I'll use this entry to upload, and occasionally update, various phylogenetic trees for New Zealand Basidiomycete fungi.
I generate these trees to understand where NZ species, often undescribed, fit within the phylogenetic classification. Position often reveals the correct genus and perhaps whether a species is likely to have been introduced, or indigenous. The published non-NZ sequences included in the trees are from various published papers, and I try to include generic type species where available (or at least sequenced labeled as generic types, but not always a sequence of the holotype). I also use them as a sanity check to ensure that genus-family relationships found in the literature make sense and are re-producible. That knowledge feeds into the classification we adopt on the Biota of NZ website, https://biotanz.landcareresearch.co.nz/. Sometimes published phylogenies do not make sense, because the authors have been over-selective in what they include, and exclude. They have over-split taxa (in my opinion), used inappropriate outgroups, haven't used data for all available loci and so stated support values are misleading. On the other hand, these trees are generated without much finesse. They are simple multi-gene concatenations of alignments using MAFFT E-INS-i followed by IQ-Tree using the auto-detected model and just 1,000 bootstraps. There is no locus-specfic partitioning. Sometimes I have manually removed misaligned or gappy segments, and sometimes I have used Trimmal to remove saturated regions. So, treat them with some caution. In the following indented classification sometimes I have left some place-holders to remind me to add tidy versions of the missing trees.
Phylum: Basidiomycota
Subphylum: Agaricomycotina
Class: Agaricomycetes
Subclass: Agaricomycetidae
Order: Agaricales
Suborder: Agaricineae
Family: Agaricaceae
Agaricus(2024) ITS+LSU+RPB2+Tef
Lycoperdaceae (2024) ITS+LSU+RPB2+Tef
Leucocoprinus/Leucoagaricus (2024) ITS+LSU+SSU+RPB2+TEF
Verrucosporaceae (2024) ITS+LSU+RPB2+Tef
Family: Bolbitiaceae
Bolbitiaceae (2025) ITS+LSU+Tef
Family: Cortinariaceae
Family: Crepidotaceae
Crepidotaceae(2025) ITS+LSU+SSU+RPB1+RPB2+Tef
Family: Hydnangiaceae
Laccaria (2024) ITS+LSU+RPB2+Tef
Family: Hymenogastraceae
Strophariaceae sensu lato (2023) ITS+LSU+RPB1+RPB2+SSU+Tef
Family: Inocybaceae
Inocybaceae (2024) ITS+LSU+RPB2
Family: Nidulariaceae
Nidulariaceae (2024) ITS+LSU+SSU+RPB2+Tef
Family: Paneaolaceae
Family: Psathyrellaceae
Coprinopsis (2024) ITS+LSU+Btub+Tef
Psathyrella (2024) ITS+LSU+BTUB+Tef
Coprinellus (2024) ITS+LSU+BTUB+SSU+Tef
Candolleomyces (2024) ITS+LSU+BTUB+Tef
Parasola (2024) ITS+LSU+BTUB+Tef
Family: Squamanitaceae
Family: Strophariaceae
Strophariaceae sensu lato (2023) ITS+LSU+RPB1+RPB2+SSU+Tef
Family: Tubariaceae
Tubariaceae (2024) ITS+LSU+SSU+RPB2+Tef
Suborder: Clavariineae
Family: Clavariaceae
Clavariaceae (2023) ITS+LSU+RPB2
Suborder: Hygrophorineae
Family: Hygrophoraceae
Hygrophoraceae (2024) ITS+LSU+SSU+RPB1+RPB2+Tef
Suborder: Marasmineae
Family: Cyphellopsidaceae
Cyphellopsidaceae (2023) ITS+LSU
Family: Marasmiaceae/Campanellaceae
Marasmiaceae/Campanellaceae (2024) ITS+LSU+SSU+RPB2+Tef
Family: Omphalotaceae
Family: Physlacriaceae
Physalacriaceae (2024) ITS+LSU
Family: Porotheleaceae/Cyphellaceae
Porotheleaceae/Cyphellaceae (2025) ITS+LSU+SSU+RPB1+RPB2+Tef
Suborder Mycenineae
Family Mycenaceae
Mycenaceae (2024) ITS+LSU+mtSSU+RPB1+RPB2+Tef
Suborder: Pluteineae
Family: Amanitaceae
Amanitaceae (2024) ITS+LSU+BTUB+MCM7+mt26S+mtSSU+RPB2+SSU+Tef
Family: Pleurotaceae
Hohenbuehelia (2025) ITS+LSU+Tef
Family: Pluteaceae
Suborders: Typhulineae/Sarcomyxineae/Phyllotopsidinea
Typhulineae/Sarcomyxineae/Phyllotopsidinea (2025) ITS+LSU+SSU+RPB1+RPB2+Tef
Suborder Tricholomatineae
Tricholomatineae (2024) ITS+LSU+SSU+ATP6+mtSSU+RPB1+RPB2+Tef
Family: Biannulariaceae
Family: Clitocybaceae
Family: Entolomataceae
Entolomataceae (2022) ITS+LSU+Tef+mtSSU+RPB2
Family: Fayodiaceae/Pseudoclitocybaceae
Family: Lyophyllaceae
Family: Tricholomataceae
Tricholomataceae (2023) ITS+LSU+SSU+RPB2+Tef
Order: Amylocorticiales/Atheliales
Atheliales/Amylocorticiales (2024) ITS+LSU+RPB2+Tef
Order: Boletales
Suborder: Boletineae
Family: Boletaceae
Boletaceae (2024) ITS+LSU+RPB1+RPB2+Tef
Suborder: Sclerodermatineae
Sclerodermatineae (2024) ITS+LSU+ATP6+RPB1+RPB2+Tef
Suborder:Suillineae
Subclass: Phallomycetidae
Phallomycetidae 2024) ITS+LSU+ATP6+mtSSU+RPB2+Tef
Order: Geastrales
Geastrum (2024) ATP6+ITS+LSU+RPB1
Order: Gomphales
Gomphales (2024) ATP6+ITS+LSU+mtSSU+RPB2+Tef
Order: Hysterangiales
Hysterangiales (2024) ATP6+ITS+LSU+mtSSU+RPB2+Tef
Order: Phallales
Phallales (2024) ITS+LSU+ATP6+mtSSU+RPB2+Tef
Subclass: unassigned
Order: Auriculariales
Auriculariales (2025) ITS+LSU+TBP2+Tef
Order: Cantharellalles
Cantharellales (2024) ITS+LSU+RPB2+SSU+Tef
Family: Clavulinaceae
Order: Corticiales
Order: Hymenochaetales
Hymenochaetales (2025) ITS+LSU+SSU+mtSSU+RPB2+Tef
Order: Polyporales
Family: Cerrenaceae/Cystostereaceae/Climacocystaceae/Panaceae
Cerrenaceae plus (2024) ITS+LSU+ATP6+mtSSU+RPB1+Tef
Family: Fomitopsidaceae
Hyphoderma (2024) ITS+LSU+mtSSU+RPB1+RPB2
Family: Hyphodermatacaeae
Fomitopsidaceae (2024) ITS+LSU+SSU+mtSSU+RPB1+RPB2+Tef
Family: Incrustoporiaceae
Incrustoporiaceae (2024) ITS+LSU+RPB1+RPB2+Tef
Family: Irpicaceae
Irpicaceae (2024) ITS+LSU+RPB1+SSU+Tef
Family: Meripilaceae
Meripilaceae (2024) ITS+LSU+RPB1+RPB2+SSU+mtSSU+Tef
Family: Meruliaceae
Meruliaceae (2025) ITS+LSU+RPB1+RPB2+Tef
Family: Phanerochaetaceae
Phanerochaetaceae (2024) ITS+LSU+RPB1+RPB2+Tef
Family: Polyporaceae
Polyporaceae (2024) ITS+LSU+BTUB+RPB1+RPB2+SSU+mtSSU+Tef
Family: Postiaceae sensu lato
Postiaceaea sensu lato (2024) ITS+LSU+mtSSU+SSU+RPB1+RPB2+Tef
Family: Steccherinaceae
Steccherinaceae (2024) ITS+LSU+RPB1+RPB2+ATP6+mtSSU+Tef
Order: Russulales
Russulales exc. NZ Russulaceae (2025) ITS+LSU+RPB1+RPB2
Family: Russulaceae
Lactarius & Multifurca (2025) ITS+LSU+RPB2
Lactifluus (2025) ITS+LSU+RPB1+RPB2
Russula (2025) ITS+LSU+mtSSU+RPB1+RPB2+Tef
Order: Sebacinales
Order: Sistotrematales
Order: Thelephorales
Theleophorales (2024) ITS+LSU+SSU+mtSSU+RPB2
Order: Tremellodendropsidales
Tremellodendropsis (2024) ITS+LSU
Order: Xenasmatales
Order Trechisporales
Class: Dacrymycetes
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