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Phylogenomic red flags: Homology errors and zombie lineages in the evolutionary diversification of placental mammals
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Waking the undead: Implications of a soft explosive model for the timing of placental mammal diversification
inferredcites →https://doi.org/10.1073/pnas.1616744114openalex-snapshot
Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary
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ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
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Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1016/j.dib.2018.04.094openalex-snapshot
Genome-scale DNA sequence data and the evolutionary history of placental mammals
inferred← citeshttps://doi.org/10.1016/j.tree.2019.01.017openalex-snapshot
Six Impossible Things before Breakfast: Assumptions, Models, and Belief in Molecular Dating
inferred← citeshttps://doi.org/10.1016/j.tree.2025.06.011openalex-snapshot
Recombination-aware phylogenomics
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.10.012openalex-snapshot
Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.106539openalex-snapshot
Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107344openalex-snapshot
Gene-tree misrooting drives conflicts in phylogenomic coalescent analyses of palaeognath birds
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107550openalex-snapshot
Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree
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Introduction: Carving Nature at Its Joints, or Why Birds Are Not Dinosaurs and Men Are Not Apes
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The Interrelationships of Organisms
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Systematics: Exposing Myths
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Monothetic and Polythetic Taxa
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Non-taxa or the Absence of –Phyly: Paraphyly and Aphyly
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Parameters of Classification:Ordo Ab Chao
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How to Study Classification
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Modern Artificial Methods and Raw Data
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How to Study Classification: Consensus Techniques and General Classifications
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How to Study Classification: ‘Total Evidence’ vs. ‘Consensus’, Character Congruence vs. Taxonomic Congruence, Simultaneous Analysis vs. Partitioned Data
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How to Study Classification
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How to Study Classification
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Beyond Classification: How to Study Phylogeny
inferred← citeshttps://doi.org/10.1017/9781139047678.021openalex-snapshot
The Separation of Classification and Phylogenetics
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Further Myths and More Misunderstandings
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Systematics Association Special Volumes
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Rolling of the jaw is essential for mammalian chewing and tribosphenic molar function
inferred← citeshttps://doi.org/10.1073/pnas.1715371114openalex-snapshot
Reply to Gatesy and Springer: Claims of homology errors and zombie lineages do not compromise the dating of placental diversification
inferred← citeshttps://doi.org/10.1073/pnas.2406494121openalex-snapshot
A new phylogeny for Aves is compromised by pervasive misalignment and homology problems
inferred← citeshttps://doi.org/10.1080/14772000.2017.1401016openalex-snapshot
On the importance of homology in the age of phylogenomics
inferred← citeshttps://doi.org/10.1093/jhered/esz076openalex-snapshot
ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets
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Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals
inferred← citeshttps://doi.org/10.1101/2020.07.31.230144openalex-snapshot
Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Non-Reversible Models for Mammals
inferred← citeshttps://doi.org/10.1101/2022.03.08.483551openalex-snapshot
Iterative deletion of gene trees detects extreme biases in distance-based phylogenomic coalescent analyses
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Conflicting signal in transcriptomic markers leads to a poorly resolved backbone phylogeny of chalcidoid wasps
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A comparison of phylogenomic inference pipelines for low‐coverage whole‐genome sequencing in Formica ants
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Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation
inferred← citeshttps://doi.org/10.1186/s12862-018-1218-xopenalex-snapshot
The soft explosive model of placental mammal evolution
inferred← citeshttps://doi.org/10.1186/s12862-019-1534-9openalex-snapshot
The effect of alignment uncertainty, substitution models and priors in building and dating the mammal tree of life
inferred← citeshttps://doi.org/10.1371/journal.pbio.3000494openalex-snapshot
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
inferred← citeshttps://doi.org/10.24272/j.issn.2095-8137.2023.189openalex-snapshot
Improved mammalian family phylogeny using gap-rare multiple sequence alignment: A timetree of extant placentals and marsupials
inferred← citeshttps://doi.org/10.3389/fgene.2019.01241openalex-snapshot
Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary
inferred← citeshttps://doi.org/10.3390/genes13050766openalex-snapshot
Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone
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Assessing confidence in root placement on phylogenies: an empirical study using non-reversible models for Mammals
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