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The topography of gene tree topology space in a plant genus with a legacy of recent polyploidy and introgression

https://doi.org/10.1101/2024.09.27.615508

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What this work says

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

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The Multispecies Coalescent

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Data‐driven guidelines for phylogenomic analyses using SNP data

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How reticulated are species?

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Phylogenetic Utility of Histone H3 Intron Sequences in the Perennial Relatives of Soybean (Glycine:Leguminosae)

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Phylogenetic Incongruence: Window into Genome History and Molecular Evolution

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Identification of high-quality single-nucleotide polymorphisms in Glycine latifolia using a heterologous reference genome sequence

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Paleopolyploidy and gene duplication in soybean and other legumes

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Phylogenomics: the beginning of incongruence?

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Horizontal Gene Transfer in Eukaryotes: Not if, but How Much?

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New Approaches for Inferring Phylogenies in the Presence of Paralogs

inferredcites →https://doi.org/10.1038/425782aopenalex-snapshot

Ending incongruence

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Genome-scale approaches to resolving incongruence in molecular phylogenies

inferredcites →https://doi.org/10.1038/nature08670openalex-snapshot

Genome sequence of the palaeopolyploid soybean

inferredcites →https://doi.org/10.1038/nrg795openalex-snapshot

Genealogical trees, coalescent theory and the analysis of genetic polymorphisms

inferredcites →https://doi.org/10.1038/s41477-022-01102-4openalex-snapshot

Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition

inferredcites →https://doi.org/10.1038/s41576-023-00620-xopenalex-snapshot

Incongruence in the phylogenomics era

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One thousand plant transcriptomes and the phylogenomics of green plants

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Diploid and polyploid reticulate evolution throughout the history of the perennial soybeans (GlycinesubgenusGlycine)

inferredcites →https://doi.org/10.1071/sb00041openalex-snapshot

A review of the Glycine clandestina species complex (Fabaceae: Phaseolae) reveals two new species

inferredcites →https://doi.org/10.1073/pnas.1810031116openalex-snapshot

Lateral transfers of large DNA fragments spread functional genes among grasses

inferredcites →https://doi.org/10.1093/bioinformatics/btaa614openalex-snapshot

Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees

inferredcites →https://doi.org/10.1093/bioinformatics/btu531openalex-snapshot

AliView: a fast and lightweight alignment viewer and editor for large datasets

inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot

Minimap2: pairwise alignment for nucleotide sequences

inferredcites →https://doi.org/10.1093/bioinformatics/bty633openalex-snapshot

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

inferredcites →https://doi.org/10.1093/bioinformatics/btz931openalex-snapshot

ShinyGO: a graphical gene-set enrichment tool for animals and plants

inferredcites →https://doi.org/10.1093/gbe/evac129openalex-snapshot

A Practical Guide to Design and Assess a Phylogenomic Study

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A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference

inferredcites →https://doi.org/10.1093/genetics/156.2.879openalex-snapshot

Consequences of Recombination on Traditional Phylogenetic Analysis

inferredcites →https://doi.org/10.1093/molbev/msaa015openalex-snapshot

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

inferredcites →https://doi.org/10.1093/molbev/msab120openalex-snapshot

MEGA11: Molecular Evolutionary Genetics Analysis Version 11

inferredcites →https://doi.org/10.1093/molbev/msab151openalex-snapshot

Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci

inferredcites →https://doi.org/10.1093/molbev/msac112openalex-snapshot

Using all Gene Families Vastly Expands Data Available for Phylogenomic Inference

inferredcites →https://doi.org/10.1093/molbev/msae084openalex-snapshot

PhyloBench: A Benchmark for Evaluating Phylogenetic Programs

inferredcites →https://doi.org/10.1093/molbev/msi121openalex-snapshot

More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic Accuracy

inferredcites →https://doi.org/10.1093/molbev/msj030openalex-snapshot

Application of Phylogenetic Networks in Evolutionary Studies

inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot

Bayesian Inference of Species Trees from Multilocus Data

inferredcites →https://doi.org/10.1093/molbev/msr048openalex-snapshot

Testing for Ancient Admixture between Closely Related Populations

inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

inferredcites →https://doi.org/10.1093/molbev/msu245openalex-snapshot

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

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PhyloNetworks: A Package for Phylogenetic Networks

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Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates

inferredcites →https://doi.org/10.1093/nargab/lqab075openalex-snapshot

Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026116openalex-snapshot

Incongruence in the diploid B-genome species complex of Glycine (Leguminosae) revisited: histone H3-D alleles versus chloroplast haplotypes

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040517openalex-snapshot

Relationships between gene trees and species trees.

inferredcites →https://doi.org/10.1093/sysbio/28.2.132openalex-snapshot

Fitting the Gene Lineage into its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences

inferredcites →https://doi.org/10.1093/sysbio/40.3.315openalex-snapshot

The Discovery and Importance of Multiple Islands of Most-Parsimonious Trees

inferredcites →https://doi.org/10.1093/sysbio/46.3.523openalex-snapshot

Gene Trees in Species Trees

inferredcites →https://doi.org/10.1093/sysbio/syab053openalex-snapshot

Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics

inferredcites →https://doi.org/10.1093/sysbio/syab097openalex-snapshot

The Frequency and Topology of Pseudoorthologs

inferredcites →https://doi.org/10.1093/sysbio/syab100openalex-snapshot

Robust Analysis of Phylogenetic Tree Space

inferredcites →https://doi.org/10.1093/sysbio/syad056openalex-snapshot

Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages

inferredcites →https://doi.org/10.1093/sysbio/syad076openalex-snapshot

Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora

inferredcites →https://doi.org/10.1093/sysbio/syq041openalex-snapshot

A Comparison of Global, Gene-Specific, and Relaxed Clock Methods in a Comparative Genomics Framework: Dating the Polyploid History of Soybean (Glycine max)

inferredcites →https://doi.org/10.1093/sysbio/syu085openalex-snapshot

Practical Performance of Tree Comparison Metrics

inferredcites →https://doi.org/10.1104/pp.16.00523openalex-snapshot

Evolution of Gene Duplication in Plants

inferredcites →https://doi.org/10.1104/pp.16.01340openalex-snapshot

Hybridization in Plants: Old Ideas, New Techniques

inferredcites →https://doi.org/10.1111/1755-0998.13993openalex-snapshot

Next‐generation bioinformatics: An ultrafast and user‐friendly tool for phylogenomic data exploration

inferredcites →https://doi.org/10.1111/j.1469-8137.2009.03118.xopenalex-snapshot

Dating the origins of polyploidy events

inferredcites →https://doi.org/10.1111/j.1558-5646.2008.00549.xopenalex-snapshot

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

inferredcites →https://doi.org/10.1111/jse.12268openalex-snapshot

Characterizing the allopolyploid species among the wild relatives of soybean: Utility of reduced representation genotyping methodologies

inferredcites →https://doi.org/10.1111/nph.19272openalex-snapshot

Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage

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/10.1139/g04-047openalex-snapshot

Mining EST databases to resolve evolutionary events in major crop species

inferredcites →https://doi.org/10.1146/annurev.genet.39.073003.114725openalex-snapshot

Orthologs, Paralogs, and Evolutionary Genomics

inferredcites →https://doi.org/10.1186/s12859-018-2129-yopenalex-snapshot

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

inferredcites →https://doi.org/10.1186/s13059-019-1832-yopenalex-snapshot

OrthoFinder: phylogenetic orthology inference for comparative genomics

inferredcites →https://doi.org/10.1186/s13059-020-02154-5openalex-snapshot

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

inferredcites →https://doi.org/10.1371/journal.pgen.1005896openalex-snapshot

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

inferredcites →https://doi.org/10.1371/journal.pone.0011147openalex-snapshot

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

inferredcites →https://doi.org/10.1371/journal.pone.0062892openalex-snapshot

The Impact of Paralogy on Phylogenomic Studies – A Case Study on Annelid Relationships

inferredcites →https://doi.org/10.1371/journal.pone.0163962openalex-snapshot

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

inferredcites →https://doi.org/10.1371/journal.pone.0197433openalex-snapshot

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

inferredcites →https://doi.org/10.1534/g3.114.012690openalex-snapshot

Complete Plastome Sequences from Glycine syndetika and Six Additional Perennial Wild Relatives of Soybean

inferredcites →https://doi.org/10.1534/genetics.105.048975openalex-snapshot

A Simple and Robust Statistical Test for Detecting the Presence of Recombination

inferredcites →https://doi.org/10.1534/genetics.166.2.987openalex-snapshot

Multiple Origins and nrDNA Internal Transcribed Spacer Homeologue Evolution in theGlycine tomentella(Leguminosae) Allopolyploid Complex

inferredcites →https://doi.org/10.1600/036364423x16758873924117openalex-snapshot

Genomic Relationships of Glycine remota, a Recently Discovered Perennial Relative of Soybean, within Glycine

inferredcites →https://doi.org/10.2307/2409415openalex-snapshot

A Chloroplast-DNA Phylogeny of the Wild Perennial Relatives of Soybean (Glycine Subgenus glycine): Congruence with Morphological and Crossing Groups

inferredcites →https://doi.org/10.2307/2412448openalex-snapshot

Distinguishing Homologous from Analogous Proteins

inferredcites →https://doi.org/10.2307/2412810openalex-snapshot

The Number of Evolutionary Trees

inferredcites →https://doi.org/10.2307/2419070openalex-snapshot

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

inferredcites →https://doi.org/10.2307/2419362openalex-snapshot

Chloroplast DNA Phylogenetic Affinities of Newly Described Species in Glycine (Leguminosae: Phaseoleae)

inferredcites →https://doi.org/10.2307/2419811openalex-snapshot

The Irrelevance of Allele Tree Topologies for Species Delimitation, and a Non-Topological Alternative

inferredcites →https://doi.org/10.2307/4119796openalex-snapshot

Phytochemical Ecology, Phytochemical Society Symposia Series no. 8

inferredcites →https://doi.org/10.3389/fpls.2021.770660openalex-snapshot

Chromosome-Scale Reference Genome of Amphicarpaea edgeworthii: A New Resource for Amphicarpic Plants Research and Complex Flowering Pattern

inferredcites →https://doi.org/10.3389/fpls.2023.1125107openalex-snapshot

Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants

inferredcites →https://doi.org/10.3390/genes9030123openalex-snapshot

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

inferredcites →https://doi.org/10.3732/ajb.1400121openalex-snapshot

The wild side of a major crop: Soybean's perennial cousins from Down Under

inferredcites →https://doi.org/10.3732/ajb.1500320openalex-snapshot

The wondrous cycles of polyploidy in plants

inferredcites →https://doi.org/10.7312/nei-92038openalex-snapshot

Molecular Evolutionary Genetics

inferredcites →https://doi.org/10.7717/peerj.16505openalex-snapshot

phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)

inferredcites →https://doi.org/10.7717/peerj.391openalex-snapshot

Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex

inferredcites →https://doi.org/10.7717/peerj.6399openalex-snapshot

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

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