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Disentangling Sources of Gene Tree Discordance in Phylogenomic Datasets: Testing Ancient Hybridizations in Amaranthaceae s.l

https://doi.org/10.1101/794370
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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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A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories
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From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales
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Phylogeny of Polycnemoideae (Amaranthaceae): Implications for biogeography, character evolution and taxonomy
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Halophyte Halogeton glomeratus, a promising candidate for phytoremediation of heavy metal-contaminated saline soils
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The Phylogenetic Association Between Salt Tolerance and Heavy Metal Hyperaccumulation in Angiosperms
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Plastome Phylogenetics: 30 Years of Inferences Into Plant Evolution
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Evolutionary ecology of fast seed germination—A case study in Amaranthaceae/Chenopodiaceae
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Gene tree discordance, phylogenetic inference and the multispecies coalescent
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Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics
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Plastid phylogenomic insights into the evolution of Caryophyllales
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Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes
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Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes
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Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: implications for biogeography and concerted evolution.
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Further analysis of the data by Akaike's information criterion and the finite corrections
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Difficulties in Detecting Hybridization
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An Approximately Unbiased Test of Phylogenetic Tree Selection
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Modeling Compositional Heterogeneity
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Differentiating between Hypotheses of Lineage Sorting and Introgression in New Zealand Alpine Cicadas (Maoricicada Dugdale)
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The Reticulate History of Medicago (Fabaceae)
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Phylogeny of Amaranthaceae and Chenopodiaceae and the Evolution of C4Photosynthesis
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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
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Plant salt tolerance: adaptations in halophytes
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Evolutionary diversification of the African achyranthoid clade (Amaranthaceae) in the context of sterile flower evolution and epizoochory
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CONSEL: for assessing the confidence of phylogenetic tree selection
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Phybase: an R package for species tree analysis
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phangorn: phylogenetic analysis in R
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Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
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treePL: divergence time estimation using penalized likelihood for large phylogenies
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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Quartet Inference from SNP Data Under the Coalescent Model
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Performance of gene expression analyses using de novo assembled transcripts in polyploid species
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Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci
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New Methods to Calculate Concordance Factors for Phylogenomic Datasets
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Testing for Ancient Admixture between Closely Related Populations
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Statistics and Truth in Phylogenomics
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PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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Discordance of Species Trees with Their Most Likely Gene Trees: A Unifying Principle
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Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees
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Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics
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Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
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TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees
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UFBoot2: Improving the Ultrafast Bootstrap Approximation
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The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments
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What Is the Danger of the Anomaly Zone for Empirical Phylogenetics?
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Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions
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Mitochondrial Phylogenomics of Early Land Plants: Mitigating the Effects of Saturation, Compositional Heterogeneity, and Codon-Usage Bias
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Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting
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Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).
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Disentangling Incomplete Lineage Sorting and Introgression to Refine Species-Tree Estimates for Lake Tanganyika Cichlid Fishes
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Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms
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Inferring Phylogenetic Networks Using PhyloNet
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Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini)
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Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting
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Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone
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Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents
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Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data
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Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence
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A broader model for C 4 photosynthesis evolution in plants inferred from the goosefoot family (Chenopodiaceae s.s.)
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DISCORDANCE BETWEEN NUCLEAR AND CHLOROPLAST PHYLOGENIES IN THE HEUCHERA GROUP (SAXIFRAGACEAE)
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IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
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Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis
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Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high‐Andean diversification (Asteraceae: Astereae:Diplostephium)
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Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)
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An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers ( Helianthus )
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Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus)
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Large‐scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near‐simultaneous evolutionary origin of all six subfamilies
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A Draft Sequence of the Neandertal Genome
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Assorted angiosperm pollen from the Edmonton Formation (Maestrichtian), Alberta, Canada
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Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting
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PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships
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A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation
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Gene flow analysis method, the D-statistic, is robust in a wide parameter space
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ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
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Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
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An invariants-based method for efficient identification of hybrid species from large-scale genomic data
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Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution
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Corset: enabling differential gene expression analysis for de novoassembled transcriptomes
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Discordance of Species Trees with Their Most Likely Gene Trees
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The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection
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Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting
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A Simple and Robust Statistical Test for Detecting the Presence of Recombination
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Phylogeny and Evolution of the Neotropical Radiation of Lachemilla (Rosaceae): Uncovering a History of Reticulate Evolution and Implications for Infrageneric Classification
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A taxonomic backbone for the global synthesis of species diversity in the angiosperm order Caryophyllales
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RNA-Seq Assembly – Are We There Yet?
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Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies
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Characterizing gene tree conflict in plastome-inferred phylogenies

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Phylogenomic conflict coincides with rapid morphological innovation
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Phylogenomic analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving the diversifications, with insights into the complex biogeographic history in the Northern Hemisphere
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