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Analyses of trait evolution and diversification reveal multiple adaptive periods in the fungal order Hymenochaetales

https://doi.org/10.1101/2024.06.06.597693

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What this work says

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

inferredcites →https://doi.org/10.1002/ajb2.1183openalex-snapshot

Stable isotope analyses reveal previously unknown trophic mode diversity in the Hymenochaetales

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Using ggtree to Visualize Data on Tree‐Like Structures

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Ectomycorrhizas of Coltricia and Coltriciella (Hymenochaetales, Basidiomycota) on Caesalpiniaceae, Dipterocarpaceae and Myrtaceae in Seychelles

inferredcites →https://doi.org/10.1007/s13225-019-00432-7openalex-snapshot

Resource diversity of Chinese macrofungi: edible, medicinal and poisonous species

inferredcites →https://doi.org/10.1007/s13225-021-00496-4openalex-snapshot

Global diversity and systematics of Hymenochaetaceae with poroid hymenophore

inferredcites →https://doi.org/10.1016/j.funbio.2022.07.001openalex-snapshot

Radiation of mushroom-forming fungi correlates with novel modes of protecting sexual fruiting bodies

inferredcites →https://doi.org/10.1016/j.mycres.2007.01.012openalex-snapshot

After the gold rush, or before the flood? Evolutionary morphology of mushroom-forming fungi (Agaricomycetes) in the early 21st century

inferredcites →https://doi.org/10.1016/j.mycres.2007.03.004openalex-snapshot

A higher-level phylogenetic classification of the Fungi

inferredcites →https://doi.org/10.1016/j.tree.2007.06.013openalex-snapshot

Estimating diversification rates from phylogenetic information

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The phylogenetic distribution of resupinate forms across the major clades of mushroom‐forming fungi (Homobasidiomycetes)

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Patterns in vascular land plant diversification

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Getting the measure of biodiversity

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Global cooling as a driver of diversification in a major marine clade

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jModelTest 2: more models, new heuristics and parallel computing

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Dimensions of biodiversity in the Earth mycobiome

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Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies

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Megaphylogeny resolves global patterns of mushroom evolution

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Basidioradulum mayi and B. tasmanicum spp. nov. (Hymenochaetales, Basidiomycota) from both sides of Bass Strait, Australia

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Temporal lags and overlap in the diversification of weevils and flowering plants

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Documenting a significant relationship between macroevolutionary origination rates and Phanerozoic pCO 2 levels

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Fruiting body form, not nutritional mode, is the major driver of diversification in mushroom-forming fungi

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Tracing the tropics across land and sea: Permian to present

inferredcites →https://doi.org/10.1080/10635150121079openalex-snapshot

Analysis of Character Correlations Among Wood Decay Mechanisms, Mating Systems, and Substrate Ranges in Homobasidiomycetes

inferredcites →https://doi.org/10.1080/10635150390235520openalex-snapshot

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

inferredcites →https://doi.org/10.1080/10635150490522610openalex-snapshot

Trends in Morphological Evolution in Homobasidiomycetes Inferred Using Maximum Likelihood: A Comparison of Binary and Multistate Approaches

inferredcites →https://doi.org/10.1080/10635150701607033openalex-snapshot

Estimating a Binary Character's Effect on Speciation and Extinction

inferredcites →https://doi.org/10.1080/21501203.2022.2103194openalex-snapshot

Fungal taxonomy: current status and research agendas for the interdisciplinary and globalisation era

inferredcites →https://doi.org/10.1080/87559129.2020.1740245openalex-snapshot

Current Status of ‘Sanghuang’ as a Group of Medicinal Mushrooms and Their Perspective in Industry Development

inferredcites →https://doi.org/10.1080/87559129.2021.1967382openalex-snapshot

Phylloporia (Hymenochaetales, Basidiomycota), a Medicinal Wood-inhabiting Fungal Genus with Much Potential for Commercial Development

inferredcites →https://doi.org/10.1089/cmb.2009.0179openalex-snapshot

How Many Bootstrap Replicates Are Necessary?

inferredcites →https://doi.org/10.1093/bioinformatics/bts492openalex-snapshot

treePL: divergence time estimation using penalized likelihood for large phylogenies

inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot

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

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/gbe/evad136openalex-snapshot

Insights into the Ecological Diversification of the Hymenochaetales based on Comparative Genomics and Phylogenomics With an Emphasis onColtricia

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/nar/gki198openalex-snapshot

MAFFT version 5: improvement in accuracy of multiple sequence alignment

inferredcites →https://doi.org/10.1093/sysbio/sys002openalex-snapshot

The Evolution of Defense Mechanisms Correlate with the Explosive Diversification of Autodigesting Coprinellus Mushrooms (Agaricales, Fungi)

inferredcites →https://doi.org/10.1093/sysbio/syt034openalex-snapshot

Identifying Hidden Rate Changes in the Evolution of a Binary Morphological Character: The Evolution of Plant Habit in Campanulid Angiosperms

inferredcites →https://doi.org/10.1093/sysbio/syu070openalex-snapshot

The Unsolved Challenge to Phylogenetic Correlation Tests for Categorical Characters

inferredcites →https://doi.org/10.1093/sysbio/syu131openalex-snapshot

Model Inadequacy and Mistaken Inferences of Trait-Dependent Speciation

inferredcites →https://doi.org/10.1093/sysbio/syz081openalex-snapshot

Estimating Diversification Rates on Incompletely Sampled Phylogenies: Theoretical Concerns and Practical Solutions

inferredcites →https://doi.org/10.1094/pdis-03-14-0335-reopenalex-snapshot

A Novel Phellinidium sp. Causes Laminated Root Rot on Qilian Juniper (Sabina przewalskii) in Northwest China

inferredcites →https://doi.org/10.1094/phyto-05-21-0181-ropenalex-snapshot

Species Diversification of the Coniferous Pathogenic Fungal Genus Coniferiporia (Hymenochaetales, Basidiomycota) in Association with Its Biogeography and Host Plants

inferredcites →https://doi.org/10.1098/rspb.2002.2123openalex-snapshot

Evolution of complex fruiting–body morphologies in homobasidiomycetes

inferredcites →https://doi.org/10.1098/rspb.2016.1334openalex-snapshot

Diversification rates and species richness across the Tree of Life

inferredcites →https://doi.org/10.1111/2041-210x.12199openalex-snapshot

BAMM tools: an R package for the analysis of evolutionary dynamics on phylogenetic trees

inferredcites →https://doi.org/10.1111/2041-210x.13153openalex-snapshot

Tip rates, phylogenies and diversification: What are we estimating, and how good are the estimates?

inferredcites →https://doi.org/10.1111/evo.13099openalex-snapshot

Is the switch to an ectomycorrhizal state an evolutionary key innovation in mushroom‐forming fungi? A case study in the Tricholomatineae (Agaricales)

inferredcites →https://doi.org/10.1111/j.1558-5646.2010.01214.xopenalex-snapshot

EFFECTS OF GASTEROID FRUITING BODY MORPHOLOGY ON DIVERSIFICATION RATES IN THREE INDEPENDENT CLADES OF FUNGI ESTIMATED USING BINARY STATE SPECIATION AND EXTINCTION ANALYSIS

inferredcites →https://doi.org/10.1111/nph.14270openalex-snapshot

Evolution of ectomycorrhizas as a driver of diversification and biogeographic patterns in the model mycorrhizal mushroom genus Laccaria

inferredcites →https://doi.org/10.1111/nph.14368openalex-snapshot

Host shifts enhance diversification of ectomycorrhizal fungi: diversification rate analysis of the ectomycorrhizal fungal generaStrobilomycesandAfroboletuswith an 80‐gene phylogeny

inferredcites →https://doi.org/10.1111/nph.15698openalex-snapshot

Timing of evolutionary innovation: scenarios of evolutionary diversification in a species‐rich fungal clade, Boletales

inferredcites →https://doi.org/10.1111/nph.18365openalex-snapshot

Biogeographic history of a large clade of ectomycorrhizal fungi, the Russulaceae, in the Neotropics and adjacent regions

inferredcites →https://doi.org/10.1111/nph.19055openalex-snapshot

The evolution of ectomycorrhizal symbiosis in the Late Cretaceous is a key driver of explosive diversification in Agaricomycetes

inferredcites →https://doi.org/10.1126/science.1161833openalex-snapshot

Superiority, Competition, and Opportunism in the Evolutionary Radiation of Dinosaurs

inferredcites →https://doi.org/10.1128/microbiolspec.funk-0036-2016openalex-snapshot

Six Key Traits of Fungi: Their Evolutionary Origins and Genetic Bases

inferredcites →https://doi.org/10.1128/microbiolspec.funk-0052-2016openalex-snapshot

Fungal Diversity Revisited: 2.2 to 3.8 Million Species

inferredcites →https://doi.org/10.1128/mmbr.00019-21openalex-snapshot

Evolutionary Morphogenesis of Sexual Fruiting Bodies in Basidiomycota: Toward a New Evo-Devo Synthesis

inferredcites →https://doi.org/10.1146/annurev.ecolsys.39.110707.173447openalex-snapshot

Phylogenetic Insights on Adaptive Radiation

inferredcites →https://doi.org/10.11646/phytotaxa.350.3.7openalex-snapshot

Rickenella danxiashanensis, a new bryophilous agaric from China

inferredcites →https://doi.org/10.11646/phytotaxa.446.4.1openalex-snapshot

Species clarification of the medicinal wood-inhabiting fungus Phylloporia (Hymenochaetales, Basidiomycota) in China

inferredcites →https://doi.org/10.1186/s12862-018-1229-7openalex-snapshot

Evolutionary dynamics of host specialization in wood-decay fungi

inferredcites →https://doi.org/10.1186/s43008-021-00059-xopenalex-snapshot

Addressing widespread misidentifications of traditional medicinal mushrooms in Sanghuangporus (Basidiomycota) through ITS barcoding and designation of reference sequences

inferredcites →https://doi.org/10.1186/s43008-021-00071-1openalex-snapshot

Taxonomy and phylogeny of Resinicium sensu lato from Asia-Pacific revealing a new genus and five new species (Hymenochaetales, Basidiomycota)

inferredcites →https://doi.org/10.1371/journal.pbio.1001854openalex-snapshot

From Dinosaurs to Modern Bird Diversity: Extending the Time Scale of Adaptive Radiation

inferredcites →https://doi.org/10.1371/journal.pone.0089543openalex-snapshot

Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees

inferredcites →https://doi.org/10.3390/jof10010022openalex-snapshot

Umbellaceae fam. nov. (Hymenochaetales, Basidiomycota) for Umbellus sinensis gen. et sp. nov. and Three New Combinations

inferredcites →https://doi.org/10.3390/jof7060478openalex-snapshot

Towards a Natural Classification of Hyphodontia Sensu Lato and the Trait Evolution of Basidiocarps within Hymenochaetales (Basidiomycota)

inferredcites →https://doi.org/10.3852/14-254openalex-snapshot

Four new species of Phylloporia (Hymenochaetales, Basidiomycota) from tropical China with a key to Phylloporia species worldwide

inferredcites →https://doi.org/10.3852/mycologia.98.6.926openalex-snapshot

Hymenochaetales: a molecular phylogeny for the hymenochaetoid clade

inferredcites →https://doi.org/10.3897/mycokeys.29.21250openalex-snapshot

Resolution of phylogenetic position of Nigrofomitaceae within Hymenochaetales (Basidiomycota) and Nigrofomes sinomelanoporus sp. nov. (Nigrofomitaceae) from China

inferredcites →https://doi.org/10.3897/mycokeys.51.33262openalex-snapshot

Reinstatement of the corticioid genus Leifia (Hymenochaetales, Basidiomycota) with a new species L. brevispora from Hubei, Central China

inferredcites →https://doi.org/10.5943/mycosphere/14/1/6openalex-snapshot

An updated taxonomic framework of Hymenochaetales (Agaricomycetes, Basidiomycota)

What points at this work

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

inferred← citeshttps://doi.org/10.3390/jof10110780openalex-snapshot

Spatiotemporal Pattern of a Macrofungal Genus Phylloporia (Basidiomycota) Revealing Its Adaptive Evolution in China

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