Damm et al.combined sequence datasets. Models of nucleotide substitutionf<strong>or</strong> each gene determined by MrModeltest v. 2.3 were included f<strong>or</strong>each gene partition. The analyses of two MCMC chains were runfrom random trees f<strong>or</strong> one million generations and sampled every100 generations. The likelihood sc<strong>or</strong>e of the two runs were 2 730and 2 170 and theref<strong>or</strong>e, the first 2 450 (the average of both) treeswere discarded as the burn-in phase of the analysis and posteri<strong>or</strong>probabilities determined from the remaining trees. Sequencesderived in this study were lodged at GenBank, the alignmentin TreeBASE (www.treebase.<strong>or</strong>g), and taxonomic novelties inMycoBank (Crous et al. 2004a).RESULTSPhylogenyThe seven sequence datasets did not show any conflicts in treetopology f<strong>or</strong> the 70 % reciprocal bootstrap trees, which allowed usto combine them. In the multigene analyses (gene boundaries ofITS: 1–561, GAPDH: 572–864, CHS-1: 875–1154, HIS3: 1164–1562, ACT: 1573–1851, TUB2: 1862–2363, CAL: 2374–2823) of87 isolates of C. boninense and related <strong>Colletotrichum</strong> <strong>species</strong>including the outgroup, 2 823 characters including the alignmentgaps were processed, of which 572 characters were parsimonyinf<strong>or</strong>mative,247 parsimony-uninf<strong>or</strong>mative and 2004 constant. Aftera heuristic search using PAUP, 958 most parsimonious trees wereretained (length = 1423 steps, CI = 0.740, RI = 0.927, RC = 0.686,HI = 0.260) of which one is shown in Fig. 1. The topology of the 958trees was similar, which was verified f<strong>or</strong> a large selection of trees.They differed in the position of taxa within the subclades and in theposition of strain <strong>CBS</strong> 130241. F<strong>or</strong> Bayesian analysis, a HKY+Gmodel was selected f<strong>or</strong> ACT and CAL, SYM+I+G f<strong>or</strong> ITS, K80+I+Gf<strong>or</strong> CHS-1, GTR+I+G f<strong>or</strong> HIS3, and HKY+I f<strong>or</strong> GAPDH and TUB2,and inc<strong>or</strong>p<strong>or</strong>ated in the analysis. The consensus tree obtainedfrom Bayesian analyses confirmed the tree topology obtained withparsimony as well as the bootstrap supp<strong>or</strong>t (Fig. 1).The analyses resulted in the detection of 18 clades, whichwe accept as representing different <strong>Colletotrichum</strong> <strong>species</strong>.M<strong>or</strong>e than half of all strains included cluster in the first clade (C.karstii) with a bootstrap supp<strong>or</strong>t of 96 % and a Bayesian posteri<strong>or</strong>probability value of 1.00. Two single strain clades, representingC. phyllanthi and C. annellatum, group with this big clade with abootstrap supp<strong>or</strong>t/Bayesian posteri<strong>or</strong> probability value of 96/0.99and 100/1.00, respectively. The C. petchii clade is well supp<strong>or</strong>ted(100/1.00) and f<strong>or</strong>ms a sister clade to the first three <strong>species</strong>. Theclade representing C. novae-zelandiae consists of two strains ona long branch (100/1.00). In contrast, the following five clades aresh<strong>or</strong>t-branched, namely C. boninense s. str. (95/1.00), C. t<strong>or</strong>ulosum(100/1.00), C. cymbidiicola (96/1.00), C. oncidii (100/1.00) and aclade containing an unnamed single strain (<strong>CBS</strong> 123921). Thesefive <strong>species</strong> f<strong>or</strong>m a sister clade (100/1.00) to another well supp<strong>or</strong>ted(100/1.00) clade f<strong>or</strong>med by two single strain clades, C. beeveriand C. brassicicola, and the C. colombiense clade (100/1.00)containing two strains. The clades representing C. hippeastri andC. brasiliense consist of three and two strains respectively, andare well supp<strong>or</strong>ted (100/1.00). They group (100/1.00) with a singlestrain clade (C. parsonsiae). The C. constrictum clade (100/1.00)containing two strains and the single strain clade representing C.dacrycarpi are on very long branches and group with a Bayesianposteri<strong>or</strong> probability value of 1.00.The individual alignments and trees of the seven single geneswere compared as well with respect to their perf<strong>or</strong>mance in <strong>species</strong>recognition. With ITS and CHS-1 only 7 and 9 <strong>species</strong> can berecognised, with TUB2 some <strong>species</strong> close to C. boninense cannot be separated, while with HIS3 and CAL some <strong>species</strong> onlydiffer in one <strong>or</strong> two bp and f<strong>or</strong>m no <strong>or</strong> only sh<strong>or</strong>t-branched clades.With GAPDH all clades are recognised, but some are also sh<strong>or</strong>tbranched,especially the single strain clades C. beeveri and C.brassicicola that are well differentiated with almost all other genesexcept f<strong>or</strong> ITS. With ACT the intraspecific variability is very high insome <strong>species</strong>, which could lead to misidentifications.TaxonomyThe 86 isolates studied (Table 1) are assigned to 18 <strong>species</strong> withinthe <strong>Colletotrichum</strong> boninense <strong>complex</strong> based on DNA sequencedata and m<strong>or</strong>phology, including 12 <strong>species</strong> that are new to science.Ten <strong>species</strong> f<strong>or</strong>m teleom<strong>or</strong>ph stages in vitro, four <strong>species</strong> haveknown anam<strong>or</strong>phs described in <strong>Colletotrichum</strong>, while one <strong>species</strong>,G. phyllanthi, has a known teleom<strong>or</strong>ph and is shown here asbelonging to the <strong>Colletotrichum</strong> boninense <strong>species</strong> <strong>complex</strong>. All<strong>species</strong> studied in culture are characterised below.Species of <strong>Colletotrichum</strong> represent anam<strong>or</strong>phic stages ofGlomerella. Anam<strong>or</strong>ph and telem<strong>or</strong>ph names of fungi will haveequal status under the International Code of Nomenclature f<strong>or</strong>algae, fungi, and plants (f<strong>or</strong>merly the International Code f<strong>or</strong>Botanical Nomenclature), with the deletion of Art. 59, which takeseffect on 1 Jan. 2013. The decision was qualified by a stipulationthat uptake of names of anam<strong>or</strong>phic genera that predate well-knowncompeting teleom<strong>or</strong>phic names should be ratified by a committeeof the International Commission f<strong>or</strong> the Taxonomy of Fungi. Thename <strong>Colletotrichum</strong> (C<strong>or</strong>da 1831) predates Glomerella (Spauld.& H. Schrenk 1903) and is m<strong>or</strong>e commonly used. Consequentlywe name the new holom<strong>or</strong>phs as <strong>species</strong> of <strong>Colletotrichum</strong> and wedo not name the new sexual m<strong>or</strong>phs separately. Furtherm<strong>or</strong>e, G.phyllanthi is combined in <strong>Colletotrichum</strong> as C. phyllanthi. There isprecedent f<strong>or</strong> this as Rojas et al. (2010) described <strong>Colletotrichum</strong>ignotum as having a teleom<strong>or</strong>ph (see Rojas et al. 2010: figs 44–47,table III), although the teleom<strong>or</strong>phic structures were not included inthe f<strong>or</strong>mal <strong>species</strong> diagnosis.<strong>Colletotrichum</strong> annellatum Damm, P.F. Cannon & Crous,sp. nov. MycoBank MB560734. Fig. 2.Etymology: The name refers to the proliferation of conidiogenouscells, which appear annellate.Teleom<strong>or</strong>ph developed on SNA. Ascomata ovoid to obpyrif<strong>or</strong>m,medium to dark brown, 180–220 × 100–150 µm, glabrous,ostiolate, neck hyaline to pale brown, wall 5–10 µm thick, outerlayer composed of flattened medium brown angular cells, 5–10 µmdiam. Interascal tissue composed of paraphyses, hyaline, septate,branched at the base, disintegrating quickly, 35–55 µm long, base3–4.5 µm diam, apically free, the apex rounded. Asci cylindricalto clavate, 58–74 × 11–16 µm, 8-sp<strong>or</strong>ed. Ascosp<strong>or</strong>es arrangedbiseriately, hyaline, smooth-walled, aseptate, cylindrical to narrowlyfabif<strong>or</strong>m, straight <strong>or</strong> rarely very slightly curved, both sides rounded,(13.5–)15–17(–18.5) × 5–6 µm, mean ± SD = 16.0 ± 1.1 × 5.6 ±0.4 µm, L/W ratio = 2.9.Teleom<strong>or</strong>ph developed on Anthriscus stem. Ascomata ovoidto obpyrif<strong>or</strong>m, medium brown. Asci cylindrical to clavate, 60–706
The <strong>Colletotrichum</strong> boninense <strong>species</strong> <strong>complex</strong>10 changes1001.001.001.00991.001001.001001.00921.00951.00731.0099 <strong>CBS</strong> 1298331.00 <strong>CBS</strong> 129834<strong>CBS</strong> 125468MAFF 305973<strong>CBS</strong> 128524MAFF 306204<strong>CBS</strong> 129832<strong>CBS</strong> 1275950.99 <strong>CBS</strong> 125388<strong>CBS</strong> 127591<strong>CBS</strong> 1298150.99 <strong>CBS</strong> 128552<strong>CBS</strong> 1298291.00 <strong>CBS</strong> 130235MAFF 305998<strong>CBS</strong> 118401<strong>CBS</strong> 508.97<strong>CBS</strong> 124969<strong>CBS</strong> 1249511.00 <strong>CBS</strong> 1130871.00 <strong>CBS</strong> 486.97<strong>CBS</strong> 112982<strong>CBS</strong> 861.72<strong>CBS</strong> 110779<strong>CBS</strong> 127535<strong>CBS</strong> 129830<strong>CBS</strong> 127536<strong>CBS</strong> 128500<strong>CBS</strong> 127596<strong>CBS</strong> 127597<strong>CBS</strong> 12854896 <strong>CBS</strong> 1285451.00 <strong>CBS</strong> 1285510.99 <strong>CBS</strong> 111860<strong>CBS</strong> 111998<strong>CBS</strong> 112762<strong>CBS</strong> 115535<strong>CBS</strong> 12992796 <strong>CBS</strong> 1265320.99 <strong>CBS</strong> 12854090 <strong>CBS</strong> 1298241.00 <strong>CBS</strong> 124956100 <strong>CBS</strong> 1275521.00 <strong>CBS</strong> 1298221.001.00<strong>CBS</strong> 128550<strong>CBS</strong> 106.91<strong>CBS</strong> 175.67<strong>CBS</strong> 129826<strong>CBS</strong> 378.94<strong>CBS</strong> 379.94<strong>CBS</strong> 118774<strong>CBS</strong> 1181931001.0087 <strong>CBS</strong> 1259571.00 100 <strong>CBS</strong> 1285051.00 <strong>CBS</strong> 13024099 <strong>CBS</strong> 1237551.00 <strong>CBS</strong> 123756MAFF 306162<strong>CBS</strong> 128549<strong>CBS</strong> 128506<strong>CBS</strong> 128546<strong>CBS</strong> 128547<strong>CBS</strong> 112115<strong>CBS</strong> 129831<strong>CBS</strong> 128526<strong>CBS</strong> 123921C. karstiiC. phyllanthiC. annellatumC. petchiiC. novae-zelandiaeC. boninense861.00<strong>Colletotrichum</strong> sp.100 <strong>CBS</strong> 128544100 1.00C. t<strong>or</strong>ulosum<strong>CBS</strong> 1026671.00 IMI 34792396 <strong>CBS</strong> 128543C. cymbidiicola91 1.00 <strong>CBS</strong> 1237571.00 100 <strong>CBS</strong> 129828C. oncidii1.00 <strong>CBS</strong> 130242<strong>CBS</strong> 128527C. beeveri100 100 <strong>CBS</strong> 1298171.00 1.00C. colombiense<strong>CBS</strong> 129818<strong>CBS</strong> 101059 C. brassicicola100 <strong>CBS</strong> 1253771.00 <strong>CBS</strong> 125376C. hippeastri<strong>CBS</strong> 241.78<strong>CBS</strong> 128525C. parsonsiae100 <strong>CBS</strong> 1285281.00 <strong>CBS</strong> 128501C. brasiliense<strong>CBS</strong> 130241C. dacrycarpi100 <strong>CBS</strong> 1285031.00C. constrictum<strong>CBS</strong> 128504<strong>CBS</strong> 112999 C. gloeosp<strong>or</strong>ioidesFig. 1. One of 958 most parsimonious trees obtained from a heuristic search of the combined ITS, GAPDH, CHS-1, ACT, HIS3, TUB2 and CAL sequences alignment of the<strong>Colletotrichum</strong> boninense <strong>species</strong> <strong>complex</strong>. Bootstrap supp<strong>or</strong>t values (500 replicates) above 70 % (bold) and Bayesian posteri<strong>or</strong> probability values above 0.95 are shown at thenodes. <strong>Colletotrichum</strong> gloeosp<strong>or</strong>ioides <strong>CBS</strong> 112999 is used as outgroup. Numbers of ex-type and ex-epitype strains are emphasised in bold.www.studiesinmycology.<strong>or</strong>g7
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Studies in Mycology (ISSN 0166-0616