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ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets
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Outgoing claims: the papers this work cites, builds on, or argues with.
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SINE insertions: powerful tools for molecular systematics
inferredcites →https://doi.org/10.1002/ajb2.1016openalex-snapshot
Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life
inferredcites →https://doi.org/10.1007/978-3-319-67979-2_4openalex-snapshot
ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches
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Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent
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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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Phylogenetic inference based on matrix representation of trees
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Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites
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Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites
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Origin of land plants using the multispecies coalescent model
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Land plant origins and coalescence confusion
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SINEs of speciation: tracking lineages with retroposons
inferredcites →https://doi.org/10.1016/j.tree.2009.01.009openalex-snapshot
Gene tree discordance, phylogenetic inference and the multispecies coalescent
inferredcites →https://doi.org/10.1016/j.ympev.2004.02.020openalex-snapshot
Phylogeny of mysticete whales based on mitochondrial and nuclear data
inferredcites →https://doi.org/10.1016/j.ympev.2009.05.033openalex-snapshot
Coalescent methods for estimating phylogenetic trees
inferredcites →https://doi.org/10.1016/j.ympev.2009.08.018openalex-snapshot
Divergence date estimation and a comprehensive molecular tree of extant cetaceans
inferredcites →https://doi.org/10.1016/j.ympev.2011.06.021openalex-snapshot
Quartet MaxCut: A fast algorithm for amalgamating quartet trees
inferredcites →https://doi.org/10.1016/j.ympev.2012.10.012openalex-snapshot
A phylogenetic blueprint for a modern whale
inferredcites →https://doi.org/10.1016/j.ympev.2014.01.018openalex-snapshot
Divergent maximum-likelihood-branch-support values for polytomies
inferredcites →https://doi.org/10.1016/j.ympev.2014.04.029openalex-snapshot
Disparate parametric branch-support values from ambiguous characters
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Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
inferredcites →https://doi.org/10.1016/j.ympev.2015.05.011openalex-snapshot
Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms
inferredcites →https://doi.org/10.1016/j.ympev.2017.05.002openalex-snapshot
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Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage
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SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space
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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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Rare genomic changes as a tool for phylogenetics
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Initial sequencing and analysis of the human genome
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Molecular evidence from retroposons that whales form a clade within even-toed ungulates
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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
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Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds
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Regulatory activities of transposable elements: from conflicts to benefits
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Origins and evolutionary consequences of ancient endogenous retroviruses
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Retrophylogenomics Place Tarsiers on the Evolutionary Branch of Anthropoids
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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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Hemiplasy and homoplasy in the karyotypic phylogenies of 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
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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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Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
inferredcites →https://doi.org/10.1073/pnas.1221121110openalex-snapshot
Concatenation versus coalescence versus “concatalescence”
inferredcites →https://doi.org/10.1073/pnas.1407950111openalex-snapshot
Maximum likelihood inference of reticulate evolutionary histories
inferredcites →https://doi.org/10.1073/pnas.1616744114openalex-snapshot
Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary
inferredcites →https://doi.org/10.1073/pnas.1715318114openalex-snapshot
Phylogenomic red flags: Homology errors and zombie lineages in the evolutionary diversification of placental mammals
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Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: Hippopotamuses are the closest extant relatives of whales
inferredcites →https://doi.org/10.1080/106351500750049851openalex-snapshot
SINE Evolution, Missing Data, and the Origin of Whales
inferredcites →https://doi.org/10.1080/10635150590905939openalex-snapshot
Mitochondrial Phylogenetics and Evolution of Mysticete Whales
inferredcites →https://doi.org/10.1080/10635150600755453openalex-snapshot
Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative
inferredcites →https://doi.org/10.1080/10635150600865419openalex-snapshot
SINEs of a Nearly Perfect Character
inferredcites →https://doi.org/10.1080/10635150701884632openalex-snapshot
Morphological and Molecular Evidence for a Stepwise Evolutionary Transition from Teeth to Baleen in Mysticete Whales
inferredcites →https://doi.org/10.1080/10635150801905535openalex-snapshot
Discordance of Species Trees with Their Most Likely Gene Trees: The Case of Five Taxa
inferredcites →https://doi.org/10.1080/10635150802164587openalex-snapshot
Hemiplasy: A New Term in the Lexicon of Phylogenetics
inferredcites →https://doi.org/10.1080/106351598260996openalex-snapshot
Is It Better to Add Taxa or Characters to a Difficult Phylogenetic Problem?
inferredcites →https://doi.org/10.1080/14772000.2017.1401016openalex-snapshot
On the importance of homology in the age of phylogenomics
inferredcites →https://doi.org/10.1090/conm/685openalex-snapshot
Algebraic and Geometric Methods in Discrete Mathematics
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DendroPy: a Python library for phylogenetic computing
inferredcites →https://doi.org/10.1093/bioinformatics/btu462openalex-snapshot
ASTRAL: genome-scale coalescent-based species tree estimation
inferredcites →https://doi.org/10.1093/bioinformatics/btu530openalex-snapshot
Quartet Inference from SNP Data Under the Coalescent Model
inferredcites →https://doi.org/10.1093/bioinformatics/btv234openalex-snapshot
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
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/gbe/evx147openalex-snapshot
Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences
inferredcites →https://doi.org/10.1093/jhered/esx089openalex-snapshot
Pinniped Diphyly and Bat Triphyly: More Homology Errors Drive Conflicts in the Mammalian Tree
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Application of Phylogenetic Networks in Evolutionary Studies
inferredcites →https://doi.org/10.1093/molbev/msj071openalex-snapshot
Baleen Whale Phylogeny and a Past Extensive Radiation Event Revealed by SINE Insertion Analysis
inferredcites →https://doi.org/10.1093/molbev/msn172openalex-snapshot
Subdivision in an Ancestral Species Creates Asymmetry in Gene Trees
inferredcites →https://doi.org/10.1093/molbev/msr048openalex-snapshot
Testing for Ancient Admixture between Closely Related Populations
inferredcites →https://doi.org/10.1093/molbev/mss086openalex-snapshot
Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis
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Activity of Ancient RTE Retroposons during the Evolution of Cows, Spiral-Horned Antelopes, and Nilgais (Bovinae)
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Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals
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Heterogeneous Models Place the Root of the Placental Mammal Phylogeny
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Discordance of Species Trees with Their Most Likely Gene Trees: A Unifying Principle
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Exploring Massive Incomplete Lineage Sorting in Arctoids (Laurasiatheria, Carnivora)
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Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
inferredcites →https://doi.org/10.1093/molbev/msx261openalex-snapshot
Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction
inferredcites →https://doi.org/10.1093/molbev/msy112openalex-snapshot
Comparative Genomics Reveals a Burst of Homoplasy-Free Numt Insertions
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Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species
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Alternative Methods of Phylogenetic Inference and their Interrelationship
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Trees within Trees: Genes and Species, Molecules and Morphology
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What Is the Danger of the Anomaly Zone for Empirical Phylogenetics?
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Radiation of Extant Cetaceans Driven by Restructuring of the Oceans
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New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
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Sources of Error Inherent in Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing among Different Methods
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Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1093/sysbio/syq100openalex-snapshot
Are Transposable Element Insertions Homoplasy Free?: An Examination Using the Avian Tree of Life
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Estimating Species Trees: Practical and Theoretical Aspects
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Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting
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On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods
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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
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Incomplete Lineage Sorting in Mammalian Phylogenomics
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Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards
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To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods
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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
Baleen boom and bust: a synthesis of mysticete phylogeny, diversity and disparity
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Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
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Spectral shifts of mammalian ultraviolet-sensitive pigments (short wavelength-sensitive opsin 1) are associated with eye length and photic niche evolution
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Mammal madness: is the mammal tree of life not yet resolved?
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The perils of intralocus recombination for inferences of molecular convergence
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Mosaic retroposon insertion patterns in placental mammals
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Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
inferredcites →https://doi.org/10.1101/gr.186668.114openalex-snapshot
Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)
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
Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family‐level tree for Mammalia
inferredcites →https://doi.org/10.1111/cla.12404openalex-snapshot
Divergence and support among slightly suboptimal likelihood gene trees
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A NEW HYBRID BETWEEN A BLUE WHALE, BALAENOPTERA MUSCULUS , AND A FIN WHALE, B. PHYSALUS : FREQUENCY AND IMPLICATIONS OF HYBRIDIZATION
inferredcites →https://doi.org/10.1126/sciadv.aap9873openalex-snapshot
Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow
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The comparative genomics and complex population history of Papio baboons
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Resolution of the Early Placental Mammal Radiation Using Bayesian Phylogenetics
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A Draft Sequence of the Neandertal Genome
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Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification
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Whole-genome analyses resolve early branches in the tree of life of modern birds
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Convergent regulatory evolution and loss of flight in paleognathous birds
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Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits
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A Polynomial Time Approximation Scheme for Inferring Evolutionary Trees from Quartet Topologies and Its Application
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A comparative study of SVDquartets and other coalescent-based species tree estimation methods
inferredcites →https://doi.org/10.1186/s12859-018-2129-yopenalex-snapshot
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
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Dispersal of an ancient retroposon in the TP53 promoter of Bovidae: phylogeny, novel mechanisms, and potential implications for cow milk persistency
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SIESTA: enhancing searches for optimal supertrees and species trees
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/10.1371/journal.pbio.1000436openalex-snapshot
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
inferredcites →https://doi.org/10.1371/journal.pone.0028199openalex-snapshot
A Genomic Approach to Examine the Complex Evolution of Laurasiatherian Mammals
inferredcites →https://doi.org/10.1371/journal.pone.0104008openalex-snapshot
Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach
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Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
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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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Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary
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Phylogenetic Signal of Indels and the Neoavian Radiation
inferredcites →https://doi.org/10.3390/genes9030123openalex-snapshot
Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets
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Protein-Coding Genes’ Retrocopies and Their Functions
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Error in Phylogenetic Estimation for Bushes in the Tree of Life
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On the Illogic of Coalescence Simulations for Distinguishing the Causes of Conflict among Gene Trees
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble
inferred← citeshttps://doi.org/10.1002/ajb2.1568openalex-snapshot
Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation
inferred← citeshttps://doi.org/10.1016/j.cell.2022.03.034openalex-snapshot
Incomplete lineage sorting and phenotypic evolution in marsupials
inferred← citeshttps://doi.org/10.1016/j.cub.2025.10.020openalex-snapshot
Phoronid genome supports a monophyletic Lophophorata
inferred← citeshttps://doi.org/10.1016/j.tpb.2025.09.004openalex-snapshot
Inconsistency of parsimony under the multispecies coalescent
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A phylogeny for the Drosophila montium species group: A model clade for comparative analyses
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Collapsing dubiously resolved gene-tree branches in phylogenomic coalescent analyses
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Gene-tree misrooting drives conflicts in phylogenomic coalescent analyses of palaeognath birds
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107463openalex-snapshot
Molecular evolutionary analyses of tooth genes support sequential loss of enamel and teeth in baleen whales (Mysticeti)
inferred← citeshttps://doi.org/10.1038/s41467-024-49769-xopenalex-snapshot
Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria
inferred← citeshttps://doi.org/10.1093/gbe/evac013openalex-snapshot
Champagne: Automated Whole-Genome Phylogenomic Character Matrix Method Using Large Genomic Indels for Homoplasy-Free Inference
inferred← citeshttps://doi.org/10.1093/gbe/evad092openalex-snapshot
Effect of Different Types of Sequence Data on Palaeognath Phylogeny
inferred← citeshttps://doi.org/10.1093/jhered/esac061openalex-snapshot
Estimating phylogenies from genomes: A beginners review of commonly used genomic data in vertebrate phylogenomics
inferred← citeshttps://doi.org/10.1093/sysbio/syab069openalex-snapshot
Accuracy in Near-Perfect Virus Phylogenies
inferred← citeshttps://doi.org/10.1093/sysbio/syab086openalex-snapshot
Theoretical and Practical Considerations when using Retroelement Insertions to Estimate Species Trees in the Anomaly Zone
inferred← citeshttps://doi.org/10.1093/sysbio/syac025openalex-snapshot
Reunion of Australasian Possums by Shared SINE Insertions
inferred← citeshttps://doi.org/10.1093/sysbio/syaf009openalex-snapshot
Improved Robustness to Gene Tree Incompleteness, Estimation Errors, and Systematic Homology Errors with Weighted TREE-QMC
inferred← citeshttps://doi.org/10.1101/2022.08.10.503388openalex-snapshot
A genomic timescale for placental mammal evolution
inferred← citeshttps://doi.org/10.1101/2022.08.11.503681openalex-snapshot
Unraveling the Myotis Morass: Ultraconserved-Element Analysis Reveals Introgression, Cryptic Diversity, and Taxonomic Trouble in the Most Species-rich Bat Genus
inferred← citeshttps://doi.org/10.1101/2025.07.10.664098openalex-snapshot
A Maximum-Likelihood Method to Construct Phylogenetic Trees Using Low-Homoplasy Markers: New Insights into Neoaves Phylogeny
inferred← citeshttps://doi.org/10.1101/gr.262261.120openalex-snapshot
The multicomparative 2-n-way genome suite
inferred← citeshttps://doi.org/10.1111/mec.70426openalex-snapshot
Genomic Insights Into the Evolutionary History of Berardius Beaked Whales: Speciation Driven by Resource Specialization, Gigantism and Thermal Barriers?
inferred← citeshttps://doi.org/10.1126/science.abl8189openalex-snapshot
A genomic timescale for placental mammal evolution
inferred← citeshttps://doi.org/10.1146/annurev-animal-061220-023149openalex-snapshot
Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation
inferred← citeshttps://doi.org/10.1186/s13015-023-00248-wopenalex-snapshot
Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model
inferred← citeshttps://doi.org/10.1186/s13015-023-00249-9openalex-snapshot
Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem
inferred← citeshttps://doi.org/10.1371/journal.pbio.3000954openalex-snapshot
Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression
inferred← citeshttps://doi.org/10.1371/journal.pbio.3002632openalex-snapshot
The promise and pitfalls of synteny in phylogenomics
inferred← citeshttps://doi.org/10.3390/d12040164openalex-snapshot
Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation
inferred← citeshttps://doi.org/10.3390/genes13030399openalex-snapshot
SINE-Based Phylogenomics Reveal Extensive Introgression and Incomplete Lineage Sorting in Myotis
inferred← citeshttps://doi.org/10.3390/genes13040709openalex-snapshot
Methodologies for the De novo Discovery of Transposable Element Families
inferred← citeshttps://doi.org/10.3390/genes13050766openalex-snapshot
Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone
inferred← citeshttps://doi.org/10.3390/genes13050774openalex-snapshot
Euarchontoglires Challenged by Incomplete Lineage Sorting
inferred← citeshttps://doi.org/10.3390/genes13060989openalex-snapshot
SINEs as Credible Signs to Prove Common Ancestry in the Tree of Life: A Brief Review of Pioneering Case Studies in Retroposon Systematics
inferred← citeshttps://doi.org/10.3390/genes13071167openalex-snapshot
Phylogenomic Coalescent Analyses of Avian Retroelements Infer Zero-Length Branches at the Base of Neoaves, Emergent Support for Controversial Clades, and Ancient Introgressive Hybridization in Afroaves
inferred← citeshttps://doi.org/10.6084/m9.figshare.26648247openalex-snapshot
Additional file 1 of Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model
inferred← citeshttps://doi.org/10.6084/m9.figshare.26665393openalex-snapshot
Additional file 1 of Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem
inferred← citeshttps://doi.org/10.64898/2026.02.14.705539openalex-snapshot
TriMouNet: An Algorithm for Inferring Level-1 Phylogenetic Networks from Multi-Locus Gene Tree Distributions
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