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Why do phylogenomic analyses of early animal evolution continue to disagree? Sites in different structural environments yield different answers

https://doi.org/10.1101/400465
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What this work says

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

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Multiple Sequence Alignment Using ClustalW and ClustalX
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Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
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How Many Bootstrap Replicates Are Necessary?
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Volume changes in protein evolution
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Position-based sequence weights
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Phylogenomics Revives Traditional Views on Deep Animal Relationships
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Multigene Phylogeny of the Green Lineage Reveals the Origin and Diversification of Land Plants
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An Alternative Root for the Eukaryote Tree of Life
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A Transcriptomic-Phylogenomic Analysis of the Evolutionary Relationships of Flatworms
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A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals
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Embracing Uncertainty in Reconstructing Early Animal Evolution
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Should phylogenetic models be trying to ‘fit an elephant’?
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The hidden biology of sponges and ctenophores
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Coalescent methods for estimating phylogenetic trees
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Deep metazoan phylogeny: When different genes tell different stories
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Identifying localized biases in large datasets: A case study using the avian tree of life
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A meeting with Enrico Fermi
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Genome-scale approaches to resolving incongruence in molecular phylogenies
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Broad phylogenomic sampling improves resolution of the animal tree of life
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Acoelomorph flatworms are deuterostomes related to Xenoturbella
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Inferring ancient divergences requires genes with strong phylogenetic signals
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The ctenophore genome and the evolutionary origins of neural systems
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Causes of evolutionary rate variation among protein sites
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Contentious relationships in phylogenomic studies can be driven by a handful of genes
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Ctenophore relationships and their placement as the sister group to all other animals
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Molecular phylogeny of choanoflagellates, the sister group to Metazoa
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Evidence for an ancient adaptive episode of convergent molecular evolution
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Phylotranscriptomic analysis of the origin and early diversification of land plants
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The two-domain tree of life is linked to a new root for the Archaea
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Error, signal, and the placement of Ctenophora sister to all other animals
inferredcites →https://doi.org/10.1073/pnas.1518127112openalex-snapshot
Genomic data do not support comb jellies as the sister group to all other animals
inferredcites →https://doi.org/10.1080/106351500750049860openalex-snapshot
Parametric Phylogenetics?
inferredcites →https://doi.org/10.1080/10635150290102339openalex-snapshot
Increased Taxon Sampling Greatly Reduces Phylogenetic Error
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Choosing the Best Genes for the Job: The Case for Stationary Genes in Genome-Scale Phylogenetics
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A Rapid Bootstrap Algorithm for the RAxML Web Servers
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How Should Species Phylogenies Be Inferred from Sequence Data?
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Empirical profile mixture models for phylogenetic reconstruction
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity
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Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution
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A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
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An Improved General Amino Acid Replacement Matrix
inferredcites →https://doi.org/10.1093/molbev/msq089openalex-snapshot
Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships
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The Phylogenetic Position of Myxozoa: Exploring Conflicting Signals in Phylogenomic and Ribosomal Data Sets
inferredcites →https://doi.org/10.1093/molbev/mss208openalex-snapshot
Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets
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Ultrafast Approximation for Phylogenetic Bootstrap
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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
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Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)
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UniProt: the Universal Protein knowledgebase
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SCRATCH: a protein structure and structural feature prediction server
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The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides
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UniProt: the universal protein knowledgebase
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025627openalex-snapshot
Combining protein evolution and secondary structure
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
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Cases in which Parsimony or Compatibility Methods will be Positively Misleading
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A Concern for Evidence and a Phylogenetic Hypothesis of Relationships among Epicrates (Boidae, Serpentes)
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Gene Trees in Species Trees
inferredcites →https://doi.org/10.1093/sysbio/syq002openalex-snapshot
Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics Is Clearly Beneficial
inferredcites →https://doi.org/10.1093/sysbio/sys036openalex-snapshot
Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny
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Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions
inferredcites →https://doi.org/10.1093/sysbio/syw084openalex-snapshot
Who Let the CAT Out of the Bag? Accurately Dealing with Substitutional Heterogeneity in Phylogenomic Analyses
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Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses
inferredcites →https://doi.org/10.1093/sysbio/syx041openalex-snapshot
Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling
inferredcites →https://doi.org/10.1098/rspb.2009.0896openalex-snapshot
Assessing the root of bilaterian animals with scalable phylogenomic methods
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The response of protein structures to amino-acid sequence changes
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Models of Molecular Evolution and Phylogeny: Table 1.
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The origin of the animals and a ‘Savannah’ hypothesis for early bilaterian evolution
inferredcites →https://doi.org/10.1111/j.1558-5646.2008.00549.xopenalex-snapshot
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
inferredcites →https://doi.org/10.1111/nyas.12747openalex-snapshot
Estimating phylogenetic trees from genome‐scale data
inferredcites →https://doi.org/10.1126/science.1242592openalex-snapshot
The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution
inferredcites →https://doi.org/10.1126/science.1253451openalex-snapshot
Whole-genome analyses resolve early branches in the tree of life of modern birds
inferredcites →https://doi.org/10.1126/science.1257570openalex-snapshot
Phylogenomics resolves the timing and pattern of insect evolution
inferredcites →https://doi.org/10.1186/1471-2148-7-s1-s4openalex-snapshot
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
inferredcites →https://doi.org/10.1186/1471-2148-9-1openalex-snapshot
Phylogenetic relationships in Cortinarius, section Calochroi, inferred from nuclear DNA sequences
inferredcites →https://doi.org/10.1186/1471-2148-9-187openalex-snapshot
An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models
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The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa
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Rooting the eutherian tree: the power and pitfalls of phylogenomics
inferredcites →https://doi.org/10.1371/journal.pbio.1000602openalex-snapshot
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
inferredcites →https://doi.org/10.1371/journal.pcbi.1002572openalex-snapshot
Bringing Molecules Back into Molecular Evolution
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Multigene Phylogeny of Choanozoa and the Origin of Animals
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Cases in which Parsimony or Compatibility Methods Will be Positively Misleading
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A Framework for the Quantitative Study of Evolutionary Trees
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R: A Language and Environment for Statistical Computing
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Animal phylogeny and large-scale sequencing: progress and pitfalls
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Error in Phylogenetic Estimation for Bushes in the Tree of Life
inferredcites →https://doi.org/10.5281/zenodo.1403224openalex-snapshot
Data For: Why Do Phylogenomic Analyses Of Early Animal Evolution Continue To Disagree? Sites In Different Structural Environments Yield Different Answers

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inferred← citeshttps://doi.org/10.1007/978-3-030-16477-5_6openalex-snapshot
Resolving the Avian Tree of Life from Top to Bottom: The Promise and Potential Boundaries of the Phylogenomic Era
inferred← citeshttps://doi.org/10.1093/sysbio/syaa023openalex-snapshot
Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses
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