Lineage-through-time (LTT) plot for the <i>Cladia aggregata</i> group, including (A) single threshold analysis and (B) multiple threshold analysis of GMYC.

<p>Lines are actual numbers of reconstructed lineages for the clade. Time is expressed as a proportion of the total time since the first cladogenesis event inferred for the taxon. The sharp increase in branching rate, corresponding to the transition from interspecies to intraspecies branching events, is indicated by the red line(s).</p

Likelihood scores for STEM analysis of species delimitation scenarios (k = number of parameters, high Δ lnL means high support for a given scenario).

<p>Likelihood scores for STEM analysis of species delimitation scenarios (k =  number of parameters, high Δ lnL means high support for a given scenario).</p

Homoplasy measures of phenotypical characters and their association with phylogenetic structure in the <i>Cladia aggregata</i> complex.

<p>Homoplasy measured using the consistency index (CI) and retention index (RI). Low values of these point toward homoplasy. The morphologically deviating <i>C. moniliformis</i> was excluded from the contingency table tests (*Only additional putative species tested for the 12-species scenario).</p

Ultrametric gene genealogy and clusters of specimens recognized as putative species by the single-threshold method of GMYC.

<p>Nodes of genetic clusters recognized as putative species are highlighted in red.</p

Maximum Likelihood tree depicting relationships within the <i>Cladia aggregata</i> complex on the basis of a concatenated data set including nuITS, IGS, protein-coding GAPDH and protein -coding Mcm7 sequences and estimated using partitioned ML analysis.

<p>Bootstrap support equal or above 70% is shown (ML) and posterior probabilities equal or above 0.95 are indicated as bold branches. The purple (single threshold) and green (multiple thresholds) shades represented species recognized by GMYC method.</p

Genealogical concordance.

<p>Presence of clades and ML bootstrap support values of putative species as suggested by the a) single threshold and b) multiple threshold methods of GMYC (+ = present, but not supported; − = not present).</p><p>Single threshold method.</p

Sequence characteristics of sampled markers used in the present study.

<p>Including alignment length (number of base pairs); variable sites for each sampled locus; and locus-specific model of evolution identified using the Akaike information criterion in JMODELTEST.</p

Using Phylogenetic and Coalescent Methods to Understand the Species Diversity in the <em>Cladia aggregata</em> Complex (Ascomycota, Lecanorales)

<div><p>The <em>Cladia aggregata</em> complex is one of the phenotypically most variable groups in lichenized fungi, making species determination difficult and resulting in different classifications accepting between one to eight species. Multi-locus DNA sequence data provide an avenue to test species delimitation scenarios using genealogical and coalescent methods, employing gene and species trees. Here we tested species delimitation in the complex using molecular data of four loci (nuITS and IGS rDNA, protein-coding GAPDH and Mcm-7), including 474 newly generated sequences. Using a combination of ML and Bayesian gene tree topologies, species tree inferences, coalescent-based species delimitation, and examination of phenotypic variation we assessed the circumscription of lineages. We propose that results from our analyses support a 12 species delimitation scenario, suggesting that there is a high level of species diversity in the complex. Morphological and chemical characters often do not characterize lineages but show some degree of plasticity within at least some of the clades. However, clades can often be characterized by a combination of several phenotypical characters. In contrast to the amount of homoplasy in the morphological characters, the data set exhibits some geographical patterns with putative species having distribution patterns, such as austral, Australasian or being endemic to Australia, New Zealand or Tasmania.</p> </div

Morphological characteristics of the putative <i>Cladia</i> species identified using the multiple threshold method of GMYC.

<p>Habits of A)  =  Putative species 1a ( = <i>C. inflata</i>, Elix 39099 [CANB]); B)  =  Putative species 1b ( = <i>C. deformis</i>, HTL 19994d [F]); C)  =  Putative species 2a (Blanchon 003104a [F]); D)  =  Putative species 2b (HTL 19975e [F]); E)  =  Putative species 3 (HTL 19975f [F]); F)  =  Putative species 4 (SP 286 [RAMK]), G)  =  Putative species 5 (Elix 39100 [CANB]), H) Putative species 6 ( = <i>C. moniliformis</i>, HTL 19991h [F]); I)  =  Putative species 7a (HTL 19976h [F]); J)  =  Putative species 7b ( = <i>C. dumicola</i>, HTL 19993h [F]); K)  =  Putative species 8 (Elix 39131 [CANB]); L)  =  Putative species 9 (HTL 19989o [F]). Scale bars  = 10 mm.</p

Ultrametric gene genealogy and clusters of specimens recognized as putative species by the multiple-threshold method of GMYC.

<p>Nodes of genetic clusters recognized as putative species are highlighted in red, light blue, violet and green.</p