The authors have declared that no competing interests exist.
Conceived and designed the experiments: HTL RL. Performed the experiments: SP. Analyzed the data: SP RL HTL. Contributed reagents/materials/analysis tools: SP. Wrote the paper: SP HTL.
Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus
Molecular data have revolutionized our understanding of the evolution of organisms and have had profound impact on classifications, especially in organisms lacking complex morphologies, such as fungi
Due to the nature of binomial nomenclature introduced by Linnaeus, in which a species name is composed of the generic name and the epitheton, changes in the classification of an organism at the generic level lead to a change in the name of the organism. Thus, systematists have been reluctant to translate phylogenetic studies into classification at the generic level when monophyletic clades lack correlating phenotypical features. When a genus-level taxon is found to be poly- or paraphyletic, it can be either split or merged with another taxon to obtain monophyly. Since genera and all higher taxonomic ranks are arbitrary, both lumping or splitting would be possible and there is no a priori scientific argument to favor either solution. Such reclassifications often lead to genera that are not distinguishable by phenotypical characters, and these have been called “cryptic genera”
Here we propose a new, quantitative approach to choose among alternative classifications, combining the technique of morphology-based phylogenetic binning with a multi-response permutation procedure (MRPP)
We used the tribe Thelotremateae in Graphidaceae, a family of lichenized fungi, to illustrate our approach
Seventy-five new sequences were generated for this study and aligned with 237 sequences downloaded from Genbank, most of them generated in our lab and included in a previous study (
Posterior probabilities equal or above 0.95 are indicated as bold branches. ML-bootstrap support equal or above 70% is shown as number at branches.
Species | Collection data | mtSSU acc. no. | nuLSU acc. no | |
|
Brazil, Lücking 31237 (F) | JX420971 | JX421438 |
|
|
Brazil, Lücking 31238a (F) | JX420972 | JX421439 | JX420936 |
|
Guatemala, Lücking 25587 (F) | JX420973 | JX421440 | JX420940 |
|
Thailand, Lumbsch 19750a (F) | JX420974 | JX421441 | JX420859 |
|
Thailand, Lücking 24011 (F) |
|
JX421445 | JX420947 |
|
Thailand, Papong 6004 (F) | JX420975 | JX421442 | JX420865 |
|
Thailand, Lücking 24008 (F) | JX420978 | JX421444 | JX420945 |
|
Thailand, Lücking 24006 (F) | JX420977 | JX421443 | JX420943 |
|
Venezuela, Kalb s.n. | JX420980 | – | JX420898 |
|
Venezuela, Lücking 32101 (F) | JX420981 | JX421446 | JX420906 |
|
Venezuela, Lücking 26143 (F) | JX420982 | JX421447 | JX420949 |
|
Brazil, Cáceres 6006a | JX420984 | – | JX420885 |
|
Brazil, Cáceres 6006b (F) |
|
– | JX420886 |
|
Brazil, Cáceres s.n. (F) | JX420983 | – | JX420883 |
|
Peru, Rivas Plata 107C (F) | JX420985 | – | JX420870 |
|
Peru, Rivas Plata 809a (F) | JX420986 |
|
|
|
Thailand, Parnmen 018486 (RAMK) |
|
|
|
|
Australia, Lumbsch 19139sa (F) | JX420988 | JX421448 | JX420831 |
|
Australia, Lumbsch 19139sb (F) | JX420989 |
|
– |
Thailand, Lücking 24007 (F) | JX420969 | JX421436 | JX420944 | |
Thailand, Lücking 24009 (F) | JX420970 | JX421437 | JX420946 | |
|
Thailand, Kalb 38794 (hb. Kalb) | JX420994 | JX421453 | JX420928 |
|
Thailand, Lumbsch 19750c (F) | JX420993 | JX421452 | JX420857 |
|
Thailand, Lücking 24004 (F) | JX420995 | JX421455 | JX420942 |
|
Philippines, Rivas Plata 1175B (F) | JX420992 |
|
|
|
Fiji, Lumbsch 20500f (F) | JX420996 |
|
|
|
Philippines, Rivas Plata 1111G (F) | JX420998 |
|
JX420860 |
|
Philippines, Rivas Plata 1200 (F) | JX420999 |
|
JX420861 |
|
Costa Rica, Lücking 17770 (F) | EU075610 | EU075655 | JF828940 |
|
Australia, Lumbsch 19125k1 (F) | EU075568 | EU075615 | – |
|
Australia, Lumbsch 19125k2 (F) | EU675274 | – | – |
|
Australia, Lumbsch 19151p1 (F) | EU075567 | FJ708487 | – |
|
Thailand, Lücking 24003 (F) | JX421003 | JX421459 | JX420941 |
|
China, Kalb 38676 (hb. Kalb) | JX421001 | JX421458 | JX420939 |
|
Australia, Mangold 39ze (F) | EU675275 |
|
|
|
Fiji, Lumbsch 20500d (F) | JX421005 |
|
|
|
Australia, Lumbsch 19100f (F) | EU075569 |
|
|
|
USA, Lücking 26573 (F) | JX421007 | JX421460 |
|
|
Thailand, Lumbsch 19750b (F) | JX421008 |
|
JX420858 |
Thailand, Parnmen 018492 (RAMK) |
|
|
|
|
|
Australia, Lumbsch 19129t (F) | EU075571 | EU075619 |
|
|
Brazil, Lücking 31200 (F) | JX421011 | JX421462 | JX420935 |
|
Brazil, Lücking 31240 (F) | JX421012 | JX421463 | JX420937 |
|
Mexico, Lücking RLD056 (F) | HQ639600 | JX421466 | JX420842 |
|
Venezuela, Lücking 32019 (F) | JX421013 |
|
JX420905 |
|
Panama, Lücking 27305 (F) |
|
|
|
|
Panama, Lücking s.n. (F) |
|
|
|
Thailand, Parnmen 018483 (RAMK) |
|
|
|
|
Fiji, Lumbsch 19815d (F) | JX421000 | JX421457 |
|
|
|
Australia, Lumbsch 19126a (F) | HQ639585 | JX421468 | – |
|
Australia, Lumbsch 5437 (F) | FJ708496 | FJ708489 | – |
|
Thailand, Papong 5118 (F) | FJ708497 | FJ708490 | – |
|
Thailand, Papong 6071 (F) |
|
– |
|
|
Thailand, Papong 6069 (F) |
|
JX421469 | JX420863 |
|
Thailand, Papong 6070 (F) |
|
|
– |
|
AFTOL-ID 328 | DQ912306 | DQ883799 | DQ883755 |
|
Venezuela, Lücking 32120 (F) | JX421077 | JX421512 |
|
|
Thailand, Lumbsch 20205b (F) | JX421081 | JX421514 | – |
|
El Salvador, Lücking 28098 (F) | HQ639611 | HQ639657 | JF828949 |
|
USA, Mangold 50d (F) | JX421084 | – | JX420846 |
|
Australia, Mangold 22zl (F) | JF828962 | – | – |
|
USA, Mangold 50a (F) |
|
|
|
|
Australia, Lumbsch 19153p (F) | EU075576 | EU075624 | – |
|
Australia, Lumbsch 19116o (F) | EU075575 | EU075623 | – |
|
Australia, Lumbsch & Mangold 19113f (F) | EU075579 | EU075627 | HM244799 |
|
Fiji, Lumbsch 20520a (F) |
|
JX421531 |
|
|
El Salvador, Lücking 28015 (F) | HQ639622 | – | JF828952 |
|
India, Lumbsch 19730i (F) | JX421344 | JX421642 | JX420851 |
|
India, Lumbsch 19737m (F) | JX421343 | JX421641 | JX420848 |
|
Thailand, Lumbsch 20200b (F) | JX421347 | JX421645 |
|
|
Thailand, Lumbsch 19756u (F) |
|
JX421644 | JX420853 |
New Zealand, Knight 61701 (F) |
|
– |
|
|
|
Australia, Mangold 27v (F) | DQ384917 | FJ708493 | – |
|
Australia, Mangold 31o (F) | JX421356 | – | JX420847 |
|
Australia, Lumbsch 19127v (F) | EU075599 | JX421649 | JX420827 |
|
Australia, Lumbsch 19151k (F) | EU075600 | EU075653 | – |
|
Australia, Lumbsch 19117k (F) | EU675293 | – | – |
|
Australia, Lumbsch 19100yb (F) | JX421360 |
|
JX420826 |
|
Australia, Lumbsch 20004c (F) | JX421370 | JX421655 | JX420868 |
|
Australia, Lumbsch 19998a (F) | JX421368 |
|
JX420866 |
|
Australia, Lumbsch 19997c (F) | JX421369 | JX421654 | JX420867 |
|
Australia, Mangold 1b (F) | JX421362 | JX421656 | JX420837 |
|
Australia, Mangold 18l (F) | JX421363 | JX421651 | JX420840 |
|
Australia, Lumbsch 19983i (F) | JX421371 |
|
– |
|
India, Lumbsch 19744i (F) | JX421365 | JX421652 | JX420850 |
|
New Zealand, Knight 61702 (F) | JX421366 | JX421653 | JX420934 |
|
UK, Scotland, Lumbsch 20100c (F) |
|
|
JX420890 |
|
USA, Lendemer 6389 (NY) | EU075602 | EU075645 |
|
|
Australia, Lumbsch 19161xb (F) | EU075596 | EU075644 | – |
|
Australia, Lumbsch 19158w (F) | EU075601 | EU075646 | – |
|
Australia, Lumbsch 19123j (F) | JX421376 | JX421660 |
|
|
Australia, Lumbsch 19100ya (F) | EU075597 | EU075647 | – |
Thailand, Lumbsch 19751f (F) | JX421408 | JX421673 | JX420854 | |
Thailand, Lumbsch 19751d (F) | JX421409 | JX421674 | JX420856 | |
|
Tanzania, Frisch 99Tz1051 (hb. Kalb) | DQ384918 | DQ431925 | – |
|
USA, Lücking 26568a (F) | JX421381 | – |
|
|
Australia, Lumbsch 19162j (F) | EU675290 | – | JX420829 |
|
UK, Scotland, Lumbsch 20100a (F) | JX421383 | JX421664 | JX420891 |
|
Australia, Lumbsch 19108d (F) | JX421384 |
|
|
Australia, Mangold 29t (F) | JX421350 | JX421646 | JX420844 | |
Australia, Lumbsch 19151zb (F) | JX421349 | – |
|
|
Australia, Lumbsch 19156d (F) | EU675291 |
|
– | |
|
Fiji, Lumbsch 20524f (F) | JX421394 | – |
|
|
Fiji, Lumbsch 20532a (F) | JX421397 |
|
|
|
Fiji, Lumbsch 20516h (F) | JX421386 |
|
|
|
Philippines, Rivas Plata 2009 (F) | HQ639603 | JX421665 | – |
|
Australia, Lumbsch 19082b (F) | EU075605 |
|
– |
|
USA, Lumbsch 19257b (F) | JX421402 | – | JX420836 |
|
Japan, Ohmura 7769 (TNS) | JX421403 | JX421668 | JX420932 |
Australia, Mangold 3e (F) | EU675297 | DQ871013 |
|
|
Australia, Mangold 3j (F) | EU075607 | EU075651 | JX420834 | |
|
Norway, Gaarder 4365 (BG) | JX421406 | JX421671 | – |
|
Norway, Gaarder 4366a (BG) | JX421407 | JX421672 | JX420832 |
|
Norway, Gaarder 4366b (BG) |
|
|
|
Australia, Mangold Am3p (F) | JX421404 | JX421669 | JX420833 | |
Australia, Mangold Am6l (F) | JX421405 | JX421670 | JX420835 | |
India, Lumbsch 19729i (F) | JX421400 | JX421667 | JX420849 | |
|
Venezuela, Lücking 32003 (F) | JX421422 | JX421681 | JX420916 |
In the phylogenetic tree, the genus
Phylogenetic binning of the 65 described
ML 2-clades | MP 2-clades | ML 4-clades | MP 4-clades | ML 5-clades | MP 5-clades | |
Clade I | 14 | 19 | 16 | 21 | – | – |
Subclade Ia | – | – | – | – | 8 | 10 |
Subclade Ib | – | – | – | – | 8 | 11 |
Clade II | 49 | 44 | – | – | – | – |
Subclade IIa | – | – | 24 | 21 | 24 | 21 |
Subclade IIb | – | – | 5 | 7 | 5 | 7 |
Subclade IIc | – | – | 20 | 16 | 20 | 16 |
Outside | 2 | 2 | 0 | 0 | 0 | 0 |
Conflicting | 12 | 19 | 20 | |||
|
|
|
|
|
|
|
The MRPP analysis resulted in non-significant or spuriously significant differences between groups for the 2-clade solution but in highly significant differences for the 4-clade solution, independent of group assignment based on ML or MP weighting and of the distance measure employed (
Euclidean | Correlation | |
ML 2-clades | 0.0732 | 0.1697 |
MP 2-clades | 0.0366 | 0.0785 |
ML 4-clades | 0.0000 | 0.0000 |
MP 4-clades | 0.0000 | 0.0000 |
ML 5-clades | 0.0000 | 0.0000 |
MP 5-clades | 0.0000 | 0.0000 |
p-values for significance of group distances based on morphological character matrix.
Kruskal-Wallis ANOVA indicates five characters as significantly discriminating between groups in a 2-clade solution using ML weighting and an additional three characters as marginally significant (
Significant (p<0.05) | Marginally significant (p<0.10) | Total | |
ML 2-clades | 5 | 3 | 8 |
MP 2-clades | 3 | 3 | 6 |
ML 4-clades | 15 | 3 | 18 |
MP 4-clades | 11 | 3 | 14 |
ML 5-clades | 14 | 4 | 18 |
MP 5-clades | 11 | 3 | 14 |
The best discriminating characters in the 4-clade and 5-clade solutions (
ML-2 | MP-2 | ML-4 | MP-4 | ML-5 | MP-5 | |
Soralia | 0.0019 | 0.0102 | 0.0002 | |||
Oxalate crystals | 0.0129 | 0.0244 | ||||
Cortex | 0.0744 | 0.0914 | 0.0089 | 0.0313 | ||
Ascoma emergence | 0.0296 | 0.0567 | ||||
Ascoma shape | 0.0962 | 0.0504 | ||||
Ascoma aggregation | 0.0975 | 0.0544 | ||||
Ascoma diameter | 0.0661 | 0.0980 | 0.0574 | 0.0596 | ||
Ascoma exposure | 0.0017 | 0.0010 | 0.0043 | 0.0026 | ||
Proper margin shape | 0.0368 | 0.0168 | 0.0057 | |||
Proper margin striation | 0.0262 | 0.0019 | 0.0741 | 0.0049 | ||
Proper margin split | 0.0007 | 0.0000 | 0.0544 | 0.0000 | ||
Thallus margin shape | 0.0003 | 0.0003 | 0.0002 | |||
Excipulum carbonization | 0.0080 | 0.0148 | 0.0123 | 0.0391 | 0.0274 | 0.0592 |
Periphysoids presence | 0.0000 | 0.0000 | ||||
Ascospores number | 0.0033 | 0.0080 | ||||
Ascospores length | 0.0037 | 0.0723 | 0.0003 | 0.0008 | ||
Ascospores width | 0.0773 | 0.0862 | 0.0077 | 0.0168 | ||
Ascospores length-to-widthratio | 0.0006 | 0.0014 | 0.0027 | |||
Ascospores endosporedevelopment | 0.0000 | 0.0000 | 0.0000 | 0.0000 | ||
Ascospores iodine reaction | 0.0000 | 0.0000 | 0.0000 | 0.0000 | ||
Ascospores transverse septa | 0.0056 | 0.0003 | 0.0919 | 0.0008 | ||
Ascospores longitudinal septa | 0.0002 | 0.0546 | 0.0005 | 0.0272 | ||
Chemistry stictic acid | 0.0366 | 0.0405 | ||||
Chemistry protocetraric acid | 0.0005 | 0.0010 |
The detection of phylogenetically defined clades lacking clearly discriminant morphological characters is not rare and particularly common in fungal groups, including lichenized species, since these organisms are composed of rather simple structures and are less differentiated than higher plants and animals
The genus
In the case of the genus
The phylogenetic binning method allows both ML and MP weighting of the morphological characters, but the underlying algorithms are different
In contrast to making phenotypical characters obsolete in systematics, our study underlines the importance of these data even in times where molecular data become increasingly available to reconstruct phylogenies. While phenotypical data itself should not be used in such reconstructions, they are indispensable when transforming phylogenies into classifications and, with powerful analytical methods, provide statistical evidence that can be used to compare alternative classification models based on an underlying phylogeny.
The results of our phylogenetic analysis and the combined binning/multiresponse permutation procedure support a classification accepting each of the four Chapsa clades as different genera. Also,
Parnmen, Lücking & Lumbsch, gen. nov. [MycoBank MB 801540] Type species:
Differing from
Thallus usually with dense cortex, rarely with loose cortex or ecorticate. Apothecia erumpent, rounded to irregular in outline; disc exposed; margin lobulate to usually recurved. Excipulum usually brown. Ascospores septate to muriform, fusiform-ellipsoid to oblong-cylindrical, with slightly thickened septa and angular lumina (subdistoseptate), colorless or rarely brown, almost exclusively I–. Secondary chemistry: no substances or frequently stictic acid and relatives; apothecial disc sometimes pigmented.
Etymology: Derived from “astro” (Greek, starry) because of the star-like morphology of the ascomata and the genus name
(Frisch) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801500] Bas.:
(Kalb) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801501] Bas.:
(Berk. & Broome) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801502] Bas.:
(Vain.) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801503] Bas.:
(Kalb) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801504] Bas.:
(Mangold) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801505] Bas.:
(Berk. & Broome) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801506] Bas.:
(Rivas Plata, Lumbsch & Lücking) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801507] Bas.:
(Mangold) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801508] Bas.:
(Kalb & Frisch) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801509] Bas.:
(Vain.) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801510] Bas.:
(Nyl.) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801511] Bas.:
(Hale) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801512] Bas.:
(G. Salisb.) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801513] Bas.:
(Hale) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801515] Bas.:
(Weerakoon, Lumbsch & Lücking) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801516] Bas.:
(Redinger) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801517] Bas.:
Parnmen, Lücking & Lumbsch, gen. nov. [MycoBank MB 801541] Type species:
Differing from
Thallus ecorticate. Apothecia erumpent, rounded; disc largely obscured by exciple; margin star-like, multi-layered. Excipulum hyaline basally, carbonized apically. Ascospores transversaly septate, fusiform, with thickened septa and lens-shaped to rounded lumina (distoseptate), colorless, I+. Secondary chemistry: no substances.
Etymology: Named after the distinguished British lichenologist Peter Crittenden (Nottingham) with whom SP and HTL collected material of the genus sequenced here on a field trip organized by the British Lichen Society. The name Crittenden is derived from the old British and Welsh and means “the cot on the lower hill”; derived from “cru” (cot); “tarn” (lower), and “dun” or “din” (hill).
(P.M. Jørg. & Brodo) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801518] Bas.:
Parnmen, Lücking & Lumbsch, gen. nov. [MycoBank MB 801542]. Type species:
Differing from
Thallus usually with loose cortex or ecorticate, very rarely with dense cortex. Apothecia erumpent, rounded to irregular in outline; disc exposed; margin usually fissured to lobulate, rarely recurved. Excipulum usually brown. Ascospores septate to muriform, fusiform-ellipsoid to oblong-cylindrical, mostly with thickened septa and lens-shaped to rounded lumina (distoseptate), colorless or very rarely brown, almost exclusively I+ violet-blue (amyloid). Secondary chemistry: no substances or frequently stictic acid and relatives; apothecial disc rarely pigmented.
Etymology: Derived from “pseudo” (Greek, false) and the genus name
(Sipman) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801519] Bas.:
Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801520] Bas.:
Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801521] Bas.:
Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801522] Bas.:
(Rivas Plata & Lücking) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801523] Bas.:
(Frisch & Kalb) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801524] Bas.:
(Frisch) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801525] Bas.:
(Kalb) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801526] Bas.:
(Nyl.) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801527] Bas.:
(Müll. Arg.) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801528] Bas.:
(Patw. & C. R. Kulk.) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801529] Bas.:
(Hale) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801530] Bas.:
(Kalb) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801531] Bas.:
(Kalb) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801532] Bas.:
(Frisch & Kalb) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801533] Bas.:
(Hale) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801534] Bas.:
Parnmen, Lücking & Lumbsch, gen. nov. [MycoBank MB 801543] Type species:
Differing from
Thallus usually with dense cortex, rarely with loose cortex. Apothecia erumpent, rounded to irregular in outline; disc pore-like; margin fissured lobulate, in concentric layers covering the disc. Excipulum hyaline to brown. Ascospores septate to muriform, fusiform-ellipsoid to oblong-cylindrical, with slightly thickened septa and angular lumina (subdistoseptate), colorless to brown, I–. Secondary chemistry: no substances.
Etymology: Derived from “pseudo” (Greek, false) and the genus name
(Hale) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801535] Bas.:
(Müll. Arg.) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801536] Bas.:
(Hale) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801537] Bas.:
(Hale) Parnmen, Lücking & Lumbsch, comb. nov. [MycoBank MB 801538] Bas.:
We assembled a three-locus data set consisting of mtSSU rDNA, nuLSU rDNA, and the protein-coding genes
Alignments were done using Geneious Pro 5.5.2
The ML analysis of the concatenated alignment was performed with the program RAxML-HPC2 (version 7.3.1) on XSEDE
The B/MCMC analysis was conducted on the concatenated data set using MrBAYES 3.1.2
Anatomical studies were conducted using standard light microscopy on hand-cut sections mounted in water. Secondary lichen substances were identified by thin-layer chromatography (TLC) and high performance thin-layer chromatography (HPTLC) according to standard methods
Our phylogenetic analyses revealed that the genus
Since the molecular data set corresponding to the genus
A multiresponse permutation procedure is a simple and effective tool to test for differences between groups of entities, in this case the groups obtained by the four alternative classifications obtained from the molecular phylogeny and subsequent binning method
The electronic version of this article in Portable Document Format (PDF) in a work with an ISSN or ISBN will represent a published work according to the International Code of Nomenclature for algae, fungi, and plants, and hence the new names contained in the electronic publication of a PLOS ONE article are effectively published under that Code from the electronic edition alone, so there is no longer any need to provide printed copies.
In addition, new names contained in this work have been submitted to MycoBank from where they will be made available to the Global Names Index. The unique MycoBank number can be resolved and the associated information viewed through any standard web browser by appending the MycoBank number contained in this publication to the prefix
(DOC)
All new sequences were generated in the Pritzker Laboratory for Molecular Systematics and evolution at The Field Museum (Chicago). We wish to thank Marcela Cáceres (Recife), Allison Knight (Auckland), Eimy Rivas Plata (Durham, NC), Khwanruan Papong (Maharasakam), Andreas Frisch (Stockholm), Klaus Kalb (Neumarkt/Opf.), Armin Mangold (Berlin), and Tor Tønsberg (Bergen) for providing material that was used in this study.