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Supplementary figures and tables
Figure S1. Chronogram for Amanita. Time scale set to millions of years. Maximum clade credibility (MCC) tree with median node heights based on the nucLSU region. Node bars represent 95% credibility intervals for node heights. Numbers above branches represent posterior probabilities. Names of outgroup taxa are in gray. The root was assigned an age prior with mean 129 Ma (standard deviation [sd] 17 Ma) and the split between Pluteus and Amanita an age prior with mean 89 Ma (sd 15 Ma). The cut off for OTUs were set to 0.01 expected substitutions per site.
Figure S2. Chronogram for Catathelasma. Time scale set to millions of years. MCC tree with median node heights based on the nucLSU region. Node bars represent 95% credibility intervals for node heights. Numbers above branches represent posterior probabilities. Names of outgroup taxa are in gray. The root was assigned an age prior with mean 129 Ma (sd 17 Ma) and the split between Tricholoma and Lyophyllum an age prior with mean 103 Ma (sd 15 Ma). The cut off for OTUs was set to 0.05 expected substitutions per site.
D. Figure S3. Chronogram for Cortinarius. The time scale set to millions of years. MCC tree with median node heights based on the ITS region. The tree is spit into four parts, and connections between figures are indicated by the sub figure annotation at collapsed nodes. Node bars represent 95% credibility intervals for node heights. Numbers above branches represents posterior probabilities. Names of outgroup taxa are in gray. The root was assigned an age prior with mean 113 Ma (sd 16 Ma) and the split between Cortinarius aurilicis and Cortinarius iodes an age prior with mean 31 Ma (sd 10 Ma). The cut off for OTUs was set to 0.01 expected substitutions per site. MEDUSA indicated two rate changes (clades marked with gray backgound). The root was inferred to have a net diversification rate = 0.11 and relative extinction rate = 0.00; the clade marked in figure A had a net diversification rate = 0.14 and relative extinction rate = 0.00; the clade marked in figure C had a net diversification rate = 0.26 and relative extinction rate = 0.00.
0.010.020.030.040.050.060.070.0
AY669606 Protoglossum luteum
FJ717596 Cortinarius variosimilis
AY669623 Cortinarius subcastanellus
DQ117928 Cortinarius norrlandicus
AY669553 Cortinarius caligatus
AF325577 Thaxterogaster porphyreus
AY669589 Cortinarius stillatitius
EU821694 Cortinarius vibratilis
AY174798 Cortinarius triumphans
GQ159859 Cortinarius cf. pseudosalor
AF325610 Cortinarius dulciolens
AY669543 Cortinarius patibilis
DQ295110 Cortinarius trivialis
DQ054564 uncultured fungus
DQ328194 Quadrispora sp.
DQ652234 Cortinarius lustrabilis
FJ157133 Cortinarius muscigenus
AY669528 Cortinarius vinaceomaculatus
AF476988 ectomycorrhizal root
FJ039670 Cortinarius nanceiensis
AF112143 Cortinarius radicatus
EF420147 Cortinarius costaricensis
AY669610 Cortinarius archeri
AY669638 Cortinarius cf. submeleagris
AY669529 Cortinarius percomis
AY669618 Cortinarius salmaster
AY669644 Cortinarius sp.
DQ328099 Thaxterogaster sp.
DQ328158 Thaxterogaster sp.
FJ157140 Cortinarius sp.
AY669616 Cortinarius quaresimalis
GQ159888 Cortinarius aff. inamoenus
AY174801 Cortinarius balteatocumatilis
DQ328110 Thaxterogaster sp.
AF325608 Cortinarius saginus
AY669575 Cortinarius caperatus
AY669552 Cortinarius coalescens
DQ295091 Cortinarius favrei
AY174790 Cortinarius varius
DQ295105 Cortinarius fennoscandicus
AF325613 Protoglossum sp.
GQ159874 Cortinarius pingue
FJ717578 Cortinarius vibratilis
AY669649 Cortinarius fulvoiubatus
GQ166892 Cortinarius sp.
FJ717595 Cortinarius sp.
AY033097 Cortinarius alboroseus
AY033106 Cortinarius taylorianus
AF325607 Cortinarius citriolens
DQ097879 Cortinarius crystallinus
AY174791 Cortinarius variiformis
AY669557 Cortinarius pseudovulpinus
AY033113 Cortinarius dulciolens
DQ328183 Thaxterogaster sp.
DQ083772 Cortinarius aurilicis
AY669541 Cortinarius serarius
AY669640 Cortinarius coelopus
EU821686 Cortinarius salor
DQ328205 Thaxterogaster sp.
AY669549 Cortinarius obsoletus
AY174786 Cortinarius cephalixus
EU660946 Cortinarius memoriaannae
AF325568 Thaxterogaster redactus
AY033101 Cortinarius meleagris
AF389149 Cortinarius ombrophilus
AY669617 Cortinarius lavendulensis
EU821651 Cortinarius sp.
AY669576 Cortinarius emodensis
AY669524 Cortinarius acidophilus
AY669619 Cortinarius austrosaginus
AY033108 Cortinarius paradoxus
AY669577 Cortinarius similis
AY174856 Cortinarius nanceiensis
FJ039600 Cortinarius salor
AF182796 Cortinarius trivialis
AY669551 Cortinarius fraudulosus
AY033111 Cortinarius subcastanellus
AY174795 Cortinarius variicolor
FJ157016 Cortinarius causticus
AF539715 Cortinarius caelicolor
FJ039633 Cortinarius cf. variicolor
AF325611 Cortinarius corrugatus
DQ328189 Thaxterogaster sp.
AY669516 Cortinarius paracephalixus
AY669522 Cortinarius claricolor
FJ157038 Cortinarius cf. vibratilis
AF389125 Cortinarius magellanicus
AY669625 Cuphocybe sp.
AY174814 Cortinarius mussivus
DQ149869_Laccaria_bicolor
AY669521 Cortinarius populinus
FJ717585 Cortinarius sp.
AF389142 Cortinarius pluvius
AY669567 Cortinarius borgsjoeensis
DQ481961 uncultured cf. Dermocybe
AY669518 Cortinarius vacciniophilus
AY174803 Cortinarius praestans
FJ717601 Cortinarius variosimilis
DQ328199 Quadrispora sp.
FJ717593 Cortinarius sp.
AY669542 Cortinarius largus
DQ083813 Cortinarius sp.
EU569251 Cortinarius sp.
AY669607 Cortinarius basipurpureus
DQ367896 Cortinarius collinitus
FM202133 Cortinarius sp.
AY669534 Cortinarius delaportei
DQ328152 Thaxterogaster sp.
AY669535 Cortinarius argutus
DQ295122 Cortinarius lividoochrascens
DQ328169 Thaxterogaster sp.
AF389143 Cortinarius croceocaeruleus
DQ083805 Cortinarius percomis
EU846306 Cortinarius magnivelatus
EU084983 Protoglossum luteum
AF325606 Cortinarius sp.
AY669605 Cortinarius erythraeus
AY669550 Cortinarius latobalteatus
EU569250 Cortinarius sp.
DQ328141 Thaxterogaster piriformis
AF539714 Cortinarius punctatisporus
FJ717519 Cortinarius sp.
AY669627 Cortinarius elaiochrous
AF539719 Cortinarius magellanicus
AY174782 Cortinarius infractus
FJ039664 Cortinarius vibratilis
AY669556 Cortinarius tiliae
AY669629 Cuphocybe sp.
AY669517 Cortinarius balteatoalbus
FJ039669 Cortinarius papulosus
DQ328081 Protoglossum violaceum
AY033104 Cortinarius elacatipus
AF325556 Thaxterogaster violaceus
AY033102 Cortinarius meleagris
AY174811 Cortinarius vulpinus
DQ328095 Thaxterogaster sp.
AY033099 Cortinarius elaiochrous
FJ195640 Cortinarius majoranae
AY669611 Cortinarius malvaceus
AF389123 Cortinarius cycneus
FJ157076 Cortinarius cf. vanduzerensis
0.42
0.04
1
0.991
0.89
0.61
1
1
0.39
0.61
1
0.92
0.88
0.91
0.38
1
0.02
0.19
0.85
0.78
0.17
0.01
0.12
1
0.62
1
0.83
0.9
0.15
0.04
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0.82
0.68
0.41
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0.95
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0
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0.82
1
0.44
0.660.25
1
0.7
1
0.5
0.05
0.6
0.09
0.5
0.68
1
0.1
1
1
1
0.02
0.98
0.96 0.77
0.52
0.62
1
1
0.96
0.780.2
0.68
0.49
1
1
0.77
0.82
0.64
0.8
0.04
1
0.19
0.01
0.96
0.05
0.28
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1
0.6
1
0.68
0.29
1
0.04
0.96
0.91
0.06
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0.98
1
1
1
0.84
0.97
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0.01
0.49
0.1
0.94
1
0.37
0.9
0.13
0.08
0.05
0.13
0.74
1
1
0.11
1
0.42
0.07
1
1
0.94
0.28
1
0.06
1
0.85
0.94
0.99
0.08
0.98
1
0.9
1
1
0.03
1
0.4
0.92
0.03
0.91
0.65
0.28
A
B
C
Figure S4. Chronogram for Descolea and allies. Time scale set to millions of years. MCC tree with median node heights based on the ITS region. Node bars represent 95% credibility intervals for node heights. Numbers above branches represents posterior probabilities. Names of outgroup taxa are in gray. The root was assigned an age prior with mean 83 Ma (sd 15 Ma) and the split between Cortinarius aurilicis and Cortinarius iodes an age prior with mean 31 Ma (sd 10 Ma). The cut off for OTUs was set to 0.02 expected substitutions per site.
0.010.020.030.040.050.060.070.080.0
DQ328167 Timgrovea sp.
DQ328177 Descomyces sp.
HQ728544 Descolea phlebophora
Cortinarius aurilicis
DQ328214 Setchelliogaster sp.
DQ328115 Descomyces sp.
DQ328108 Timgrovea sp.
DQ328069 Descomyces sp.
DQ328195 Timgrovea sp.
AF389133 Cortinarius iodes
AF325649 Descolea recedens
DQ328061 Descomyces sp.
AF325652 Descolea gunnii
AF325647 Descolea antarctica
DQ328116 Timgrovea ferruginea
AF325644 Descomyces sp.
AF325651 Descolea maculata
AF325656 Descolea phlebophora
DQ328063 Descomyces sp.
DQ192181 Descolea maculata
DQ328175 Timgrovea sp.
DQ328168 Descomyces albus
DQ328162 Timgrovea sp.
DQ328184 Setchelliogaster sp.
AF325645 Descomyces albellus
DQ328163 Timgrovea sp.
DQ328058 Descomyces angustisporus
Bolbitius vitellinus
DQ328209 Descomyces albus
DQ328207 Timgrovea sp.
1
1
1
0.93
1
1
0.46
0.99
1
1
1
0.99
0.96
0.95
0.38
1
1
1
0.68
0.98
0.99
1
1
0.99
1
1
1
1
Figure S5. Chronogram for Hebelomateae. Time scale set to millions of years. MCC tree with median node heights based on the ITS region. Node bars represent 95% credibility intervals for node heights. Numbers above branches represents posterior probabilities. Names of outgroup taxa are in gray. The root was assigned an age prior with mean 85 Ma (sd 14 Ma) and the split between Hebelomateae and Agrocybe an age prior with mean 60 Ma (sd 14 Ma). The cut off for OTUs was set to 0.005 expected substitutions per site. MEDUSA indicated one rate change (clade marked with gray backgound). The root was inferred to have a net diversification rate = 0.11 and relative extinction rate = 0.00; the clade marked in gray had a net diversification rate = 0.27 and relative extinction rate = 0.00.
0.010.020.030.040.050.060.070.0
EU375717 uncultured ectomycorrhiza
AY308582 Hebeloma aestivale
AY900095 Hebeloma submelinoides
AY818352 Anamika lactariolens
EU570183 Hebeloma sp.
AY311516 Hebeloma helodes var. capitata
EU554717 uncultured fungus
EU554800 uncultured fungus
AF430254 Hebeloma velutipes
AF124715 Hebeloma sarcophyllum
EF218766 uncultured ectomycorrhiza
AY900054 Alnicola umbrina
AY900073 Alnicola sp.
AF124712 Naucoria bohemica
AF124693 Hebeloma birrum
FJ717490 Hebeloma sp.
EU570167 Hebeloma hiemale
AY634136 uncultured ectomycorrhiza
AY097047 uncultured cf. Hebeloma
AY309963 Hebeloma cylindrosporum
AY575919 Anamika angustilamellata
AF325633 Hymenogaster tener
EF451057 Hebeloma mesophaeum
EU570180 Hebeloma theobrominum
AY900087 Alnicola sp.
AY312986 Hebeloma saliciphilum
AF325640 Hymenogaster subalpinus
AY320396 Hebeloma vaccinum
AY900089 Alnicola amarescens
AF124683 Hebeloma crustuliniforme
AY303581 Alnicola amarescens
DQ822802 Hebeloma sp.
AY351629 uncultured ectomycorrhiza
EU570185 Hebeloma erumpens
AF325639 Hymenogaster gardneri
AJ875387 uncultured fungus
EU784364 Hymenogaster tener
AY311525 Hebeloma oculatum
AY311520 Hebeloma marginatulum
FM993246 uncultured ectomycorrhiza
AY945302 Hymenogaster raphanodorus
AY351621 Hebeloma funariophilum
DQ328132 Hymenogaster australis
AY309959 Hebeloma brunneifolium
EU570189 Naucoria celluloderma
EU784360 Hymenogaster citrinus
AY900094 Hebeloma submelinoides
AY303584 Alnicola tantilla
AY818348 Agrocybe praecox
AF325637 Hymenogaster populetorum
AY748855 uncultured ectomycorrhiza
EU570194 Hebeloma cf. erumpens
EU570170 Hebeloma sp.
AF430291 Hebeloma incarnatulum
AF325638 Hymenogaster parksii
AY309958 Hebeloma bruchetii
AY900088 Alnicola salabertii
FM993174 uncultured ectomycorrhiza
EU784359 Hymenogaster arenarius
EU784363 Hymenogaster tener
AY308583 Hebeloma albocolossum
FM993124 uncultured ectomycorrhiza
FM203019 uncultured ectomycorrhiza
AY312977 Hebeloma polare
EF434074 uncultured fungus
AY320393 Hebeloma subconcolor
EU346884 Hebeloma sp.
AM882885 Naucoria submelinoides
AY309964 Hebeloma fragilipes
DQ365636 Hebeloma incarnatulum
AJ875382 uncultured fungus
AF124697 Hebeloma helodes
DQ481994 uncultured ectomycorrhiza
DQ328124 Hymenogaster arenarius
AM882996 Crepidotus mollis
FM992926 uncultured ectomycorrhiza
AY311526 Hebeloma pallidoluctuosum
AY900093 Alnicola cholea
AF124675 Hebeloma danicum
AY918956 Hymenogaster boozeri
FM993273 uncultured ectomycorrhiza
EU784365 Hymenogaster vulgaris
EU554998 uncultured fungus
AF124680 Hebeloma tomentosum
AY312985 Hebeloma sacchariolens
AY310842 uncultured ectomycorrhiza
AY303582 Alnicola geraniolens
EU570177 Hebeloma cistophilum
AY900103 Alnicola macrospora
AB211274 Hebeloma pusillum
EU784361 Hymenogaster griseus
AJ920024 uncultured fungus
AY900090 Alnicola tantilla
AY309961 Hebeloma calyptrosporum
AJ893225 uncultured ectomycorrhiza
DQ447994 uncultured Agaricomycetes
AY945303 Hymenogaster rubyensis
AY900031 Alnicola badia
EF644129 uncultured ectomycorrhiza Hebeloma
AY900040 Alnicola sp.
AY320394 Hebeloma subsaponaceum
FJ789604 Hymenogaster sp.
AY312987 Hebeloma senescens
AY312982 Hebeloma pusillum
AF325636 Hymenogaster griseus
AY833049 uncultured basidiomycete
EU847262 uncultured ectomycorrhiza
AF407163 Anamika indica
AF325632 Hymenogaster alnicola
AY278767 Hebeloma radicosum
AF124673 Hebeloma bulbiferum
AF124698 Hebeloma edurum
AY900081 Naucoria escharoides
FM993206 uncultured ectomycorrhiza
AY312981 Hebeloma pumilum
FM992925 uncultured ectomycorrhiza
AY900074 Alnicola sphagneti
AY311518 Hebeloma longicaudum
AF124682 Hebeloma sinapizans
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Figure S6. Chronogram for Hydnangiaceae. Time scale set to millions of years. MCC tree with median node heights based on the ITS region. Node bars represent 95% credibility intervals for node heights. Numbers above branches represents posterior probabilities. Names of outgroup taxa are in gray. The root was given an age prior with mean 112 Ma (sd 17 Ma) and the split between Hydnangiaceae and Mythicomyces an age prior with mean 72 Ma (sd 17 Ma). The cut off for OTUs was set to 0.01 expected substitutions per site.
0.010.020.030.040.050.060.070.080.090.0100.0
AY825516 uncultured ectomycorrhiza
DQ404393 Mythicomyces corneipes
EF644110 Laccaria laccata
EU486434 Laccaria montana
GQ240912 uncultured Laccaria
AB211273 Laccaria laccata
EU597085 Laccaria bicolor
AM161523 uncultured ectomycorrhiza
DQ149871 Laccaria pseudomontana
DQ974699 Laccaria cf. laccata
AF389133 Cortinarius iodes
FJ168606 Laccaria sp.
FJ168603 Laccaria sp.
FJ168599 Hydnangium carneum
AB211271 Laccaria murina
AJ699074 Laccaria laccata
GQ205354 uncultured fungus
GQ240913 uncultured Laccaria
EF218783 uncultured ectomycorrhiza
AB211143 uncultured mycorrhiza
DQ149864 Laccaria pumila
AB459516 Laccaria vinaceoavellanea
FJ168602 Laccaria sp.
EF530940 Laccaria amethystina
FJ168600 Laccaria ochropurpurea
DQ421089 uncultured fungus
GQ267477 Laccaria proxima
DQ149861 Laccaria nobilis
EF634114 uncultured ectomycorrhiza
EU819476 Laccaria amethystina
AM113953 Laccaria amethystina
AY880933 uncultured ectomycorrhiza
AY702728 uncultured fungus
FJ168598 Laccaria sp.
FN393140 uncultured Laccaria
DQ149865 Laccaria montana
EU819478 Laccaria laccata var. pallidifolia
GQ205355 uncultured fungus
FJ168595 Hydnangium sp.
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1
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1
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Figure S7. Chronogram for Hygrophorus. Time scale set to millions of years. MCC tree with median node heights based on the nucLSU region. Node bars represent 95% credibility intervals for node heights. Numbers above branches represents posterior probabilities. Names of outgroup taxa are in gray. The root was assigned an age prior with mean 154 Ma (sd 20 Ma). The cut off for OTUs was set to 0.01 expected substitutions per site.
0.025.050.075.0100.0125.0150.0
AY635769 Hygrophorus flavodiscus
DQ071733 Hygrophorus chrysodon
AF430273 Hygrophorus discoideus
AF430270 Hygrophorus pustulatus
AF042623 Hygrophorus bakerensis
AF430280 Hygrophorus leucophaeus
AY684167 Hygrocybe aff. conica
AY586660 Hygrophorus agathosmus
AY586662 Hygrophorus olivaceoalbus
EU712607 Uncultured Russulaceae
FJ627029 Hygrophorus sp.
DQ457678 Hygrophorus pudorinus
EU292415 Uncultured fungus
AF042562 Hygrophorus sordidus
FJ943241 Hygrophorus sp.
DQ974809 Hygrophorus chrysodon
FJ196924 Uncultured ectomycorrhiza
AY635775 Agaricus bisporus
DQ273522 Uncultured Hygrophoraceae
FJ196923 Uncultured ectomycorrhiza
AY586663 Hygrophorus russula
AF430279 Hygrophorus eburneus
AF430272 Hygrophorus capreolarius
0.53
0.64
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A. 0.010.020.030.040.050.060.070.080.0
AY380398 Mallocybe subtilisior
JN975007 Inocybe aff. nivevelata
EU600903 Inocybe sp.
AM882784 Inocybe spuria
AM882941 Inocybe bongardii
AM882945 Inocybe cf. calamistrata
JN975013 Inocybe umbrinella
AM882769 Inocybe obsoleta
JN975018 Inocybe calamistrata
JN975017 Inocybe sp.
EU569871 Inocybe sp.
AY702014 Inocybe cookei
HQ201348 Inocybe curreyi ss Hesler
AY380368 Inocybe calamistrata
AY038315 Mallocybe dulcamara
AM882956 Inocybe cookei
GU062739 Auritella sp.
AM882786 Inocybe cf. rimosa
AY380403 Mallocybe unicolor
EU555446 Inocybe sp
JN975009 Inocybe sp.
JN975028 Mallocybe sp.
AY380371 Auritella dolichocystis
AM882866 Inocybe gymnocarpa
EU600890 Inocybe sp.
AM882960 Inocybe quietiodor
JN975025 Inocybe maculata
EU569858 Mallocybe leucoblema
AY380366 Mallocybe agardhii
JN975005 Inocybe aff. rimosa
JN975032 Inocybe sp.
EU600831 Inocybe sp.
JN975026 Inocybe maculata group
EU600887 Tubariomyces sp.
EU600834 Inocybe sp.
AM882762 Inocybe rimosa
AY038321 Inocybe cf. maculata
AM882964 Inocybe maculata
AY745700 Inocybe maculata
AY380386 Inocybe lilacinosquamosa
EU600851 Inocybe rimosa
AY380395 Auritella geoaustralis
JN975034 Inocybe lanatodisca
AY380379 Mallocybe heimii
EU569847 Inocybe fastiella
AM882771 Inocybe perlata
JN975008 Inocybe rimosa
EU563510 uncultured ectomycorrhiza
EU569854 Inocybe hirsuta var. maxima
AY038327 Mallocybe flavicothurnata
GU907094 Tubariomyces inexpectata
AM882765 Inocybe bulbosissima
EF417792 uncultured ectomycorrhiza
EU600883 Inocybe sp.
AY702013 Cortinarius iodes
JN975016 Inocybe sp.
AM882951 Inocybe erubescens
AM882948 Inocybe calamistrata
JN975006 Inocybe rimosa
GQ892938 Inocybe sp.
JN974916 Mallocybe cf. subtilisior
AY239018 Inocybe ayangannae
EU600885 Inocybe sp.
AM882938 Inocybe calamistrata
JN975015 Inocybe fastigiata ss Kauffman
EU569836 Mallocybe dulcamara
AY380374 Inocybe fastiella
JN975021 Inocybe apiosmota
AF205694 Crepidotus applanatus var. applanatus
JN975010 Inocybe umbrinella
JN975012 Inocybe actinocephala
AY380382 Inocybe lanatodisca
JN975014 Inocybe sp.
EU600847 Inocybe rimosa
EU600829 Inocybe sp.
EU569868 Inocybe maculata
JN642235 Inocybe sp.
EU522733 Inocybe sp.
EU569844 Inocybe sp.
EU600870 Inocybe sp.
AY380394 Mallocybe sp
EU555466 Inocybe cf. renispora
AM882774 Inocybe flavella
EU569870 Inocybe malenconii
EU555454 Inocybe calamistrata
AF518622 Inocybe sp
EU569855 Tubariomyces inexpectata
AY700196 Mallocybe dulcamara
AM882706 Inocybe adaequata
EU555452 Inocybe calamistrata
GQ892937 Inocybe sp.
AY635766 Auritella aureoplumosa
EU569834 Mallocybe dulcamara
AF347101 Inocybe cervicolor
EU600877 Inocybe sp.
AM882944 Inocybe calamistrata
JN975019 Inocybe aff. calamistrata
EU600852 Inocybe rimosa
AM882782 Inocybe flavella
EU555463 Inocybe cf. reisneri
AM882939 Inocybe cervicolor
JN975020 Inocybe sp.
EF561633 Inocybe rimosa
AY038317 Inocybe hirsuta var. maxima
AM882781 Inocybe mimica
EU600863 Inocybe sororia
AY380400 Mallocybe sp.
DQ071697 Inocybe rimosa
AY732213 Inocybe sp.
JN975033 Inocybe cyanotincta
FJ627030 Inocybe aff. calamistrata
GU907092 Tubariomyces inexpectata
AM882864 Mallocybe terrigena
EU600840 Inocybe sp.
AY732212 Inocybe mutata
JN975011 Inosperma sp.
HQ201353 Inocybe jurana ss Hesler
EU600879 Inocybe sp
EU600853 Inocybe rimosa
JN975024 Inocybe latericia
EU604546 Inocybe sp.
AM882776 Inocybe flavella
JN975023 Inocybe aff. latericia
HQ201340 Inocybe calamistrata var. mucidiolens
EU569874 Inocybe misakaensis
AY380369 Inocybe calamistratoides
JN975022 Inocybe apiosmota
AY380381 Mallocybe jarrahae
JN975004 Inosperma aff. sororia
AY038325 Auritella serpentinocystis
EU555451 Inocybe sp.
JN975027 Inocybe regisii
AM882952 Inocybe cookei
1
1
0.55
0.4
0.64
0.05
0.25
1
0.17
0.29
0.37
0.09
0.57
1
0.67
1
0.851
0.99
0.97
1
1
0.33
0.99
0.4
0.52
0.02
0.98
0.89
0.07
0.36
0.97
0.05
0.14
1
1
0.12
0.48
0.27
0.61
0.28
1
0.56
1
1
1
1
0.81
0.55
0.21
0.99
0.99
0.95
1
0.76
1
0.63
0.99
0.84
0.75
1
0.92
1
0.99
1
0.82
0.96
1
0.18
0.34
0.08
1
0.47
1
0.65
1
0.83
0.76
0.91
1
0.85
0.22
1
0.99
0.82
0.16
0.11
0.17
0.77
0.75
0.98
1
0.81
1
0.24
1
0.94
0.23
0.05
0.98
1
0.95
1
0.86
0.95
1
0.64
1
0.22
1
1
0.55
0.02
0.75
0.79
1
0.49
0.94
0.67
0.99
1
0.75
0.38
0.95
0.99
0.59
0.57
0.57
0.99
1
1
0.97
1
B, C
B 0.010.020.030.040.050.060.070.080.0
EU600884 Inocybe sp.
FN557549 uncultured ectomycorrhizal
AM882721 Inocybe cf. praetervisa
GQ892974 Inocybe sp.
EU600844 Inocybe sp.
AM882713 Inocybe nematoloma
GQ892949 Inocybe aff. sphaerospora
EU691943 uncultured fungus
AM882823 Inocybe lacera
AY038324 Inocybe relicina
JN974994 Inocybe crucifera
JN975029 Inocybe sp.
JN642241 Inocybe pulchella
AM882923 Inocybe acutella
AM882760 Inocybe calida
EU307818 Inocybe sp.
AM882931 Inocybe subporospora
JN974976 Inocybe jacobi
JN974931 Inocybe sp.
EU600865 Inocybe sp.
EU600838 Inocybe sp.
EU600894 Inocybe sp.
JN974987 Inocybe soluta
EU569857 Inocybe lasseri
EU600900 Inocybe sp.
GQ892971 Inocybe hydrocybiformis
AM882930 Inocybe cf. assimilata
GQ892948 Inocybe sphaerospora
AM882929 Inocybe assimilata
EU600854 Inocybe scissa
EU569860 Inocybe sp.
EU307835 Inocybe intricata
GQ892976 Inocybe sp.
AY380370 Inocybe cerasphora
AY732211 Inocybe tubarioides
AF261510 Inocybe petinosa
JN974995 Inocybe sp.
JN974989 Inocybe subfulva
JN974984 Inocybe sp.
AY038320 Inocybe leptophylla
GQ892977 Inocybe sp.
AY239024 Inocybe napipes
GQ892952 Inocybe aff. pileosulcata
JN974988 Inocybe sp.
HQ641104 Inocybe aff. xanthomelas
JN974927 Inocybe sp.
JN974973 Inocybe cf. diminuta
EU499603 Inocybe splendens
JN974977 Inocybe albodisca
FJ207485 uncultured Inocybe
EU600897 Inocybe sp
FJ567525 uncultured basidiomycete
EU555474 Inocybe sp.
AM882754 Inocybe subcarpta
JN974975 Inocybe asterospora
AY038318 Inocybe lacera
GQ892959 Inocybe sp
AY380363 Inocybe sp.
AM882759 Inocybe calospora
GQ892957 Inocybe sp.
AM882846 Inocybe fibrosa
AY702013 Cortinarius iodes
JN974978 Inocybe aff albodisca
AY038313 Inocybe calospora
JN974979 Inocybe albodisca
JN974999 Inocybe praetervisa
JN974997 Inocybe hebes
EU307845 Inocybe subexilis
AF205694 Crepidotus applanatus var. applanatus
JN974986 Inocybe sp.
FJ567238 uncultured basidiomycete
EU600875 Inocybe sp.
AM882921 Inocybe pseudoasterospora
AM882717 Inocybe saliceticola
GQ892964 Inocybe sp.
EU555456 Inocybe sp.
AM882722 Inocybe cf. asterospora
GQ892956 Inocybe sp.
JN974981 Inocybe fallax
HQ201350 Inocybe diabolica
FJ566668 uncultured basidiomycete
HQ641112 Inocybe rufofusca
JN974980 Inocybe sp.
JN974990 Inocybe sp.
EU307819 Inocybe albodisca
GQ892960 Inocybe sp
AM882755 Inocybe soluta
JN974974 Inocybe cf. umbrinous
AM882821 Inocybe impexa
JN974992 Inocybe sp.
JN974983 Inocybe graveolens
EU600874 Inocybe sp.
AM882757 Inocybe sambucina
GQ892947 Inocybe sp.
GQ892963 Inocybe sp.
AM882789 Inocybe teraturgus
GQ892975 Inocybe sp.
JN974996 Inocybe fuscescentipes
JN974991 Inocybe sp.
JN974932 Inocybe sp.
AY239027 Inocybe teraturgus
AM882711 Inocybe subexilis
AY702015 Inocybe aff. asterospora
AM882715 Inocybe rennyi
HQ641095 Inocybe cf. straminipes
GQ892958 Inocybe sp.
GQ892970 Inocybe sp.
GQ892973 Inocybe aff. hydrocybiformis
EU861785 uncultured fungus
AM882897 Inocybe asterospora
AM882724 Inocybe salicis
EU569853 Inocybe glaucodisca
AY509115 Inocybe sp.
GQ892941 Inocybe sp.
JN974985 Inocybe cf. scissa
EU555442 Inocybe aff. antillana
AM882815 Inocybe lacera var. helobia
EU692212 uncultured fungus
AM882720 Inocybe praetervisa
GQ892950 Inocybe sp.
GQ892962 Inocybe sp.
AY038319 Inocybe lanunosa
AY748869 uncultured_ectomycorrhiza
GQ892955 Inocybe sp.
HQ201342 Inocybe chalcodoxantha
AY239022 Inocybe curvipes
GQ892968 Inocybe sp.
JN974993 Inocybe lacera
AY380399 Inocybe tahquamenonensis
EU569840 Inocybe epidendron
JN642237 Inocybe amazoniensis
AY038322 Inocybe praetervisa
EU555471 Inocybe conspicuospora
EU307838 Inocybe sp.
FM993253 uncultured ectomycorrhiza
GQ892954 Inocybe sp.
EU600880 Inocybe xerophytica
EU555441 Inocybe aff. antillana
EU307837 Inocybe sp.
AM882708 Inocybe petinosa
GQ892967 Inocybe sp.
JN974998 Inocybe aff. margaritispora
1
0.3
1
0.49
0.06
1
0.46
0.02
1
1
0.61
0.81
0.29
0.83
0.48
0.48
1
1
0.25
0.8
0.97
0.80.33
0.04
0.05
0.57
1
0.69
1
0.97
1
0.180.14
0.87
1
1
1
0.01
0.04
0.67
0.58
0.07
0.99
0.65
0.84
1
0.84
1
1
0.98
1
1
1
1
0.99
0.27
0.8
0.98
0.95
0.98
0.88
1
0.55
1
0.08
1
0.28
0.96
0.01
1
0.92
0.72
0.21
0.78
0.63
0.98
0.08
0.88
1
0.94
1
1
0.88
1
1
0.53
0.99
0.03
0.66
0.89
0.68
0.01
0.37
1
1
0.24
0.96
0.05
0.32
0.12
1
0.99
0.49
0.36
1
0.94
0.84
0.92
0.34
0.77
0.96
1
1
1
1
1
0.18
0
1
0.81
0.7
1
1
1
1
0.21
0.29
0.56
1
0.04
0.68
1
0.61
0.07
0.99
0.99
1
0.74
0.16
1
0.44
0.39
0.75
0.61
0.96
1
A
C
C. Figure S8. Chronograms for Inocybaceae (tree spitted in three parts A-C). Time scales are set in million years. MCC tree with median node heights based on the nucLSU region. Node bars represent 95% credibility intervals for node heights. Numbers above branches represents posterior probabilities. Names of outgroup taxa are in gray. The root was assigned an age prior with mean 93 Ma (sd 15 Ma) and the split between Inocybaceae and Crepidotus an age prior with mean 50 Ma (sd 12 Ma). The cut off for OTUs was set to 0.01 expected substitutions per site.
Figure S9. Chronogram for Phaeocollybia. Time scale set to millions of years. MCC tree with median node heights based on the ITS region. Node bars represent 95% credibility intervals for node heights. Numbers above branches represents posterior probabilities. Names of outgroup taxa are in gray. The root was assigned an age prior with mean 85 Ma (sd 14 Ma) and the split between Phaeocollybia, Hebeloma, and Galerina an age prior with mean 60 Ma (sd 15 Ma). The cut off for OTUs was set to 0.02 expected substitutions per site. MEDUSA indicated one rate change (clade marked with gray backgound).The root was inferred to have a net diversification rate = 0.02 and relative extinction rate = 0.00; the clade marked in gray had a net diversification rate = 0.07 and relative extinction rate = 0.00.
0.010.020.030.040.050.060.070.080.0
EU846282 Phaeocollybia fallax
EU846284 Phaeocollybia fallax
GQ165693 Phaeocollybia pleurocystidia
AY818348 Agrocybe praecox
GQ165636 Phaeocollybia benzokauffmanii
EU570185 Hebeloma erumpens
GQ165647 Phaeocollybia californica
EU669366 Phaeocollybia fallax
Galerina semilanceata
GQ165657 Phaeocollybia lilacifolia
GQ165666 Phaeocollybia luteosquamulosa
GQ165634 Phaeocollybia attenuata
EU669354 Phaeocollybia dissiliens
GQ165622 Phaeocollybia ammiratii
GQ165702 Phaeocollybia scatesiae
GQ165696 Phaeocollybia radicata
EU846268 Phaeocollybia piceae
GQ165655 Phaeocollybia gregaria
GQ165682 Phaeocollybia oregonensis
AM882996 Crepidotus mollis
EU644706 Phaeocollybia sipei
EU852801 Phaeocollybia pseudofestiva
EU697255 Phaeocollybia pseudofestiva
EU697249 Phaeocollybia piceae
EU669234 Phaeocollybia olivacea
DQ494682 Phaeocollybia festiva
AF501567 Phaeocollybia graveolens
0.32
0.76
1
0.4
1
1
1
1
0.65
1
1
0.97
0.83
0.6
0.94
0.73
0.68
1
0.3
0.84
0.57
1
0.11
1
0.42
Figure S10. Chronogram for Tricholoma. Time scale set to million of years. MCC tree with median node heights based on the ITS region. Node bars represent 95% credibility intervals for node heights. Numbers above branches represents posterior probabilities. Names of outgroup taxa are in gray. The root was given an age prior with mean 103 Ma (sd 15 Ma) and the split between Tricholoma and Entoloma an age prior with mean 91 Ma (sd 15 Ma). The cut off for OTUs were set to 0.025 expected substitutions per site.
Table S1. Probabilities of stem origins during different epochs. Jurrassic Cretaceous Paleogene ECM lineage
of Agaricales Late Early Late Total Paleocene Eocene Oligocene Total Amanita 0.00 0.49 0.51 1.00 0.00 0.00 0.00 0.00 Catathelasma 0.00 0.13 0.76 0.89 0.07 0.04 0.00 0.11 Cortinarius* 0.00 0.05 0.71 0.76 0.17 0.08 0.00 0.25 Descolea* 0.00 0.01 0.50 0.51 0.24 0.23 0.01 0.48 Hebelomateae 0.00 0.00 0.34 0.34 0.36 0.30 0.00 0.66 Hydnangiaceae 0.00 0.03 0.65 0.68 0.2 0.12 0.00 0.32 Hygrophorus 0.13 0.65 0.15 0.80 0.01 0.00 0.00 0.01 Inocybaceae 0.00 0.00 0.34 0.34 0.39 0.26 0.00 0.65 Phaeocollybia 0.00 0.00 0.26 0.26 0.34 0.39 0.01 0.74 Tricholoma 0.00 0.19 0.80 0.99 0.01 0.00 0.00 0.01 * Including gasteroid allies. Table S2. Ancestral plant association. The ancestral plant association reconstructed for most trees in the posterior distribution using parsimony and the proportion of the posterior distribution (P), for which this state was reconstructed. The median probability (and 95% credibility interval) for each state given the Bayesian ancestral state reconstruction is also provided.
Table S3. Diversification rate model comparison using DivBayes. Taxa given the same number are defined to have the same rate for net diversification (N; speciation rate – extinction rate) and relative extinction rate (E; extinction rate/speciation rate), respectively. If no numbers are given for relative extinction rate, the Yule model was used (extinction rate = 0 for all taxa). The mean and standard deviation (SD) of the normal distributed age prior and the number of species (No.) for each group are also given.
Models Age prior 1 2 3 4 5 6 7 8 9 10 11
ECM lineage of Agaricales
No. Mean SD N E N E N E N E N E N E N E N E N E N E N E Amanita 500 99 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Catathelasma 4 91 18 0 0 0 1 1 0 1 1 1 0 1 0 1 1 Cortinarius* 2011 75 15 0 0 0 2 2 0 2 2 0 1 2 1 0 2 Descolea* 30 66 15 0 0 0 3 3 0 3 3 0 0 0 0 0 0 Hebelomateae 281 61 11 0 0 0 4 4 0 4 4 0 0 0 1 0 2 Hydnangiaceae 76 73 13 0 0 0 5 5 0 5 5 0 0 0 0 0 0 Hygrophorus 100 125 25 0 0 0 6 6 0 6 6 0 0 0 0 1 1 Inocybaceae 507 62 10 0 0 0 7 7 0 7 7 0 0 0 1 0 2 Phaeocollybia 50 59 11 0 0 0 8 8 0 8 8 0 0 0 0 0 0 Tricholoma 200 90 11 0 0 0 9 9 0 9 9 0 0 0 0 0 0 Table S4. Bayes factors for each model in Table S3 as estimated from harmonic means of the log likelihood in the DivBayes runs. The estimated net diversification rate (N) and relative extinction rate (E) are given for each category (indexed as in Table S3). Model Log Bayes factor Estimated rates