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Coalescent-based phylogenetic inference from genes with unequivocal historical signal suggests a polytomy at the root of the placental mammal tree of life

https://doi.org/10.1101/423996
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What this work says

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

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ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches
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Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
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Deciphering ancient rapid radiations
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Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased
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The gene tree delusion
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Molecular phylogenetics and the origins of placental mammals
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ModelFinder: fast model selection for accurate phylogenetic estimates
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Contentious relationships in phylogenomic studies can be driven by a handful of genes
inferredcites →https://doi.org/10.1073/pnas.0704342104openalex-snapshot
Genomics, biogeography, and the diversification of placental mammals
inferredcites →https://doi.org/10.1073/pnas.0809297106openalex-snapshot
Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals
inferredcites →https://doi.org/10.1073/pnas.1211733109openalex-snapshot
Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
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Correction for Song et al., Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
inferredcites →https://doi.org/10.1080/10635150290069913openalex-snapshot
An Approximately Unbiased Test of Phylogenetic Tree Selection
inferredcites →https://doi.org/10.1080/10635150601146041openalex-snapshot
Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence
inferredcites →https://doi.org/10.1093/gbe/evv261openalex-snapshot
The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference
inferredcites →https://doi.org/10.1093/molbev/msm136openalex-snapshot
Phylogenomic Data Analyses Provide Evidence that Xenarthra and Afrotheria Are Sister Groups
inferredcites →https://doi.org/10.1093/molbev/msn104openalex-snapshot
Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets
inferredcites →https://doi.org/10.1093/molbev/msq166openalex-snapshot
Mammalian Evolution May not Be Strictly Bifurcating
inferredcites →https://doi.org/10.1093/molbev/mst116openalex-snapshot
Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals
inferredcites →https://doi.org/10.1093/molbev/mst117openalex-snapshot
Heterogeneous Models Place the Root of the Placental Mammal Phylogeny
inferredcites →https://doi.org/10.1093/molbev/mst118openalex-snapshot
Making the Impossible Possible: Rooting the Tree of Placental Mammals
inferredcites →https://doi.org/10.1093/molbev/msu132openalex-snapshot
OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/sysbio/syp047openalex-snapshot
What Is the Danger of the Anomaly Zone for Empirical Phylogenetics?
inferredcites →https://doi.org/10.1093/sysbio/syx063openalex-snapshot
Why Concatenation Fails Near the Anomaly Zone
inferredcites →https://doi.org/10.1101/gr.090647.108openalex-snapshot
Mosaic retroposon insertion patterns in placental mammals
inferredcites →https://doi.org/10.1101/gr.125864.111openalex-snapshot
Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
inferredcites →https://doi.org/10.1101/gr.5918807openalex-snapshot
Using genomic data to unravel the root of the placental mammal phylogeny
inferredcites →https://doi.org/10.1111/1467-9868.00125openalex-snapshot
Smoothing Parameter Selection in Nonparametric Regression Using an Improved Akaike Information Criterion
inferredcites →https://doi.org/10.1111/j.1558-5646.1985.tb00420.xopenalex-snapshot
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
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/10.1126/science.1211028openalex-snapshot
Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification
inferredcites →https://doi.org/10.1126/science.1229237openalex-snapshot
The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals
inferredcites →https://doi.org/10.1186/1471-2148-13-1openalex-snapshot
New approaches for unravelling reassortment pathways
inferredcites →https://doi.org/10.1186/1471-2148-7-1openalex-snapshot
Differential impact of simultaneous migration on coevolving hosts and parasites.
inferredcites →https://doi.org/10.1186/1471-2148-7-108openalex-snapshot
A web-database of mammalian morphology and a reanalysis of placental phylogeny
inferredcites →https://doi.org/10.1186/1471-2148-7-8openalex-snapshot
Site specific rates of mitochondrial genomes and the phylogeny of eutheria.
inferredcites →https://doi.org/10.1186/1471-2148-8-162openalex-snapshot
Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations
inferredcites →https://doi.org/10.1186/gb-2007-8-9-r199openalex-snapshot
Rooting the eutherian tree: the power and pitfalls of phylogenomics
inferredcites →https://doi.org/10.1371/journal.pbio.0040091openalex-snapshot
Retroposed Elements as Archives for the Evolutionary History of Placental Mammals
inferredcites →https://doi.org/10.1371/journal.pgen.0020068openalex-snapshot
Discordance of Species Trees with Their Most Likely Gene Trees
inferredcites →https://doi.org/10.1371/journal.pgen.0030002openalex-snapshot
Early History of Mammals Is Elucidated with the ENCODE Multiple Species Sequencing Data

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inferred← citeshttps://doi.org/10.1093/sysbio/syac006openalex-snapshot
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi
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