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Retroposon Insertions within a Multispecies Coalescent Framework Suggest that Ratite Phylogeny is not in the ‘Anomaly Zone’
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Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1521-1878(200002)22:2<148::aid-bies6>3.0.co;2-zopenalex-snapshot
SINE insertions: powerful tools for molecular systematics
inferredcites →https://doi.org/10.1007/978-3-319-67979-2_4openalex-snapshot
ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches
inferredcites →https://doi.org/10.1007/s0033501-1015-4openalex-snapshot
Evolution of CHR-2 SINEs in cetartiodactyl genomes: possible evidence for the monophyletic origin of toothed whales
inferredcites →https://doi.org/10.1016/j.cub.2016.10.029openalex-snapshot
Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites
inferredcites →https://doi.org/10.1016/j.gene.2015.06.064openalex-snapshot
A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla)
inferredcites →https://doi.org/10.1016/j.tplants.2014.02.012openalex-snapshot
Land plant origins and coalescence confusion
inferredcites →https://doi.org/10.1016/j.tree.2004.08.002openalex-snapshot
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.2009.05.033openalex-snapshot
Coalescent methods for estimating phylogenetic trees
inferredcites →https://doi.org/10.1016/j.ympev.2013.01.020openalex-snapshot
Quantification and relative severity of inflated branch-support values generated by alternative methods: An empirical example
inferredcites →https://doi.org/10.1016/j.ympev.2014.08.013openalex-snapshot
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.2018.10.001openalex-snapshot
Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses
inferredcites →https://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
inferredcites →https://doi.org/10.1038/nature04240openalex-snapshot
Natural selection on protein-coding genes in the human genome
inferredcites →https://doi.org/10.1038/nature15697openalex-snapshot
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
inferredcites →https://doi.org/10.1038/nature19417openalex-snapshot
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
inferredcites →https://doi.org/10.1038/ncomms1448openalex-snapshot
Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds
inferredcites →https://doi.org/10.1038/nrg.2016.139openalex-snapshot
Regulatory activities of transposable elements: from conflicts to benefits
inferredcites →https://doi.org/10.1038/sj.hdy.6800724openalex-snapshot
The evolutionary ecology of the major histocompatibility complex
inferredcites →https://doi.org/10.1038/srep01756openalex-snapshot
Retrophylogenomics Place Tarsiers on the Evolutionary Branch of Anthropoids
inferredcites →https://doi.org/10.1038/srep43562openalex-snapshot
The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads
inferredcites →https://doi.org/10.1073/pnas.0603797103openalex-snapshot
Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions
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
inferredcites →https://doi.org/10.1073/pnas.1221121110openalex-snapshot
Concatenation versus coalescence versus “concatalescence”
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.96.18.10261openalex-snapshot
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/10.1080/10635150801905535openalex-snapshot
Discordance of Species Trees with Their Most Likely Gene Trees: The Case of Five Taxa
inferredcites →https://doi.org/10.1080/14772000.2017.1401016openalex-snapshot
On the importance of homology in the age of phylogenomics
inferredcites →https://doi.org/10.1093/bioinformatics/btq228openalex-snapshot
DendroPy: a Python library for phylogenetic computing
inferredcites →https://doi.org/10.1093/bioinformatics/btt394openalex-snapshot
Naive binning improves phylogenomic analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btu462openalex-snapshot
ASTRAL: genome-scale coalescent-based species tree estimation
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/evu256openalex-snapshot
Multiple Lineages of Ancient CR1 Retroposons Shaped the Early Genome Evolution of Amniotes
inferredcites →https://doi.org/10.1093/jhered/esx089openalex-snapshot
Pinniped Diphyly and Bat Triphyly: More Homology Errors Drive Conflicts in the Mammalian Tree
inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot
Bayesian Inference of Species Trees from Multilocus Data
inferredcites →https://doi.org/10.1093/molbev/msq019openalex-snapshot
Rodent Evolution: Back to the Root
inferredcites →https://doi.org/10.1093/molbev/msr319openalex-snapshot
Retroposon Insertion Patterns of Neoavian Birds: Strong Evidence for an Extensive Incomplete Lineage Sorting Era
inferredcites →https://doi.org/10.1093/molbev/mss158openalex-snapshot
Activity of Ancient RTE Retroposons during the Evolution of Cows, Spiral-Horned Antelopes, and Nilgais (Bovinae)
inferredcites →https://doi.org/10.1093/molbev/mst160openalex-snapshot
Discordance of Species Trees with Their Most Likely Gene Trees: A Unifying Principle
inferredcites →https://doi.org/10.1093/molbev/msv188openalex-snapshot
Exploring Massive Incomplete Lineage Sorting in Arctoids (Laurasiatheria, Carnivora)
inferredcites →https://doi.org/10.1093/molbev/msv347openalex-snapshot
Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)
inferredcites →https://doi.org/10.1093/molbev/msw079openalex-snapshot
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/sysbio/46.3.537openalex-snapshot
Trees within Trees: Genes and Species, Molecules and Morphology
inferredcites →https://doi.org/10.1093/sysbio/syp031openalex-snapshot
Estimating Species Phylogenies Using Coalescence Times among Sequences
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/syp061openalex-snapshot
Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes
inferredcites →https://doi.org/10.1093/sysbio/syq047openalex-snapshot
Sources of Error Inherent in Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing among Different Methods
inferredcites →https://doi.org/10.1093/sysbio/syr027openalex-snapshot
Estimating Species Trees from Unrooted Gene Trees
inferredcites →https://doi.org/10.1093/sysbio/syu063openalex-snapshot
Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1093/sysbio/syv016openalex-snapshot
On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods
inferredcites →https://doi.org/10.1093/sysbio/syw001openalex-snapshot
Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).
inferredcites →https://doi.org/10.1093/sysbio/syw082openalex-snapshot
Incomplete Lineage Sorting in Mammalian Phylogenomics
inferredcites →https://doi.org/10.1093/sysbio/syx063openalex-snapshot
Why Concatenation Fails Near the Anomaly Zone
inferredcites →https://doi.org/10.1093/sysbio/syx077openalex-snapshot
To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods
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/10.1101/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
Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family‐level tree for Mammalia
inferredcites →https://doi.org/10.1126/science.1142430openalex-snapshot
Human Genome Ultraconserved Elements Are Ultraselected
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.1250463openalex-snapshot
Statistical binning enables an accurate coalescent-based estimation of the avian tree
inferredcites →https://doi.org/10.1126/science.aat7244openalex-snapshot
Convergent regulatory evolution and loss of flight in paleognathous birds
inferredcites →https://doi.org/10.1186/1471-2148-10-302openalex-snapshot
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
inferredcites →https://doi.org/10.1186/1471-2164-15-s6-s11openalex-snapshot
BBCA: Improving the scalability of *BEAST using random binning
inferredcites →https://doi.org/10.1186/1471-2164-16-s10-s3openalex-snapshot
ASTRID: Accurate Species TRees from Internode Distances
inferredcites →https://doi.org/10.1186/s12864-015-1235-8openalex-snapshot
Dispersal of an ancient retroposon in the TP53 promoter of Bovidae: phylogeny, novel mechanisms, and potential implications for cow milk persistency
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.1002224openalex-snapshot
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.0060019openalex-snapshot
Coalescent-Based Genome Analyses Resolve the Early Branches of the Euarchontoglires
inferredcites →https://doi.org/10.1371/journal.pone.0129183openalex-snapshot
Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
inferredcites →https://doi.org/10.2307/2419070openalex-snapshot
Gene Trees and Species Trees: Molecular Systematics as One-Character Taxonomy
inferredcites →https://doi.org/10.3390/genes9030123openalex-snapshot
Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets
inferredcites →https://doi.org/10.3390/v9040080openalex-snapshot
Protein-Coding Genes’ Retrocopies and Their Functions
inferredcites →https://doi.org/10.4172/2329-9002.1000110openalex-snapshot
Error in Phylogenetic Estimation for Bushes in the Tree of Life
inferredcites →https://doi.org/10.4172/2329-9002.1000205openalex-snapshot
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.
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
inferred← citeshttps://doi.org/10.1101/709477openalex-snapshot
An ABBA-BABA Test for Introgression Using Retroposon Insertion Data
inferred← citeshttps://doi.org/10.1111/zsc.12512openalex-snapshot
Gene tree quality affects empirical coalescent branch length estimation
inferred← citeshttps://doi.org/10.1186/s40657-020-00194-wopenalex-snapshot
Whole genome phylogeny of Gallus: introgression and data-type effects
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/d13110555openalex-snapshot
Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds
inferred← citeshttps://doi.org/10.6084/m9.figshare.11992323openalex-snapshot
Additional file 6 of Whole genome phylogeny of Gallus: introgression and data-type effects
inferred← citeshttps://doi.org/10.6084/m9.figshare.11992332openalex-snapshot
Additional file 7 of Whole genome phylogeny of Gallus: introgression and data-type effects
inferred← citeshttps://doi.org/10.6084/m9.figshare.11992338openalex-snapshot
Additional file 8 of Whole genome phylogeny of Gallus: introgression and data-type effects
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