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185 lines
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<document ID-DOI="10.1111/bij.12553" ID-GBIF-Dataset="90fff1c5-81bc-44d6-acb6-8d83e92c265b" ID-ISSN="0024-4082" ID-Zenodo-Dep="7848603" IM.bibliography_approvedBy="tatiana" IM.illustrations_approvedBy="tatiana" IM.metadata_approvedBy="tatiana" IM.tables_approvedBy="tatiana" IM.taxonomicNames_approvedBy="tatiana" IM.treatments_approvedBy="tatiana" checkinTime="1681221366312" checkinUser="felipe" docAuthor="Dentinger, BTM, Gaya, E, O'Brien, H, Suz, LM, Lachlan, R, Diaz-Valderrama, JR, Koch, RA & Aime, MC" docDate="2016" docId="03A2EB6EFFD2FFDDFF063943FA998658" docLanguage="en" docName="BiolJourLinnSoc.117.11-32.pdf" docOrigin="Biological Journal of the Linnean Society 117" docStyle="DocumentStyle:9003E61B240086A483DF5C949807DC7E.1:BiolJourLinnSoc.2003-.journal_article" docStyleId="9003E61B240086A483DF5C949807DC7E" docStyleName="BiolJourLinnSoc.2003-.journal_article" docStyleVersion="1" docTitle="Pluteineae Dentinger & Gaya & O'Brien & Suz & Lachlan & Diaz-Valderrama & Koch & Aime 2016, subord. nov." docType="treatment" docVersion="2" lastPageNumber="27" masterDocId="FF9B9316FFC2FFCDFF963F07FFAA855B" masterDocTitle="Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life" masterLastPageNumber="32" masterPageNumber="11" pageNumber="27" updateTime="1681984990381" updateUser="ExternalLinkService">
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<mods:mods xmlns:mods="http://www.loc.gov/mods/v3">
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<mods:titleInfo>
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<mods:title>Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life</mods:title>
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</mods:titleInfo>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Dentinger, BTM</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Gaya, E</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>O'Brien, H</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Suz, LM</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Lachlan, R</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Diaz-Valderrama, JR</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Koch, RA</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Aime, MC</mods:namePart>
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</mods:name>
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<mods:typeOfResource>text</mods:typeOfResource>
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<mods:relatedItem type="host">
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<mods:titleInfo>
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<mods:title>Biological Journal of the Linnean Society</mods:title>
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</mods:titleInfo>
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<mods:part>
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<mods:date>2016</mods:date>
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<mods:detail type="pubDate">
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<mods:number>2015-03-26</mods:number>
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</mods:detail>
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<mods:detail type="volume">
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<mods:number>117</mods:number>
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</mods:detail>
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<mods:extent unit="page">
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<mods:start>11</mods:start>
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<mods:end>32</mods:end>
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</mods:extent>
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</mods:part>
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</mods:relatedItem>
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<mods:classification>journal article</mods:classification>
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<mods:identifier type="DOI">10.1111/bij.12553</mods:identifier>
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<mods:identifier type="GBIF-Dataset">90fff1c5-81bc-44d6-acb6-8d83e92c265b</mods:identifier>
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<mods:identifier type="ISSN">0024-4082</mods:identifier>
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<mods:identifier type="Zenodo-Dep">7848603</mods:identifier>
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</mods:mods>
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<treatment ID-DOI="http://doi.org/10.5281/zenodo.7848629" ID-Zenodo-Dep="7848629" LSID="urn:lsid:plazi:treatment:03A2EB6EFFD2FFDDFF063943FA998658" httpUri="http://treatment.plazi.org/id/03A2EB6EFFD2FFDDFF063943FA998658" lastPageNumber="27" pageId="16" pageNumber="27">
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<subSubSection box="[144,725,1604,1626]" pageId="16" pageNumber="27" type="nomenclature">
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<paragraph blockId="16.[144,759,199,1901]" box="[144,725,1604,1626]" pageId="16" pageNumber="27">
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<taxonomicName authority="Dentinger & Gaya & O'Brien & Suz & Lachlan & Diaz-Valderrama & Koch & Aime, 2016" authorityName="Dentinger & Gaya & O'Brien & Suz & Lachlan & Diaz-Valderrama & Koch & Aime" authorityYear="2016" box="[144,282,1604,1626]" class="Agaricomycetes" kingdom="Fungi" order="Agaricales" pageId="16" pageNumber="23" phylum="Basidiomycota" rank="subOrder" status="subord. nov." subOrder="Pluteineae">
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<emphasis bold="true" box="[144,282,1604,1626]" pageId="16" pageNumber="27">Pluteineae</emphasis>
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</taxonomicName>
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Aime, Dentinger & Gaya
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<emphasis box="[584,725,1604,1626]" italics="true" pageId="16" pageNumber="27">
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<taxonomicNameLabel box="[584,725,1604,1626]" pageId="16" pageNumber="27" rank="subOrder">subord. nov.</taxonomicNameLabel>
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</emphasis>
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</paragraph>
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</subSubSection>
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<subSubSection box="[168,498,1635,1657]" pageId="16" pageNumber="27" type="description">
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<paragraph blockId="16.[144,759,199,1901]" box="[168,498,1635,1657]" pageId="16" pageNumber="27">
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<emphasis box="[168,375,1635,1657]" italics="true" pageId="16" pageNumber="27">Name registration</emphasis>
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: IF551140
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</paragraph>
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</subSubSection>
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<subSubSection pageId="16" pageNumber="27" type="type_taxon">
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<paragraph blockId="16.[144,759,199,1901]" pageId="16" pageNumber="27">
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<emphasis box="[168,312,1665,1687]" italics="true" pageId="16" pageNumber="27">
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<typeStatus box="[168,222,1666,1687]" pageId="16" pageNumber="27">Type</typeStatus>
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family
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</emphasis>
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:
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<taxonomicName authority="Kotl. & Pouzar, Ceska Mykol." authorityName="Kotl. & Pouzar, Ceska Mykol." class="Agaricomycetes" family="Pluteaceae" kingdom="Fungi" order="Agaricales" pageId="16" pageNumber="27" phylum="Basidiomycota" rank="family">Pluteaceae Kotl. & Pouzar, Ceska Mykol.</taxonomicName>
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26: 218 (1972).
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</paragraph>
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</subSubSection>
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<subSubSection pageId="16" pageNumber="27" type="discussion">
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<paragraph blockId="16.[144,759,199,1901]" lastBlockId="16.[806,1422,199,1718]" pageId="16" pageNumber="27">Basidiomata agaricoid, mostly fleshy, the majority with angiocarpic development and free lamellae. Hyphae monomitic; clamp connections present or absent; non-amyloid. Basidia 2–4 spored; basidiospores hyaline or with pink pigmentation, the vast majority smooth, some amyloid. Cystidia often present. Hymenophoral tramal regular, bilateral or inverse.</paragraph>
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<paragraph blockId="16.[806,1422,199,1718]" pageId="16" pageNumber="27">
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<emphasis box="[831,1101,260,282]" italics="true" pageId="16" pageNumber="27">Representative families</emphasis>
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:
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<taxonomicName authority="R. Heim ex Pouzar" authorityName="Pouzar" class="Agaricomycetes" family="Amanitaceae" kingdom="Fungi" order="Agaricales" pageId="16" pageNumber="27" phylum="Basidiomycota" rank="family">Amanitaceae R. Heim ex Pouzar</taxonomicName>
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,
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<taxonomicName box="[902,1029,291,313]" class="Agaricomycetes" family="Pluteaceae" kingdom="Fungi" order="Agaricales" pageId="16" pageNumber="27" phylum="Basidiomycota" rank="family">Pluteaceae</taxonomicName>
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.
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</paragraph>
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<paragraph blockId="16.[806,1422,199,1718]" pageId="16" pageNumber="27">
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<emphasis box="[831,894,322,343]" italics="true" pageId="16" pageNumber="27">Notes</emphasis>
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:
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<taxonomicName authority="Dentinger & Gaya & O'Brien & Suz & Lachlan & Diaz-Valderrama & Koch & Aime, 2016" authorityName="Dentinger & Gaya & O'Brien & Suz & Lachlan & Diaz-Valderrama & Koch & Aime" authorityYear="2016" box="[909,1031,321,343]" class="Agaricomycetes" kingdom="Fungi" order="Agaricales" pageId="16" pageNumber="23" phylum="Basidiomycota" rank="subOrder" status="subord. nov." subOrder="Pluteineae">Pluteineae</taxonomicName>
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contains most angiocarpic species of
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<taxonomicName box="[835,957,351,373]" class="Agaricomycetes" kingdom="Fungi" order="Agaricales" pageId="16" pageNumber="27" phylum="Basidiomycota" rank="order">Agaricales</taxonomicName>
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, although some species (primarily members of
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<taxonomicName box="[895,980,382,403]" class="Agaricomycetes" family="Pluteaceae" genus="Pluteus" kingdom="Fungi" order="Agaricales" pageId="16" pageNumber="27" phylum="Basidiomycota" rank="genus">
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<emphasis box="[895,980,382,403]" italics="true" pageId="16" pageNumber="27">Pluteus</emphasis>
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</taxonomicName>
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) do not develop veils. Most
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<taxonomicName class="Agaricomycetes" family="Amanitaceae" kingdom="Fungi" order="Agaricales" pageId="16" pageNumber="27" phylum="Basidiomycota" rank="family">Amanitaceae</taxonomicName>
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are ectomycorrhizal, except
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<taxonomicName box="[1196,1363,413,434]" class="Agaricomycetes" family="Amanitaceae" genus="Aspidella" kingdom="Fungi" order="Agaricales" pageId="16" pageNumber="27" phylum="Basidiomycota" rank="species" species="undetermined">
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<emphasis box="[1196,1303,413,434]" italics="true" pageId="16" pageNumber="27">Aspidella</emphasis>
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spp.
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</taxonomicName>
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, and most
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<taxonomicName box="[871,995,443,465]" class="Agaricomycetes" family="Pluteaceae" kingdom="Fungi" order="Agaricales" pageId="16" pageNumber="27" phylum="Basidiomycota" rank="family">Pluteaceae</taxonomicName>
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are saprobes. This lineage was first recovered with bootstrap support in
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<bibRefCitation author="Moncalvo JM & Vilgalys R & Redhead SA & Johnson JE & James TY & Aime MC & Hofstetter V & Verduin SJW & Larsson E & Baroni TJ & Thorn RG & Jacobsson S & Clemencon H & Miller OK Jr." pageId="16" pageNumber="27" pagination="357 - 400" refId="ref15350" refString="Moncalvo JM, Vilgalys R, Redhead SA, Johnson JE, James TY, Aime MC, Hofstetter V, Verduin SJW, Larsson E, Baroni TJ, Thorn RG, Jacobsson S, Clemencon H, Miller OK Jr. 2002. One hundred and seventeen clades of euagarics. Molecular Phylogenetics and Evolution 23: 357 - 400." type="journal article" year="2002">
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Moncalvo
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<emphasis box="[1363,1421,474,495]" italics="true" pageId="16" pageNumber="27">et al.</emphasis>
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(2002)
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</bibRefCitation>
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but without a formal clade designation. Limnoperdonaceae may also belong here (
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<bibRefCitation author="Matheny PB & Curtis JM & Hofstetter V & Aime MC & Moncalvo JM & Ge ZW & Slot JC & Ammirati JF & Baroni TJ & Bougher NL & Hughes KW & Lodge DJ & Kerrigan RW & Seidl MT & Aanen DK & DeNitis M & Daniele GM & Desjardin DE & Kropp BR & Norvell LL & Parker A & Vellinga EC & Vilgalys R & Hibbett DS" pageId="16" pageNumber="27" pagination="982 - 995" refId="ref15027" refString="Matheny PB, Curtis JM, Hofstetter V, Aime MC, Moncalvo JM, Ge ZW, Slot JC, Ammirati JF, Baroni TJ, Bougher NL, Hughes KW, Lodge DJ, Kerrigan RW, Seidl MT, Aanen DK, DeNitis M, Daniele GM, Desjardin DE, Kropp BR, Norvell LL, Parker A, Vellinga EC, Vilgalys R, Hibbett DS. 2006. Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98: 982 - 995." type="journal article" year="2006">
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Matheny
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<emphasis box="[1356,1414,535,556]" italics="true" pageId="16" pageNumber="27">et al.</emphasis>
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, 2006
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</bibRefCitation>
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). This group was not supported in the ASTRAL tree (
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<figureCitation box="[875,943,596,618]" captionStart="Figure 4" captionStartId="10.[144,223,1027,1046]" captionTargetBox="[901,1419,209,987]" captionTargetId="graphics-286@10.[901,1419,209,985]" captionTargetPageId="10" captionText="Figure 4. Consensus trees of individual gene trees. Left: extended majority-rule consensus (MRE) tree based on bootstrap replicates of individual gene analyses for all genes with no missing taxa (N = 175). Numbers above branches are internode certainty (IC) and internode certainty all (ICA) values for all individual bootstrap trees compared to the MRE tree. Numbers in bold represent nodes that are not present in the ASTRAL tree (right). Right: coalescentbased consensus tree recovered by ASTRAL using 208 single gene maximum likelihood trees from RAXML analysis. Numbers in bold above branches are IC, ICA values for all individual bootstrap trees that are not present in the MRE tree (left). Numbers below branches are bootstrap supports based on single gene bootstrap analysis (100 replicates each)." figureDoi="http://doi.org/10.5281/zenodo.7848615" httpUri="https://zenodo.org/record/7848615/files/figure.png" pageId="16" pageNumber="27">Fig. 4</figureCitation>
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) and the tree based on ranked genes using
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<collectingCountry box="[878,912,627,648]" name="Russia" pageId="16" pageNumber="27">RF</collectingCountry>
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distances (see Supporting information,
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<figureCitation captionStart="Figure 2" captionStartId="8.[807,886,1791,1810]" captionTargetBox="[817,1413,1214,1723]" captionTargetId="graphics-594@8.[876,1413,1216,1698]" captionTargetPageId="8" captionText="Figure 2. Summary of data quality. A, distribution of alignment lengths for 208 loci after GBlocks processing. B, correlation of assembly quality (N50) and percent alignment coverage." figureDoi="http://doi.org/10.5281/zenodo.7848609" httpUri="https://zenodo.org/record/7848609/files/figure.png" pageId="16" pageNumber="27">Fig. S2C</figureCitation>
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), and some previous studies have not recovered
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<taxonomicName box="[807,931,687,709]" class="Agaricomycetes" family="Pluteaceae" kingdom="Fungi" order="Agaricales" pageId="16" pageNumber="27" phylum="Basidiomycota" rank="family">Pluteaceae</taxonomicName>
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with
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<taxonomicName authority="(Bodensteiner et al., 2004)" baseAuthorityName="Bodensteiner" baseAuthorityYear="2004" class="Agaricomycetes" family="Amanitaceae" kingdom="Fungi" order="Agaricales" pageId="16" pageNumber="27" phylum="Basidiomycota" rank="family">
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Amanitaceae (
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<bibRefCitation author="Bodensteiner P & Binder M & Moncalvo J-M & Agerer R & Hibbett DS" pageId="16" pageNumber="27" pagination="501 - 515" refId="ref12642" refString="Bodensteiner P, Binder M, Moncalvo J-M, Agerer R, Hibbett DS. 2004. Phylogenetic relationships of cyphelloid homobasidiomycetes. Molecular Phylogenetics and Evolution 33: 501 - 515." type="journal article" year="2004">
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Bodensteiner
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<emphasis box="[1356,1414,687,709]" italics="true" pageId="16" pageNumber="27">et al.</emphasis>
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, 2004
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</bibRefCitation>
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)
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</taxonomicName>
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or
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<taxonomicName box="[916,1041,718,739]" class="Agaricomycetes" family="Pluteaceae" genus="Volvariella" kingdom="Fungi" order="Agaricales" pageId="16" pageNumber="27" phylum="Basidiomycota" rank="genus">
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<emphasis box="[916,1041,718,739]" italics="true" pageId="16" pageNumber="27">Volvariella</emphasis>
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</taxonomicName>
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within
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<taxonomicName authority="(Justo et al., 2011)" baseAuthorityName="Justo" baseAuthorityYear="2011" class="Agaricomycetes" family="Pluteaceae" kingdom="Fungi" order="Agaricales" pageId="16" pageNumber="27" phylum="Basidiomycota" rank="family">
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Pluteaceae (
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<bibRefCitation author="Justo A & Vizzini A & Minnis AM & Menolli N Jr & Capelari M & Rodriguez O & Malysheva E & Contu M & Ghignone S & Hibbett DS" pageId="16" pageNumber="27" pagination="1 - 20" refId="ref14128" refString="Justo A, Vizzini A, Minnis AM, Menolli N Jr, Capelari M, Rodriguez O, Malysheva E, Contu M, Ghignone S, Hibbett DS. 2011. Phylogeny of the Pluteaceae (Agaricales, Basidiomycota): taxonomy and character evolution. Fungal Biology 115: 1 - 20." type="journal article" year="2011">
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Justo
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<emphasis box="[1356,1414,718,740]" italics="true" pageId="16" pageNumber="27">et al.</emphasis>
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, 2011
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</bibRefCitation>
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)
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</taxonomicName>
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, and further investigation is warranted.
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</paragraph>
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</subSubSection>
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</treatment>
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</document>
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