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Can We Avoid “SIN” in the House of “No Common Mechanism”?

https://doi.org/10.1093/sysbio/syq069
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What this work says

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

inferredcites →https://doi.org/10.1006/aama.2001.0759openalex-snapshot
Geometry of the Space of Phylogenetic Trees
inferredcites →https://doi.org/10.1006/mpev.2000.0816openalex-snapshot
Slicing Hyperdimensional Oranges: The Geometry of Phylogenetic Estimation
inferredcites →https://doi.org/10.1007/978-1-4612-1694-0_15openalex-snapshot
Information Theory and an Extension of the Maximum Likelihood Principle
inferredcites →https://doi.org/10.1007/bf01659396openalex-snapshot
Rate of change of concomitantly variable codons
inferredcites →https://doi.org/10.1007/bf02459467openalex-snapshot
Links between maximum likelihood and maximum parsimony under a simple model of site substitution
inferredcites →https://doi.org/10.1007/pl00008277openalex-snapshot
The Performance of Neighbor-Joining Methods of Phylogenetic Reconstruction
inferredcites →https://doi.org/10.1007/s00026-009-0023-zopenalex-snapshot
Inverting Random Functions III: Discrete MLE Revisited
inferredcites →https://doi.org/10.1007/s00440-009-0246-2openalex-snapshot
Evolutionary trees and the Ising model on the Bethe lattice: a proof of Steel’s conjecture
inferredcites →https://doi.org/10.1007/s11538-007-9293-yopenalex-snapshot
Mixed-up Trees: the Structure of Phylogenetic Mixtures
inferredcites →https://doi.org/10.1007/s11538-009-9446-2openalex-snapshot
Revisiting an Equivalence Between Maximum Parsimony and Maximum Likelihood Methods in Phylogenetics
inferredcites →https://doi.org/10.1016/0025-5564(78)90089-5openalex-snapshot
Taxonomy with confidence
inferredcites →https://doi.org/10.1016/0025-5564(81)90087-0openalex-snapshot
Tests of phylogenetic hypotheses under generalized models
inferredcites →https://doi.org/10.1016/b978-0-12-172651-5.x5000-3openalex-snapshot
Probability and Random Processes
inferredcites →https://doi.org/10.1016/b978-0-12-307550-5.50005-8openalex-snapshot
MOLECULAR STUDIES OF EVOLUTION: A SOURCE OF NOVEL STATISTICAL PROBLEMS**This investigation was supported in part by research grant GM 10525-08 from the National Institutes of Health, Public Health Service.
inferredcites →https://doi.org/10.1016/j.aam.2004.03.003openalex-snapshot
Peeling phylogenetic ‘oranges’
inferredcites →https://doi.org/10.1016/j.aml.2004.06.006openalex-snapshot
Two further links between MP and ML under the poisson model
inferredcites →https://doi.org/10.1016/j.jtbi.2009.01.007openalex-snapshot
Phylogenetic information complexity: Is testing a tree easier than finding it?
inferredcites →https://doi.org/10.1016/j.jtbi.2009.12.022openalex-snapshot
Rate-variation need not defeat phylogenetic inference through pairwise sequence comparisons
inferredcites →https://doi.org/10.1016/j.jtbi.2013.08.012openalex-snapshot
Consistency of Bayesian inference of resolved phylogenetic trees
inferredcites →https://doi.org/10.1016/j.mbs.2003.10.004openalex-snapshot
A phase transition for a random cluster model on phylogenetic trees
inferredcites →https://doi.org/10.1016/j.mbs.2007.09.001openalex-snapshot
Identifying evolutionary trees and substitution parameters for the general Markov model with invariable sites
inferredcites →https://doi.org/10.1016/j.ympev.2005.03.027openalex-snapshot
A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous
inferredcites →https://doi.org/10.1016/j.ympev.2007.06.020openalex-snapshot
An independent heterotachy model and its implications for phylogeny and divergence time estimation
inferredcites →https://doi.org/10.1016/s0025-5564(96)00075-2openalex-snapshot
Full reconstruction of Markov models on evolutionary trees: Identifiability and consistency
inferredcites →https://doi.org/10.1017/cbo9780511819049openalex-snapshot
The Phylogenetic Handbook
inferredcites →https://doi.org/10.1038/369363a0openalex-snapshot
Hobgoblin of phylogenetics?
inferredcites →https://doi.org/10.1038/383130a0openalex-snapshot
Inferring complex phytogenies
inferredcites →https://doi.org/10.1080/106351501753462876openalex-snapshot
A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data
inferredcites →https://doi.org/10.1080/10635150490445788openalex-snapshot
Inconsistency of Maximum Parsimony Revisited
inferredcites →https://doi.org/10.1080/10635150701627304openalex-snapshot
Phylogenetic Mixtures on a Single Tree Can Mimic a Tree of Another Topology
inferredcites →https://doi.org/10.1080/10635150802166046openalex-snapshot
A Bayesian Perspective on a Non-parsimonious Parsimony Model
inferredcites →https://doi.org/10.1086/383584openalex-snapshot
Inferring Phylogenies.
inferredcites →https://doi.org/10.1089/cmb.1994.1.153openalex-snapshot
Reconstructing Trees When Sequence Sites Evolve at Variable Rates
inferredcites →https://doi.org/10.1089/cmb.1995.2.39openalex-snapshot
Classifying and Counting Linear Phylogenetic Invariants for the Jukes–Cantor Model
inferredcites →https://doi.org/10.1089/cmb.2006.0126openalex-snapshot
Phylogeny of Mixture Models: Robustness of Maximum Likelihood and Non-Identifiable Distributions
inferredcites →https://doi.org/10.1089/cmb.2006.13.1101openalex-snapshot
The Identifiability of Tree Topology for Phylogenetic Models, Including Covarion and Mixture Models
inferredcites →https://doi.org/10.1093/acprof:oso/9780199297306.001.0001openalex-snapshot
Parsimony, Phylogeny, and Genomics
inferredcites →https://doi.org/10.1093/acprof:oso/9780199297306.003.0009openalex-snapshot
Maximum parsimony and the phylogenetic information in multistate characters
inferredcites →https://doi.org/10.1093/genetics/49.4.725openalex-snapshot
THE NUMBER OF ALLELES THAT CAN BE MAINTAINED IN A FINITE POPULATION
inferredcites →https://doi.org/10.1093/oso/9780198509424.001.0001openalex-snapshot
Phylogenetics
inferredcites →https://doi.org/10.1093/oso/9780198572237.001.0001openalex-snapshot
Probability and Random Processes
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040433openalex-snapshot
A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony.
inferredcites →https://doi.org/10.1093/sysbio/27.4.401openalex-snapshot
Cases in which Parsimony or Compatibility Methods will be Positively Misleading
inferredcites →https://doi.org/10.1093/sysbio/syq028openalex-snapshot
The Akaike Information Criterion Will Not Choose the No Common Mechanism Model
inferredcites →https://doi.org/10.1093/sysbio/syq089openalex-snapshot
Biologically Inspired Phylogenetic Models Strongly Outperform the No Common Mechanism Model
inferredcites →https://doi.org/10.1093/sysbio/syr023openalex-snapshot
On Rogers' Proof of Identifiability for the GTR + Γ + I Model
inferredcites →https://doi.org/10.1109/tcbb.2008.107openalex-snapshot
Shrinkage Effect in Ancestral Maximum Likelihood
inferredcites →https://doi.org/10.1111/j.1096-0031.2008.00214.xopenalex-snapshot
Parsimony and explanatory power
inferredcites →https://doi.org/10.1137/s089548010138790xopenalex-snapshot
Inverting Random Functions II: Explicit Bounds for Discrete Maximum Likelihood Estimation, with Applications
inferredcites →https://doi.org/10.1186/1471-2148-5-50openalex-snapshot
Heterotachy and long-branch attraction in phylogenetics
inferredcites →https://doi.org/10.1214/aoms/1177729952openalex-snapshot
Note on the Consistency of the Maximum Likelihood Estimate
inferredcites →https://doi.org/10.1239/aap/1208358894openalex-snapshot
Identifiability of a Markovian model of molecular evolution with gamma-distributed rates
inferredcites →https://doi.org/10.1371/journal.pone.0007891openalex-snapshot
Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics
inferredcites →https://doi.org/10.2307/1447682openalex-snapshot
Molecular Systematics
inferredcites →https://doi.org/10.2307/2412923openalex-snapshot
Cases in which Parsimony or Compatibility Methods Will be Positively Misleading
inferredcites →https://doi.org/10.5860/choice.46-2076openalex-snapshot
Evidence and evolution: the logic behind the science

What points at this work

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

inferred← citeshttps://doi.org/10.11646/zootaxa.3825.1.1zenodo-depositor-declared
Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria
inferred← citeshttps://doi.org/10.1002/9781118301081.biblioopenalex-snapshot
Bibliography
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Large-Scale Multiple Sequence Alignment and Phylogeny Estimation
inferred← citeshttps://doi.org/10.1007/s00285-016-1055-8openalex-snapshot
Phylogenetic mixtures and linear invariants for equal input models
inferred← citeshttps://doi.org/10.1016/b978-0-443-15750-9.00085-9openalex-snapshot
Maximum Likelihood Phylogenetic Inference
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.04.012openalex-snapshot
Global phylogeny and biogeography of the fern genus Ctenitis (Dryopteridaceae), with a focus on the Indian Ocean region
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.001.0001openalex-snapshot
Molecular Evolution
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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/gbe/evr013openalex-snapshot
Detecting Phylogenetic Breakpoints and Discordance from Genome-Wide Alignments for Species Tree Reconstruction
inferred← citeshttps://doi.org/10.1093/sysbio/syaa031openalex-snapshot
Complex Ecological Phenotypes on Phylogenetic Trees: A Markov Process Model for Comparative Analysis of Multivariate Count Data
inferred← citeshttps://doi.org/10.1093/sysbio/syad063openalex-snapshot
Is Over-parameterization a Problem for Profile Mixture Models?
inferred← citeshttps://doi.org/10.1093/sysbio/sys043openalex-snapshot
Gaps: An Elusive Source of Phylogenetic Information
inferred← citeshttps://doi.org/10.1093/sysbio/sys064openalex-snapshot
When Do Phylogenetic Mixture Models Mimic Other Phylogenetic Models?
inferred← citeshttps://doi.org/10.1093/sysbio/syy077openalex-snapshot
Morphological Data Sets Fit a Common Mechanism Much More Poorly than DNA Sequences and Call Into Question the Mkv Model
inferred← citeshttps://doi.org/10.1093/sysbio/syz051openalex-snapshot
GHOST: Recovering Historical Signal from Heterotachously Evolved Sequence Alignments
inferred← citeshttps://doi.org/10.1101/640334openalex-snapshot
Complex ecological phenotypes on phylogenetic trees: a hidden Markov model for comparative analysis of multivariate count data
inferred← citeshttps://doi.org/10.1111/cla.12205openalex-snapshot
Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology
inferred← citeshttps://doi.org/10.1186/s12864-020-6608-yopenalex-snapshot
Integrated likelihood for phylogenomics under a no-common-mechanism model
inferred← citeshttps://doi.org/10.1371/journal.pone.0094534openalex-snapshot
On the Validity of Evolutionary Models with Site-Specific Parameters
inferred← citeshttps://doi.org/10.48550/arxiv.1501.06623openalex-snapshot
A consistency lemma in statistical phylogenetics
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