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Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria

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What this work says

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

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Geological constraints on the origin of oxygenic photosynthesis

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UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis

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Comparison of phylogenetic trees

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Patterns of speciation and limits to phylogenetic resolution

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Elevated rates of horizontal gene transfer in the industrialized human microbiome

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A Neoproterozoic Transition in the Marine Nitrogen Cycle

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Cyanobacteria evolution: Insight from the fossil record

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A renaissance for the pioneering 16S rRNA gene

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The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains

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The prokaryotic tree of life: past, present…and future?

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DiscoVista: Interpretable visualizations of gene tree discordance

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RAD sequencing resolves the phylogeny, taxonomy and biogeography of Trichophoreae despite a recent rapid radiation (Cyperaceae)

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Exploring syntenic conservation across genomes for phylogenetic studies of organisms subjected to horizontal gene transfers: A case study with Cyanobacteria and cyanolichens

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Archaeal genomics: Do archaea have a mixed heritage?

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Lateral genomics

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Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima

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A comparison of homologous recombination rates in bacteria and archaea

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Dating the rise of atmospheric oxygen

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Inferring ancient divergences requires genes with strong phylogenetic signals

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ModelFinder: fast model selection for accurate phylogenetic estimates

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Microbial biogeography: putting microorganisms on the map

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Coherence of Microcystis species revealed through population genomics

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The rates of global bacterial and archaeal dispersal

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Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

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Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding

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Contentious relationships in phylogenomic studies can be driven by a handful of genes

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Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition

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Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

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A New Phylogenomic Approach For Quantifying Horizontal Gene Transfer Trends in Prokaryotes

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Origin of marine planktonic cyanobacteria

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The evolutionary diversification of cyanobacteria: Molecular–phylogenetic and paleontological perspectives

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Genome evolution in cyanobacteria: The stable core and the variable shell

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Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

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Horizontal gene transfer: A critical view

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Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750)

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Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria

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Phylogenetic structure of the prokaryotic domain: The primary kingdoms

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Molecular archaeology of the Escherichia coli genome

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Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence

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Discordance of Species Trees with Their Most Likely Gene Trees: The Case of Five Taxa

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More Characters or More Taxa for a Robust Phylogeny—Case Study from the Coffee Family (Rubiaceae)

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Assessing the fit of the multi-species network coalescent to multi-locus data

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APE: Analyses of Phylogenetics and Evolution in R language

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Empirical profile mixture models for phylogenetic reconstruction

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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

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PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

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The Newick utilities: high-throughput phylogenetic tree processing in the U nix shell

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BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

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Taxonomic Uncertainty and the Anomaly Zone: Phylogenomics Disentangle a Rapid Radiation to Resolve Contentious Species ( Gila robusta Complex) in the Colorado River

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Cycad Coralloid Roots Contain Bacterial Communities Including Cyanobacteria and Caulobacter spp. That Encode Niche-Specific Biosynthetic Gene Clusters

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Complete Genomes of Symbiotic Cyanobacteria Clarify the Evolution of Vanadium-Nitrogenase

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Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution

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ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy

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Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

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Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus

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Rooting the Animal Tree of Life

inferredcites →https://doi.org/10.1093/molbev/msac215openalex-snapshot

Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees

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A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process

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

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PAML 4: Phylogenetic Analysis by Maximum Likelihood

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Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times

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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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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

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Coalescent Methods Are Robust to the Simultaneous Effects of Long Branches and Incomplete Lineage Sorting

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PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

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PhyloNetworks: A Package for Phylogenetic Networks

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UFBoot2: Improving the Ultrafast Bootstrap Approximation

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Genomic Changes Associated with the Evolutionary Transitions of Nostoc to a Plant Symbiont

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MAFFT version 5: improvement in accuracy of multiple sequence alignment

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PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

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OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

inferredcites →https://doi.org/10.1093/nar/gkz342openalex-snapshot

MAFFT-DASH: integrated protein sequence and structural alignment

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Species and speciation without sex

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Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study on Pseudapis Bees

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Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere

inferredcites →https://doi.org/10.1093/sysbio/syaa100openalex-snapshot

The Asymptotic Behavior of Bootstrap Support Values in Molecular Phylogenetics

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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

inferredcites →https://doi.org/10.1093/sysbio/syv033openalex-snapshot

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference

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The Phylogeny ofRickettsiaUsing Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution?

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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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Estimating Bayesian Phylogenetic Information Content

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Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes

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Why Concatenation Fails Near the Anomaly Zone

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Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

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The Past Sure is Tense: On Interpreting Phylogenetic Divergence Time Estimates

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Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?

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Phylogenomic Analysis of the Explosive Adaptive Radiation of the Espeletia Complex (Asteraceae) in the Tropical Andes

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Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets

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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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The Relative Importance of Modeling Site Pattern Heterogeneity Versus Partition-Wise Heterotachy in Phylogenomic Inference

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Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents

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How big is the iceberg of which organellar genes in nuclear genomes are but the tip?

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Phylogenetic mixture models for proteins

inferredcites →https://doi.org/10.1101/gr.187002openalex-snapshot

A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History

inferredcites →https://doi.org/10.1101/gr.213959.116openalex-snapshot

metaSPAdes: a new versatile metagenomic assembler

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Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events

inferredcites →https://doi.org/10.1111/evo.12832openalex-snapshot

Irrational exuberance for resolved species trees

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POLYTOMIES AND THE POWER OF PHYLOGENETIC INFERENCE

inferredcites →https://doi.org/10.1126/science.1147112openalex-snapshot

Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer

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Phylogenetic Classification and the Universal Tree

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A rooted phylogeny resolves early bacterial evolution

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16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls

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Inheritance of DNA methylation in Coprinus cinereus.

inferredcites →https://doi.org/10.1128/mra.00258-21openalex-snapshot

Metagenome Sequencing to Explore Phylogenomics of Terrestrial Cyanobacteria

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T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees

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Cyanocohniella calida gen. et sp. nov. (Cyanobacteria: Aphanizomenonaceae) a new cyanobacterium from the thermal springs from Karlovy Vary, Czech Republic

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High-throughput genome sequencing of lichenizing fungi to assess gene loss in the ammonium transporter/ammonia permease gene family

inferredcites →https://doi.org/10.1186/gb-2008-9-10-r151openalex-snapshot

A simple, fast, and accurate method of phylogenomic inference

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

inferredcites →https://doi.org/10.1186/s12862-015-0423-0openalex-snapshot

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

inferredcites →https://doi.org/10.1186/s12864-018-4620-2openalex-snapshot

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees

inferredcites →https://doi.org/10.1186/s12864-018-4743-5openalex-snapshot

Distinctive characters of Nostoc genomes in cyanolichens

inferredcites →https://doi.org/10.1186/s12866-018-1250-4openalex-snapshot

Genotyping and phylogenetic placement of Bacillus anthracis isolates from Finland, a country with rare anthrax cases

inferredcites →https://doi.org/10.1186/s13059-021-02393-0openalex-snapshot

GUNC: detection of chimerism and contamination in prokaryotic genomes

inferredcites →https://doi.org/10.1371/journal.pbio.1000602openalex-snapshot

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

inferredcites →https://doi.org/10.1371/journal.pbio.3001007openalex-snapshot

ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference

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.pgen.1005896openalex-snapshot

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

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Comparison of French and Worldwide Bacillus anthracis Strains Favors a Recent, Post-Columbian Origin of the Predominant North-American Clade

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A Comprehensive Study of Cyanobacterial Morphological and Ecological Evolutionary Dynamics through Deep Geologic Time

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Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia

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R: A Language and Environment for Statistical Computing

inferredcites →https://doi.org/10.3389/fmicb.2017.02132openalex-snapshot

Ecogenomics and Taxonomy of Cyanobacteria Phylum

inferredcites →https://doi.org/10.7287/peerj.preprints.27522v1openalex-snapshot

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

inferredcites →https://doi.org/10.7717/peerj.1660openalex-snapshot

AMAS: a fast tool for alignment manipulation and computing of summary statistics

What points at this work

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

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Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy

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Phylogenetic heterogeneity within the Cuspidothrix clade (Nostocales, Cyanobacteria): Dolichospermum longicellulare as a black sheep of its genus

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Rapid Radiations Outweigh Reticulations During the Evolution of a 750-Million-Year-Old Lineage of Cyanobacteria

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A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data

inferred← citeshttps://doi.org/10.1111/cla.70049openalex-snapshot

Evolutionary framework and tribal circumscription of Amaranthaceae sensu stricto based on a comprehensive phylogenomic analysis

inferred← citeshttps://doi.org/10.1111/nph.70699openalex-snapshot

Evolution of molecular communication in the permanent Azolla symbiosis

inferred← citeshttps://doi.org/10.1111/pce.15010openalex-snapshot

Biosynthesis and differential spatial distribution of the 3‐deoxyanthocyanidins apigenidin and luteolinidin at the interface of a plant‐cyanobacteria symbiosis exposed to cold

inferred← citeshttps://doi.org/10.1126/sciadv.adq5232openalex-snapshot

Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea

inferred← citeshttps://doi.org/10.12697/fce.2023.60.10openalex-snapshot

Peltigera (Ascomycota) living in open and shady environments depend on different Nostoc photobionts

inferred← citeshttps://doi.org/10.3389/fpls.2023.1289199openalex-snapshot

Molecular diversity and evolution of far-red light-acclimated photosystem I

inferred← citeshttps://doi.org/10.3390/bioengineering11050480openalex-snapshot

Common Methods for Phylogenetic Tree Construction and Their Implementation in R

inferred← citeshttps://doi.org/10.64898/2026.03.16.712229openalex-snapshot

A New Information Theoretic Approach Shows that Mixture Models Outperform Partitioned Models for Phylogenetic Analyses of Amino Acid Data

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