from pairwise differences is biased
resolves10.1007/BF00486096
An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution
resolves10.1093/molbev/msg171
Functional Divergence Prediction from Evolutionary Analysis: A Case Study of Vertebrate Hemoglobin
resolves10.1007/BF02101694
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
resolves10.1093/oxfordjournals.molbev.a025552
Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA
resolves10.1016/S1055-7903(03)00061-7
RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences
resolves10.1111/j.0022-1112.2005.00746.x
<i>Sundasalanx</i>(Sundasalangidae) is a progenetic clupeiform, not a closely‐related group of salangids (Osmeriformes): mitogenomic evidence
resolves10.1093/oxfordjournals.molbev.a004221
Bayesian Phylogenetics Using an RNA Substitution Model Applied to Early Mammalian Evolution
resolves10.1093/oxfordjournals.molbev.a003811
Performance of a Divergence Time Estimation Method under a Probabilistic Model of Rate Evolution
resolves10.1093/molbev/msh112
A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
resolves10.1080/10635150490423520
The Importance of Proper Model Assumption in Bayesian Phylogenetics
resolves10.1046/j.1095-8312.2002.00108.x
Molecular phylogeny and historical biogeography of the large carpenter bees, genus Xylocopa (Hymenoptera: Apidae)
resolves10.1073/pnas.93.5.1930
Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis.
resolves10.1111/j.1095-8312.2005.00483.x
The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences
resolves10.1080/10635150490468675
A Phylogenetic Mixture Model for Detecting Pattern-Heterogeneity in Gene Sequence or Character-State Data
resolves10.1007/BF02407359
Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: Calibration of the molecular clock
resolves10.1080/10635150290102429
Identifiability of Parameters in MCMC Bayesian Inference of Phylogeny
resolves10.1093/oxfordjournals.molbev.a003974
Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach
resolves10.1016/j.ympev.2004.08.016
Opening the black box: phylogenetics and morphological evolution of the Malagasy fossorial lizards of the subfamily “Scincinae”
resolves10.1093/aesa/87.6.651
Evolution, Weighting, and Phylogenetic Utility of Mitochondrial Gene Sequences and a Compilation of Conserved Polymerase Chain Reaction Primers
resolves10.1093/oxfordjournals.molbev.a025660
Large differences in substitutional pattern and evolutionary rate of 12S ribosomal RNA genes
resolves10.1007/BF02339010
Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules
resolves10.1093/molbev/msi099
Consideration of RNA Secondary Structure Significantly Improves Likelihood-Based Estimates of Phylogeny: Examples from the Bilateria
resolves10.1080/10635150290102456
Divergence Time and Evolutionary Rate Estimation with Multilocus Data
resolves10.1093/oxfordjournals.molbev.a025892
Estimating the rate of evolution of the rate of molecular evolution
resolves10.1093/genetics/134.2.597
Rates and patterns of base change in the small subunit ribosomal RNA gene.
resolves10.1080/10635150590947212
Molecular Dates for the “Cambrian Explosion”: The Influence of Prior Assumptions
resolves10.1007/BF00160154
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
resolves10.1080/10635150390235557
Comparison of Likelihood and Bayesian Methods for Estimating Divergence Times Using Multiple Gene Loci and Calibration Points, with Application to a Radiation of Cute-Looking Mouse Lemur Species
The 7 references without a DOI — listed, not checked
no DOI — not checkedHow do insect nuclear ribosomal genes compare to protein-coding genes in phylogenetic utility and nucleotide substitution patterns? Syst
no DOI — not checkedIs character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis? Syst
no DOI — not checkedA simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
no DOI — not checkedRambaut A. Drummond A. J. Tracer v1.3 2003 http://evolve.zoo.ox.ac.uk/Available from
no DOI — not checkedSeq-Gen: An application for the Monte-Carlo simulation of DNA sequence evolution along phylogenetic trees
no DOI — not checkedAmong-site rate variation and phylogenetic analysis of 12S rRNA in Sigmodontine rodents
no DOI — not checkedPaired sequence difference in ribosomal RNAs: Evolutionary and phylogenetic implications
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work were clean at the dated check: each resolved to a known work in a public registry, and none
carried a retraction notice at that time. It says nothing about the quality, findings,
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