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An ABBA-BABA Test for Introgression Using Retroposon Insertion Data

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What this work says

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

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Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

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ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches

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The More the Merrier? A Large Cladistic Analysis of Mysticetes, and Comments on the Transition from Teeth to Baleen

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Land plant origins and coalescence confusion

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Gene tree discordance, phylogenetic inference and the multispecies coalescent

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Phylogeny of mysticete whales based on mitochondrial and nuclear data

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Coalescent methods for estimating phylogenetic trees

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Divergence date estimation and a comprehensive molecular tree of extant cetaceans

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A phylogenetic blueprint for a modern whale

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The gene tree delusion

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Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses

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Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts

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Molecular evidence from retroposons that whales form a clade within even-toed ungulates

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Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds

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The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads

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Retroelements and the human genome: New perspectives on an old relation

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Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions

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Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals

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Retroposon analysis of major cetacean lineages: The monophyly of toothed whales and the paraphyly of river dolphins

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SINE Evolution, Missing Data, and the Origin of Whales

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Mitochondrial Phylogenetics and Evolution of Mysticete Whales

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Morphological and Molecular Evidence for a Stepwise Evolutionary Transition from Teeth to Baleen in Mysticete Whales

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DendroPy: a Python library for phylogenetic computing

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Quartet Inference from SNP Data Under the Coalescent Model

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ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

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The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

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Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences

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Pinniped Diphyly and Bat Triphyly: More Homology Errors Drive Conflicts in the Mammalian Tree

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Baleen Whale Phylogeny and a Past Extensive Radiation Event Revealed by SINE Insertion Analysis

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Testing for Ancient Admixture between Closely Related Populations

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Activity of Ancient RTE Retroposons during the Evolution of Cows, Spiral-Horned Antelopes, and Nilgais (Bovinae)

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Heterogeneous Models Place the Root of the Placental Mammal Phylogeny

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Detection and Polarization of Introgression in a Five-Taxon Phylogeny

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Inconsistency of Species Tree Methods under Gene Flow

inferredcites →https://doi.org/10.1093/sysbio/syw082openalex-snapshot

Incomplete Lineage Sorting in Mammalian Phylogenomics

inferredcites →https://doi.org/10.1093/sysbio/syy076openalex-snapshot

True Homoplasy of Retrotransposon Insertions in Primates

inferredcites →https://doi.org/10.1093/sysbio/syz019openalex-snapshot

Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone

inferredcites →https://doi.org/10.1098/rsos.140434openalex-snapshot

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inferredcites →https://doi.org/10.1098/rspb.2012.0683openalex-snapshot

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inferredcites →https://doi.org/10.1098/rspb.2015.1817openalex-snapshot

Spectral shifts of mammalian ultraviolet-sensitive pigments (short wavelength-sensitive opsin 1) are associated with eye length and photic niche evolution

inferredcites →https://doi.org/10.1098/rstb.2015.0140openalex-snapshot

Mammal madness: is the mammal tree of life not yet resolved?

inferredcites →https://doi.org/10.1101/643296openalex-snapshot

Retroposon Insertions within a Multispecies Coalescent Framework Suggest that Ratite Phylogeny is not in 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.210948.116openalex-snapshot

Speciation network in Laurasiatheria: retrophylogenomic signals

inferredcites →https://doi.org/10.1111/cla.12170openalex-snapshot

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A NEW HYBRID BETWEEN A BLUE WHALE, BALAENOPTERA MUSCULUS , AND A FIN WHALE, B. PHYSALUS : FREQUENCY AND IMPLICATIONS OF HYBRIDIZATION

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Resolution of the Early Placental Mammal Radiation Using Bayesian Phylogenetics

inferredcites →https://doi.org/10.1126/science.1188021openalex-snapshot

A Draft Sequence of the Neandertal Genome

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.1253451openalex-snapshot

Whole-genome analyses resolve early branches in the tree of life of modern birds

inferredcites →https://doi.org/10.1126/science.aat7244openalex-snapshot

Convergent regulatory evolution and loss of flight in paleognathous birds

inferredcites →https://doi.org/10.1186/s13100-018-0143-2openalex-snapshot

Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation

inferredcites →https://doi.org/10.13140/rg.2.1.4466.9927openalex-snapshot

Holm-Bonferroni Sequential Correction: An EXCEL Calculator

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Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions

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The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

inferredcites →https://doi.org/10.1371/journal.pcbi.1004812openalex-snapshot

Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data

inferredcites →https://doi.org/10.1371/journal.pgen.0020068openalex-snapshot

Discordance of Species Trees with Their Most Likely Gene Trees

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A Genomic Approach to Examine the Complex Evolution of Laurasiatherian Mammals

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Gene Trees and Species Trees: Molecular Systematics as One-Character Taxonomy

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A Simple Sequentially Rejective Multiple Test Procedure

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Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets

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Protein-Coding Genes’ Retrocopies and Their Functions

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inferred← citeshttps://doi.org/10.1038/s41586-020-2486-3openalex-snapshot

Six reference-quality genomes reveal evolution of bat adaptations

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