Abstract
Recent taxonomic and DNA sequence-based studies in several groups of lichen-forming fungi have revealed incongruence between the morphological and molecule-based circumscriptions of species. While the cosmopolitan genus Usnea is well-known and easily recognized by the yellowish beard-like thallus with central cord, delimitation of many Usnea species is difficult due to the high variation and complexity of diagnostic characters. In this study, we assessed the monophyly of 18 species from section Usnea occurring in North America and Europe, including sorediate and sexually reproducing taxa with both pendent and shrubby thalli. Six nuclear markers (ribosomal internal transcribed spacer (ITS) and intergenic spacer (IGS), and protein-coding beta-tubulin, MCM7, RPB1 and RPB2) were sequenced for 144 samples. All analyzed loci show weak genetic structure and short branch lengths in single-locus topologies, suggesting recent diversification history of the sampled taxa. Concatenated, multi-locus analyses conducted in Bayesian and maximum likelihood frameworks, as well as coalescent-based species delimitation and species tree methods, recover several distinct clades, some represent traditional morphology-based species (Usnea cavernosa, U. praetervisa, U. silesiaca, U. wasmuthii), while others form clusters of two or more species (Usnea florida–U. subfloridana, U. fulvoreagens–U. glabrescens, U. barbata–U. chaetophora–U. dasopoga–U. diplotypus, U. barbata–U. intermedia–U. lapponica–U. substerilis). We propose synonymization of U. substerilis under U. lapponica. The status of several other species within intermixed clusters requires further evaluation with more extensive sampling and the inclusion of more variable markers before taxonomic consequences can be considered. A new species, Usnea parafloridana is described from Wisconsin, USA.
Similar content being viewed by others
Avoid common mistakes on your manuscript.
Introduction
Incongruence between the morphological circumscriptions of species and phylogenetic delimitation based on DNA sequence data is known from several groups of lichen-forming fungi. In some cases, overestimation of the species diversity based on morphology and chemistry has been demonstrated (Velmala et al. 2009; Leavitt et al. 2011b; Saag et al. 2014; Velmala et al. 2014), while in others, new lineages, often representing undescribed species, have also been found (Wirtz et al. 2006; Wirtz et al. 2008; Lumbsch et al. 2011; Molina et al. 2011; Kraichak et al. 2015b; Singh et al. 2015). Finding and applying the appropriate character sets is one of the most challenging aspects in species delimitation and can be especially difficult in groups with high morphological plasticity. Effectively integrating ecological, biogeographical, and other independent sources of data has provided more robust species delimitations than use of any single kind of data (Edwards and Knowles 2014).
Usnea Dill. ex Adans. represents an iconic example in which a lack of recognizable, diagnostic characters, and the use of homoplastic characters has led to the circumscription of many nonmonophyletic species (Clerc 1998). It is one of the largest genera in the family Parmeliaceae (Lecanorales, Ascomycota), comprising ca. 350 species (Thell et al. 2012). Its members are characterized by beard-like, finely branched pendent or erect thalli with a stiff central axis that is exposed when a branch is stretched and the cortex breaks apart. All Usnea species produce usnic acid in the cortex, giving the thallus a slightly yellow appearance. The monophyletic genus is well circumscribed, conspicuous, and easily recognized even by nonexperts, but the delimitation of many species in this genus is very difficult due to transitional forms and the complexity of diagnostic characters. This genus is also famous for its complicated taxonomy—more than 770 names have been published worldwide and about half of these could be considered synonyms (Clerc 1998), illustrating the necessity for taxonomic revisions in this group.
Several attempts to organize this species-rich genus into higher taxonomic units have been made based solely on morphological traits (Motyka 1936), or together with molecular characters (Ohmura 2001, 2002; Articus 2004a; Wirtz et al. 2006; Truong et al. 2013). Ohmura (2001, 2002) divided the genus Usnea into subgenera Usnea, Dolichousnea, and Eumitria. Articus (2004a) elevated these subgenera to generic rank and supported the earlier view of Neuropogon as a separate genus forming a monophyletic sister clade to the nonmonophyletic Usnea based on internal transcribed spacer (ITS) sequences. Other authors have instead retained either the three (Ohmura and Kanda 2004; Wirtz et al. 2006) or the four (Truong et al. 2013) groups at a subgeneric rank. The majority of Usnea species are included in the subgenus Usnea, which consists of sections (sect.) Usnea, Ceratinea, and according to earlier studies (Ohmura 2001, 2002; Ohmura and Kanda 2004), also Neuropogon. A multi-locus phylogenetic study by Truong et al. (2013) showed that Neuropogon forms a sister clade to subgenus Usnea, and the latter includes four groups, of which clades “Usnea-2” and “Usnea-4” correspond to previously defined sections Usnea and Ceratinea, respectively.
For this study, we focus on the sect. Usnea. It comprises a group of closely related species with a wide distribution across the Northern Hemisphere and includes the type species of the genus—U. florida (L.) Weber ex F.H. Wigg. This group consists of taxa with both pendulous and shrubby growth forms, and also both vegetatively (sorediate/isidiate) and sexually (apotheciate) reproducing species. The variation in lichen secondary metabolites is also high, with most species including more than one chemotype. Traditionally, thallus growth form (shrubby/subpendent/pendent), reproductive mode, ramification type, pigmentation of basal parts, presence of special structures on branches (papillae/tubercules/fibrils), morphology of soralia, presence of isidiomorphs, the morphology and thickness of the cortex, the medulla and the axis, and lichen chemistry have proven to be useful characters in delimiting taxa in Usnea (Clerc 2011). Many species exhibit transitional forms, and this has led to uncertainties in species boundaries and taxonomic confusion. Previous molecular studies, including species from sect. Usnea, have shown that some morphological species belonging in this group are monophyletic (Kelly et al. 2011; Saag et al. 2011; Truong et al. 2013); however, these analyses included only a few specimens per species. In contrast, the sequence-based study of Saag et al. (2011) evaluated the monophyly of nine shrubby species from sect. Usnea and found only U. wasmuthii Räsänen monophyletic—illustrating the extent of conflict between genetic data and traditional phenotypic species boundaries in sect. Usnea.
A rapid, postglacial radiation has been proposed to explain the short branch lengths and unresolved relationships between taxa in this group (Saag et al. 2011; Truong et al. 2013). Indeed, the genus Usnea is a rapidly evolving group, with exceptionally high speciation rates compared to many other genera in Parmeliaceae (Kraichak et al. 2015a). Estimating phylogenetic relationships and accurately delimiting species in recent rapid radiations can be difficult due to incomplete lineage sorting (ILS) and slow mutation rates in some markers relative to the speciation rate (Sistrom et al. 2013; Willis et al. 2013; Edwards and Knowles 2014; Saag et al. 2014; Velmala et al. 2014; Giarla and Esselstyn 2015). Even though coalescent-based species tree inferences account for ILS and hybridization, they typically require a priori assignment to putative species (Carstens et al. 2013). A priori assignment of species is difficult when phenotypic boundaries are unclear and/or they are in conflict with genetic data. In such cases, genetic clusters or clades, instead of phenotypic species, are used as putative species. However, this is problematic in young species complexes where low divergence of genetic markers and conflicts between loci are common (Saag et al. 2014; Velmala et al. 2014). In groups with recent and rapid diversification (Givnish 2015), vast amounts of genetic data are required to recover species (Wagner et al. 2013), but integrative approaches, including morphological, chemical, or geographical data, can also be effective in delimiting species (Edwards and Knowles 2014).
In our study, we use genetic, morphological, and chemical data to estimate phylogenetic relationships and delimit species boundaries in sect. Usnea. More specifically, we attempt to (1) reconstruct evolutionary relationships in sect. Usnea using DNA data from six markers, (2) identify evolutionarily independent lineages using multiple coalescent-based species delimitation approaches, (3) evaluate the utility of some traditionally used characters, and (4) provide morphology-based perspectives of species in sect. Usnea in light of molecular data.
Material and methods
Taxon sampling and species identification
In total, over 200 samples from the genus Usnea were studied. In this paper, we present a dataset of 144 specimens from which sequences of the six studied markers were obtained. The dataset represents 18 phenotypically circumscribed species from section Usnea collected from different parts of Europe and North America, including specimens with both sorediate and sexual reproductive modes, as well as pendent and shrubby species. Usnea ceratina Ach., from section Ceratinea, was represented with two samples and was selected as an outgroup based on earlier studies (Ohmura 2001; Ohmura and Kanda 2004; Kelly et al. 2011; Truong et al. 2013). Voucher information for samples included in this study is presented in Table 1.
Morphological and anatomical characters of specimens were studied using an Olympus SZ51 stereomicroscope. Thallus chemistry was examined with standardized thin layer chromatography (TLC) or high-performance thin layer chromatography (HPTLC) using solvent system A (Orange et al. 2001). Specimen identifications of the collected material were based on morphological and chemical characters described in previous publications (Halonen et al. 1998, 1999; Halonen 2000; Clerc 2004; McCune 2005; Tõrra and Randlane 2007; Randlane et al. 2009; Clerc 2011). We followed the taxonomy of Randlane et al. (2009) for species known both in Europe and North America, and Halonen (2000) and Clerc (2011) for U. pacificana (Pacific North America) and U. cylindrica (Northern Europe), respectively, as these are not present in Randlane et al. (2009). The orthography of Usnea dasopoga follows Linda in Arcadia (2013). After preliminary identification, the morphology of specimens with poorly expressed diagnostic characters was rechecked in the light of phylogenetic analyses, and the determination was corrected, if reasonable. The thickness of the cortex (C) and medulla (M) was measured, and percentages of the whole width of the measured branch were calculated (CMA values; Clerc 1987) for U. barbata (L.) Weber ex F.H. Wigg., U. chaetophora Stirt., U. cylindrica P. Clerc, U. dasopoga (Ach.) Nyl., U. diplotypus Vain., U. intermedia Jatta, U. lapponica Vain., and U. substerilis Motyka. The measurements were plotted using the BoxPlotR online tool (Spitzer et al. 2014), available at http://boxplot.tyerslab.com. The degree of medullary density was evaluated visually under stereomicroscope following the categories as defined in Clerc (2011). Significant difference in structure thickness between studied morphological species and genetic clusters was tested with the nonparametric Kruskal-Wallis test using the online tool at http://www.mathcracker.com/kruskal-wallis.php.
Molecular methods
The newly collected samples were carefully examined under a stereomicroscope for the presence of lichenicolous and other contaminating fungi. About 5 mg of vegetative thallus from each specimen was ground in 2 ml microtubes. Total genomic DNA was extracted using the High Pure PCR Template Preparation Kit (Roche Diagnostics, Mannheim, Germany) according to the manufacturer’s instructions, with an extra phase separation step using chloroform or alternatively using the Prepease DNA Isolation Kit (USB, Cleveland, Ohio, USA) following the plant leaf extraction protocol. Sequence data for six fungal nuclear markers were generated: two loci from the nuclear ribosomal cistron, the entire internal transcribed spacer (ITS) region and partial intergenic spacer (IGS); and fragments from four low-copy protein-coding genes, beta-tubulin (Bt), MCM7, and RPB1 and RPB2 (domains 6–7). Ready-To-Go PCR Beads (GE Healthcare, Pittsburgh, PA, USA) or 12.5 μl PCR Master Mix 2× (Fermentas) were used for polymerase chain reaction (PCR) amplifications, following the manufacturer’s instructions. PCR cycling parameters for amplifying ITS, IGS, Bt, and RPB1 followed Wedin et al. (2009) and Schmitt et al. (2009) for MCM7. For RPB2, the cycling parameters were initial denaturation for 10 min at 94 °C, followed by 35 cycles of 45 s at 94 °C, 50 s at 50 °C, 1 min at 72 °C, and a final elongation for 10 min at 72 °C or touch-down PCR with initial denaturation for 4 min at 95 °C, followed by 6 cycles of 30 s at 95 °C, 30 s at 55–50 °C, 1 min at 72 °C, and 30 cycles of 30 s at 95 °C, 30 s at 49 °C, 1 min at 72 °C, and a final elongation for 5 min at 72 °C. Touch-down PCR following Lindblom and Ekman (2006) was also used in some cases for IGS, Bt, MCM7, RPB1 (IGS protocol of 55–40 °C) and ITS (IGS protocol of 66–56 °C). Amplification of low-copy genes MCM7, RPB1, and RPB2 usually required a nested PCR approach to obtain high-quality sequences. Using the newly generated RPB1 and RPB2 primers in the nested-PCR second step increased the PCR success of these genes to the level of other markers. Primers used in PCR amplifications and cycle sequencing temperature profiles are shown in Table 2. All PCR products were stained with ethidium bromide and visualized on a 1 % agarose gel. Successful PCR products were purified with ExoSAP-IT (USB, Ohio, USA) or via SAP/EXO treatment (Fermentas). Complementary strands of DNA were sequenced using the BigDye Terminator v3.1 Ready Reaction Cycle Sequencing Kit (Applied Biosystems, Foster City, CA, USA) with the same primers used for PCR amplifications. The products were run on ABI 3730xl DNA Analyzers (Applied Biosystems) in the DNA Genotyping and Sequencing Core Facility of the Estonian Biocentre and Institute of Molecular and Cell Biology at the University of Tartu (Tartu, Estonia), or in the Pritzker Laboratory for Molecular Systematics at the Field Museum (Chicago, IL, USA).
Data analyses
Sequence alignment
Complementary sequence strands were viewed in 4Peaks (mekentosj.com), and assembled and edited in Sequencher v4.2 (Gene Codes Corp., Ann Arbor, Michigan, USA) and Mesquite v2.75 (Maddison and Maddison 2011). Sequence identity was checked using the “megaBLAST” function in GenBank (Madden 2002). Alignments were performed using the program MAFFT v7 (Katoh and Standley 2013) where the G-INS-i alignment algorithm (Katoh and Toh 2008) with “1PAM/K = 2” scoring matrix was implemented for all loci. For protein-coding genes, the offset value of 0.8 was applied. MEGA 5.1 (Tamura et al. 2011) was used to quantify basic parameters of genetic variability, including the number of variable and parsimony informative sites for the whole matrices and section Usnea only, and estimates of average evolutionary divergence within section Usnea. Standard error estimates were obtained by a bootstrap procedure (1000 replicates). Analyses were conducted using the Kimura 2-parameter model (Kimura 1980). The rate variation among sites was modeled with a gamma distribution (shape parameter = 6).
Single gene analyses
Single-locus alignments were analyzed using both maximum likelihood (ML) and a Bayesian approach. The ML criterion was implemented in the program RAxML v7.3.1 (Stamatakis 2006) where the evolutionary model for each single-locus dataset was set to GTRGAMMA and branch supports were assessed using 1000 “fastbootstrap” replicates (Stamatakis et al. 2008). Bayesian analyses (B/MCMC) were conducted using BEAST v1.7.2 (Drummond et al. 2012). DNA sequence evolution models for each marker were chosen in jModeltest v2.1.4 (Darriba et al. 2012) using the AIC criterion (Akaike 1974). A likelihood ratio test (LRT) was used to establish the applicability of a strict molecular clock, using clock and nonclock trees obtained in MrBayes v3.1.2 (Huelsenbeck and Ronquist 2001; Ronquist et al. 2012). In MrBayes default, priors were used except for the partition-specific rates prior that was set to “variable” (flat Dirichlet). Substitution models were set as chosen in jModeltest and are shown in Table 3. Two simultaneous analyses were run for 10 million generations, both with four chains and each starting from random trees. The LRT rejected a strict clock, and after preliminary tests with different settings, an exponential relaxed clock was applied in the BEAST analyses with a Yule model for branching events. Two independent BEAST analyses for each locus were run for 10 million generations, sampling every 1000th generation. We assessed convergence by examining likelihood plots and various statistics’ effective sample sizes (ESS) values for various parameter estimates in Tracer v1.5 (Rambaut and Drummond 2007). The runs were combined in LogCombiner v1.7.4 (Rambaut and Drummond 2012a), with the first 10 % of trees discarded as burn-in. All ESS values for combined runs were over 200. Trees were summarized with TreeAnnotator v1.7.4 (Rambaut and Drummond 2012b) and visualized in FigTree v1.3.1 (Rambaut 2009).
Data congruence, recombination, and gene concatenation analyses
Gene trees do not always reflect species relationships due to gene tree estimation errors, introgression, gene paralogy, and/or deep coalescence (Maddison 1997; Edwards 2009; Knowles and Kubatko 2010). Concatenation allows better estimation of phylogenetic relationships and species boundaries (Wiens 1998; Leaché 2009) and proves especially important in cases of low variation in sequence data and low resolution of gene trees (Spinks et al. 2013; Willis et al. 2013). Before combining the datasets, agreement between single-locus trees was evaluated. First, trees were visually compared to check for topological differences between ML and B/MCMC approaches, and for strongly supported conflicts between the loci (Mason-Gamer and Kellogg 1996). A conflict was considered strong when supported by both tree construction methods (≥70 % for ML trees and ≥95 % for B/MCMC trees). Second, the recombination detection package RDP v4 (Martin et al. 2010) and the GARD method (Kosakovsky Pond et al. 2006), implemented in the Datamonkey server (Delport et al. 2010), were used to scan for possible recombination events in all matrices. The following methods in the RDP package were tested: RDP (Martin and Rybicki 2000), GENECONV (Padidam et al. 1999), Chimaera (Posada and Crandall 2001), Maxchi (Maynard Smith 1992), Bootscan (Gibbs et al. 2000; Martin et al. 2005), SiSscan (Weiller 1998; Gibbs et al. 2000), PhylPro (Weiller 1998), and 3Seq (Boni et al. 2007).
We then conducted ML and B/MCMC analyses on the concatenated six-locus dataset. In RAxML v7.3.1 (Stamatakis 2006; Stamatakis et al. 2008), each locus was treated as a separate partition with its own mutation rate and parameters. We used the same substitution models and parameters as in the single-locus analyses. Six independent B/MCMC analyses were run in BEAST v1.7.4 (Drummond et al. 2012), each for 200 million generations, sampling every 2000, and starting with a UPGMA tree. Convergence and burn-in length were assessed using Tracer v1.5. The first 10,000 trees were discarded as burn-in, and independent runs were combined in LogCombiner, resampling every 8000th tree (Rambaut and Drummond 2012a). A maximum clade credibility (MCC) tree, with posterior probabilities (PP) as branch support, was constructed in TreeAnnotator and visualized in FigTree. Alternatively, we conducted concatenated analyses for the dataset where strongly supported conflicts between gene trees (identified by visual comparison of trees) were discarded. For this, 17 samples were removed, and a 6-locus dataset of 127 specimens was analyzed in ML and B/MCMC approach. The same evolutionary models and analysis parameters as described above were used.
Species delimitation and phylogeny under the multispecies coalescent model
The multispecies coalescent model is a widely applied approach for species tree estimation, but more recently also for species delimitation (Yang and Rannala 2010; Jones et al. 2014; Yang and Rannala 2014). To estimate putative species in our study group, we implemented the package STACEY v1.0.1 (Jones 2015) in BEAST v2.2 (Bouckaert et al. 2014). The first part of this method works similarly to *BEAST (Heled and Drummond 2010), but with the difference that every individual can be treated as a potential species, and minimal split heights in species or minimal clusters tree (SMC-tree) are collapsed with a birth-death-collapse prior. This prior is controlled with CollapseHeight (ε) and CollapseWeight (ω) parameters, that were set in our analysis at 1.0E-4 and estimated β(4;2), respectively. Substitution models and other parameters were set as in the BEAST analysis of the concatenated data as described above. Ten MCMC analyses were run for 200 million generations, sampling every 4000 generations. Parameter ESS values were above 130. The resulting SMC-trees were combined in LogCombiner, resampling every 8000 after removing 10 % as burn-in. A maximum clade credibility tree with PP support values was constructed in TreeAnnotator and visualized in FigTree. Assignment of individuals into minimal clusters was then assessed in SpeciesDelimitationAnalyser (Jones et al. 2014) where collapseHeight was set to one fraction lower than ε (τ = 0.001). The output of posterior probabilities of individuals belonging in the same cluster was visualized in a similarity matrix constructed in R v2.15.1 (R Core Team 2014).
Additionally, we conducted species tree analysis implemented in BEAST v1.8.0 (*BEAST; Heled and Drummond 2010). *BEAST is widely used in constructing species trees but requires the user to assign samples a priori to putative lineages (Carstens et al. 2013). We used results from STACEY and gene concatenation analyses to delineate candidate species. Not only all strongly supported (PP ≥ 0.95) minimal clusters from STACEY but also the weakly supported lineages “glabrescens” (PP = 0.81) and “pacificana” (n.a.), with 8 and 1 accessions, respectively, were considered as candidate species. Altogether, 13 candidate species were delimited (excl. outgroup) and assigned in the *BEAST analysis. Independent evolutionary models were set for each locus (see Table 3) with an uncorrelated relaxed exponential clock (Drummond et al. 2006). We selected a Yule tree prior and “piecewise linear with constant root” as the population size model. Two independent MCMC analyses were run for 300 million generations, sampling every 5000 steps and excluding the first 90 million generations of each run as burn-in. Convergence of runs was assessed in Tracer v1.5; ESS of parameters were all above 200, and the trees from two runs were summarized using LogCombiner and TreeAnnotator. An MCC tree with PP support values was constructed in TreeAnnotator and visualized in FigTree.
To test species boundaries in the studied Usnea taxa, the marginal posterior probabilities of speciation events were calculated for the 13 minimal clusters or species identified in the STACEY analysis using the program BP&P v3 (Yang and Rannala 2014). The method uses reversible-jump Markov chain Monte Carlo (rjMCMC) algorithms to estimate the posterior distribution of different species delimitation models. BP&P accommodates the species phylogeny, represented by a user-specified guide tree, and accounts for lineage sorting due to ancestral polymorphism. BP&P v3 includes the nearest-neighbor interchange (NNI) algorithm that allows changes in species tree topology (Yang and Rannala 2014). The species trees from *BEAST analyses were used to generate a fully resolved guide tree. We used both algorithms 0 and 1 in BP&P. Theta (θ) and tau (τ) gamma priors were assessed using species tree analyses and were set to G(2, 259) and G(2, 57) corresponding to distribution means of 0.0077 and 0.0351, respectively. Preliminary analyses were run with various fine-tuning parameters to find appropriate values. Each rjMCMC analysis was run for 200,000 generations sampling every five with a burn-in of 20,000 and run at least twice to confirm consistency of results.
Results
Molecular data
We were able to generate high-quality sequences of all six loci for 144 specimens, resulting in 864 sequences; these specimens were used for the molecular analyses reported here. Six additional specimens of the new species Usnea parafloridana had sequences of five loci (Table 1); they are included in the reports of morphology and chemistry but not in the reported molecular analyses. Online Resources 2 and 3 include concatenated phylogenies of the Usnea fulvoreagens and U. glabrescens clade, and U. parafloridana clade, respectively, where additional specimens with incomplete sequence data (one to five sequenced loci) have been added (specimens included in Table 1). Sequences generated for this study have been deposited in GenBank under accession nos. KU351849–KU352712 (Table 1) and full single locus matrices and trees in TreeBASE, under study number S18645 (https://treebase.org/). The combined dataset for phylogenetic analyses included 3225 aligned nucleotides (ITS 495 bp, IGS 354 bp, Bt 341 bp, MCM7 541 bp, RPB1 728 bp, RPB2 776 bp). The summary statistics of studied loci with their genetic variability are given in Table 3. The overall genetic variability in all loci was low considering that 19 species from different locations in Europe and North America were included. The highest number of variable sites was recovered in RPB2 (n = 118), although both the RPB2 and RPB1 markers gave the lowest percentage of parsimony informative (PI) sites compared to the matrix length (n = 73, 9.4 % and n = 64, 8.9 %, respectively). MCM7 had the highest number of PI sites (n = 79) but relative to the marker’s length, IGS was the most informative from the studied loci (n = 69, 19.5 %). In sect. Usnea, the highest overall mean genetic distance was in IGS (0.026 subst./bp) and the lowest was in the protein-coding genes RPB2 (0.009 subst./bp), Bt (0.011 subst./bp), and RPB1 (0.011 subst./bp). Sect. Usnea with 142 sequences included 317 PI sites in the concatenated matrix, constituting 9.8 % of the full length, and the average evolutionary divergence over sequence pairs was estimated 0.013 subst./bp.
Data congruence and recombination
No credible recombination events were detected within or between loci with any tested recombination detection methods. By visual comparison, no strong conflicts were found between inference methods, but several conflicts were found between loci (see Online Resource 1 for single-locus trees). As the nodal support in individual gene topologies was generally low, most of the conflicts were only weakly supported and were often within delimited clades. Concatenated analysis where strongly supported conflicts between gene trees were discarded resulted in similar topology, but with even weaker branch supports. We concluded that data exclusion diminished tree construction power more significantly than strongly supported conflicts distort phylogeny and proceeded with the full dataset of 144 taxa.
Single-locus and concatenated gene trees
The single-locus gene trees inferred from ML analyses together with nonparametric bootstrap probability (BP) and posterior probability (PP) values from Bayesian inference are given in Online Resource 1 (Fig. S1–S6). Clades with BP ≥ 70 and PP ≥ 0.95 were considered strongly supported. In general, individual gene trees showed weak genetic structure and short branch lengths for all studied loci. Similar results with no significant topological or branch support differences were obtained with both applied inferences. Nodal supports in gene trees for significant clades from the concatenated analyses are summarized in Table 4.
The majority-rule consensus tree with posterior probabilities from the Bayesian six-locus concatenation analysis applied in BEAST, together with nonparametric ML bootstrap support from RAxML, is shown in Fig. 1. Combining loci allowed better differentiation among samples. Even though the backbone of the tree remains poorly resolved, several strongly supported groups are revealed: (1) the Usnea cavernosa clade (BP = 100; PP = 1); (2) the U. silesiaca clade (BP = 100; PP = 1); (3) a clade of specimens from Wisconsin, USA, with distinct morphology and chemistry that do not clearly fit to any of the currently accepted species and, in this paper, are described as a new shrubby Usnea species, U. parafloridana (BP = 100; PP = 1; see the “Taxonomy” section for detailed description of morphology and chemistry of this species); (4) the U. wasmuthii clade (BP = 94; PP = 1); (5) the fulvoreagens-glabrescens clade (BP = 100; PP = 1) that includes the species U. fulvoreagens, U. glabrescens and U. pacificana; (6) the florida-subfloridana clade (BP = 100; PP = 1) with U. florida and U. subfloridana; (7) the U. praetervisa clade (BP = 100; PP = 1); (8) the barbata-chaetophora-dasopoga-diplotypus clade that includes specimens with the morphology of U. barbata (in part), U. chaetophora, U. cylindrica, U. dasopoga, and U. diplotypus (PP = 0.78); and (9) the barbata-intermedia-lapponica-substerilis clade that includes mainly specimens with the morphology of U. barbata (in part), U. intermedia, U. lapponica, and U. substerilis (BP = 100; PP = 1).
Bayesian 50 % consensus tree of 18 currently accepted Usnea species based on six concatenated loci, inferred by BEAST. Major groups and secondary chemistry are indicated right of the tree. Branch supports are given in circles: Black circles reflect strong support from both inferences (PP ≥ 95 % for BEAST and BP ≥ 70 % for RAxML), and gray circles strong support from BEAST only. Location and laboratory code are given in brackets. Scale bar shows the number of substitutions per site. Secondary metabolites: BAR barbatic acid, BMY baeomycesic acid, DIFF diffractic acid, FPRO/fpro fumarprotocetraric acid, NSTI norstictic acid, PAN pannaric acid, pan6 pannaric acid-6-methylester, PRO/pro protocetraric acid, PSO psoromic acid, SAL salazinic acid, SQU squamatic acid, STI stictic acid, STI-comp stictic acid complex with connorstictic cryptostictic acids, THA thamnolic acid, w/o med comp without medullary compounds, unid rfcl x unidentified substance from reference class x. Capital letters denotes major compounds in chemotype; lower case denotes accessory substances
In the fulvoreagens-glabrescens clade, two strongly supported subclades are present. The clade fulv-1 consists of U. fulvoreagens specimens from Portugal and Wisconsin (USA) and positions at the base of the clade. A second subclade includes a strongly supported group of U. fulvoreagens (four specimens) from northern Europe (fulv-2), U. glabrescens (eight specimens), and U. pacificana (one specimen). “Fulv-1” and “fulv-2” are both strongly supported in the concatenated tree (BP = 100; PP = 1), while the internal structure of the second subclade, and especially the monophyly of U. glabrescens, remains questionable. Florida-subfloridana is divided into two subclades, “subflo-1” and “florida-subloridana s.str.” Subflo-1 consists of a few U. subfloridana specimens from North America and positions at the base of the florida-subfloridana clade. Florida-subfloridana s.str. gathers all U. florida and other U. subfloridana samples. The latter subclade is not monophyletic in any of the gene trees but forms a distinct group in the six-locus concatenated tree with high support from BEAST analysis (BP = 63; PP = 0.96). The substructure inside this clade is weakly supported and inconsistent through different analyses. The monophyletic and strongly supported U. praetervisa clade is positioned with low support at the base of the barbata-chaetophora-dasopoga-diplotypus clade in the concatenated tree (BP = 65; PP = 0.78). The structure inside the barbata-chaetophora-dasopoga-diplotypus clade is weakly supported and does not support separation of any included traditional species. The barbata-intermedia-lapponica-substerilis clade is sister clade to the barbata-chaetophora-dasopoga-diplotypus and praetervisa clades. This relationship is weakly supported in RPB2 (BP = 35; PP = 0.76) and in BEAST concatenated (PP = 0.62) trees. Several weakly supported subclades are present inside this clade that seem to partly correlate with morphology (clades that include taxa with irregular, excavate to concave soralia = U. lapponica and U. substerilis, or clades including taxa with apothecia or small punctiform soralia with isidiomorphs = U. barbata and U. intermedia).
Morphological and chemical characters
Multi-locus, concatenated ML and B/MCMC analyses clustered specimens of Usnea barbata, U. chaetophora, U. cylindrica, U. dasopoga, U. diplotypus, U. intermedia, U. lapponica, and U. substerilis into two closely related clades, where one constituted species mostly with a relatively thick cortex and a thin, compact medulla (i.e., Usnea chaetophora, U. cylindrica, U. dasopoga), while specimens in the other had a relatively thin cortex with a thick and more lax medulla (U. intermedia, U. lapponica, U. substerilis). Specimens of U. barbata were divided between these two clades (Fig. 1). We measured the CMA values and evaluated medullary density of specimens in these two clades and found that members of the barbata-chaetophora-dasopoga-diplotypus clade had a significantly thicker cortex (p = 0.0001) and thinner medulla (p = 0.0007), compared to barbata-intermedia-lapponica-substerilis specimens. Such significant differences were also found in U. barbata samples—specimens related to U. dasopoga had a significantly thicker cortex (p = 0.0059) and thinner medulla (p = 0.0206). The groups differed also in medulla density, where the majority of specimens in the barbata-intermedia-lapponica-substerilis clade had a lax medulla, while those in the barbata-chaetophora-dasopoga-diplotypus clade formed a compact medulla. A similar trend was observed in U. barbata specimens from different clades. Box plots illustrating the differences in cortex and medulla thickness, and bar charts showing the distribution of medulla density categories between genetic groups are shown in Fig. 2. The percentages of cortex (C) and medulla (M) thickness were as follows: [(minimum) average ± standard deviation (maximum)] for barbata-dasopoga-chaetophora-diplotypus clade C = [(9.3) 13.2 ± 2.7 (19.2)], M = [(10) 15.1 ± 3.4 (24)], (n = 21); barbata-intermedia-lapponica-substerilis clade C = [(4.1) 8.3 ± 2.1 (15)], M = [(8.2) 20.1 ± 6.6 (47.6)], (n = 44); U. barbata related to U. dasopoga C = [(9.5) 13.2 ± 2.9 (19.2)], M = [(10.3) 15.6 ± 2.9 (18.9)], (n = 12); and U. barbata related to U. intermedia C = [(4.1) 8.0 ± 2.2 (12.1)], M = [(9.5) 18.6 ± 5.4 (27.4)], n = 14). Morphological species within the clades did not have significantly different CMA values and are not described here (additional information in Table 5).
Box plots of cortex (a, d) and medulla (b, e) thickness measurements and bar charts of medulla density categories (c, f) in clades barbata-chaetophora-dasopoga-diplotypus (bar-das-dip) and barbata-intermedia-lapponica-substerilis (bar-int-lap; first row of charts), and between Usnea barbata specimens from these clades (second row of charts). Box plots show the percentages of the whole width of the measured branch. Center lines are the medians, box limits indicate the 25th and 75th percentiles as determined by R software, whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles, outliers are represented by dots; notches are defined as ±1.85*interquartile range/sqrt(n), which gives roughly 95 % confidence that two medians are different. Bar charts show the distribution of medulla density categories between genetic groups, given in percentage of specimens for density group. Sample points for data are, bar-das-dip clade, n = 20; bar-int-lap clade, n = 43; U. barbata in bar-das-dip clade, n = 11; U. barbata in bar-int-lap clade, n = 13
Chemotypic variation was detected in most of the species studied (Table 5). We do not discuss the variation in accessory substances (e.g., protocetraric acids) or unidentified substances (ref. class 1, 3 and 4) where several new combinations were identified. We concentrate on the major compounds and their distribution over clades from multi-locus analyses. In general, chemotypic variation had some correlation with genetic clusters in sect. Usnea (Fig. 1, Table 5). Salazinic acid was the most dominant compound—it was present as the major compound in U. cavernosa, U. silesiaca, and U. glabrescens, in the barbata-chaetophora-dasopoga-diplotypus clade, and in the barbata-intermedia-lapponica-substerilis clade, and as a minor substance in U. wasmuthii and U. parafloridana. Besides salazinic acid and chemotypes with psoromic (in U. lapponica) and pannaric acid, usually together with pannaric acid-6-methylester and/or salazinic acid (in U. barbata, U. substerilis, and U. lapponica), were found in the barbata-intermedia-lapponica-substerilis clade. Norstictic acid was the major compound in U. praetervisa (in our data together with stictic acid) and U. parafloridana (often together with salazinic acid), and was dominant in the fulvoreagens-glabrescens clade. In this clade, a chemotype with squamatic (major), baeomycesic (major), and barbatic acid (minor) was present from U. pacificana and U. cf. fulvoreagens. In the florida-subfloridana clade, chemotypes with either squamatic acid or with thamnolic acid were both present, but they did not correlate with morphological species or subclades based on molecular data.
Species delimitation and validation analyses under the multispecies coalescent model
A maximum clade credibility SMC-tree, with PP supports from STACEY analysis together with a similarity matrix showing posterior probabilities of individuals belonging in the same cluster, is shown in Fig. 3. The structure and support of the SMC-tree are discussed in more detail under the next paragraph. Minimal distinct clusters in the STACEY analysis that formed monophyletic and strongly supported clades (except pacificana and glabrescens with weaker support) in the SMC-tree were considered as candidate species for subsequent species validation and species tree analyses. These 13 clusters are shown in Fig. 3 and include cavernosa (PP = 1), silesiaca (PP = 1), wasmuthii (PP = 1), parafloridana (PP = 1), subfloridana-1 (PP = 1), florida-subfloridana s.str. (PP = 0.99), fulvoreagens-1 (PP = 1), fulvoreagens-2 (PP = 1), pacificana (n.a.), glabrescens (PP = 0.81), praetervisa (PP = 1), barbata-chaetophora-dasopoga-diplotypus (PP = 0.99), and barbata-intermedia-lapponica-substerilis (PP = 0.99). BP&P results support the presence of 13 groups delimited with highest posterior probability (PP = 0.99204). Posterior probabilities of all delimited lineages were 1.00000 except for pacificana and glabrescens (PP = 0.99204). The 12-species scenario, where pacificana and glabrescens were clustered, was supported weakly (PP = 0.00796).
STACEY maximum clade credibility SMC-tree with posterior probabilities (PP) from STACEY (above branches) and *BEAST (below) analyses together with similarity matrix for the section Usnea dataset. The squares represent posterior probabilities (white = 0, black = 1) for pairs of individuals to belong to the same cluster. The lines in the matrix separate major groups (named above matrix), while labels next to the cartooned clades of the SMC-tree represent the 13 species or minimal clusters delimited in STACEY analysis. Braches and probabilities scores with strong support (PP ≥ 0.95) from STACEY and/or *BEAST analysis are marked in bold. Scale bar shows the number of substitutions per site
Phylogenetic relationships in species tree analyses
The STACEY SMC-tree corresponded with the *BEAST maximum clade credibility species tree, and therefore, only the SMC-tree is shown together with PP supports from STACEY (S-PP) and *BEAST (*PP) analyses (Fig. 3). In species tree analysis, section Usnea formed a monophyletic group on a long branch (S-PP = 0.99; *PP = 1). The backbone of the tree was not supported, and overall supports for the relationships among the putative species remained weak just as in the single-gene analyses and the concatenated multilocus phylogeny. Usnea cavernosa and U. silesiaca positioned more distantly, closer to the base of the section Usnea with weak support. Three strongly supported groups formed in the sect. Usnea. (1) The florida-subfloridana clade clustered with wasmuthii and parafloridana (S-PP = 0.91; *PP = 0.95). Inside this clade, florida-subfloridana s.str. and subfloridana-1 clustered together with low support (S-PP = 0.9; *PP = 0.88), and wasmuthii grouped with parafloridana at low support (S-PP = 0.76; *PP = 0.65). (2) The fulvoreagens-glabrescens clade was strongly supported (S-PP = 0.99; *PP = 0.99), but branch supports for candidate species inside this clade remained low. (3) The putative species barbata-intermedia-lapponica-substerilis clustered, with strong support, with barbata-chaetophora-dasopoga-diplotypus and praetervisa (S-PP = 0.98; *PP = 1), and inside, candidate species barbata-chaetophora-dasopoga-diplotypus and praetervisa clustered together with lower support (S-PP = 0.79; *PP = 0.75).
Discussion
Traditionally used diagnostic taxonomic characters and circumscribed species in light of molecular data
Here, we utilize a six-locus dataset to evaluate traditional, morphology-based species circumscription in sect. Usnea. The genus Usnea is considered one of the most taxonomically difficult macrolichen genera, as a majority of its species are highly variable in morphology and chemistry, and some traditionally used characters have proven to be homoplasious (Clerc 1998; Wirtz et al. 2012). The general appearance of specimens, e.g., whether being pendulous or shrubby and whether bearing apothecia or reproducing vegetatively, has played an important role in species identification. However, thallus length can greatly vary with age and with environmental conditions. Also, reproductive mode can vary between lineages and transitions between sexuality and asexuality, which may occur (Scherrer et al. 2005; Tehler and Irestedt 2007; Cornejo et al. 2009). Furthermore, asexual lineages have been reported as co-occurring with fertile species in the genus Usnea (Articus et al. 2002; Wirtz et al. 2008; Saag et al. 2011). Finally, several generally accepted species from sect. Usnea have been suggested as morphotypes or ecotypes (i.e., Usnea chaetophora as a morphotype of U. barbata and U. dasopoga; U. diplotypus as the epilithic form of U. dasopoga; U. fulvoreagens as the morphotype of U. glabrescens where most of the soralia are deeply excavate; Clerc 2011).
Eighteen morphologically circumscribed species from sect. Usnea were included in our study, but only four of them—Usnea cavernosa, U. praetervisa, U. silesiaca, and U. wasmuthii—were recovered as monophyletic in phylogenetic analyses, while others formed clusters of two or more species (Usnea florida–U. subfloridana, U. fulvoreagens–U. glabrescens–U. pacificana; U. barbata–U. chaetophora–U. cylindrica–U. dasopoga–U. diplotypus; U. barbata–U. intermedia–U. lapponica–U. substerilis). Our data suggest that using most diagnostic morphological characters together with branch anatomy and thallus chemistry are useful for delimiting of some genetic lineages in sect. Usnea, while other clades (e.g., barbata-chaetophora-dasopoga-diplotypus and barbata-intermedia-lapponica-substerilis) have very wide morphological variation (Table 5), and many currently accepted diagnostic morphological characters do not prove useful for delimiting these clades. Despite limited genetic variation, genotyping might be useful for separating groups in sect. Usnea and identifying morphological intermediates, juvenile forms, or subgroups/cryptic species within clades. At the same time, this study demonstrates that several traditional, morphology-based species are in need of reevaluation to specify their actual species boundaries.
Our study supports the view that several nominal species included in sect. Usnea could merely represent intraspecific phenotypes. The barbata-chaetophora-dasopoga-diplotypus clade includes several morphospecies (i.e., U. barbata, U. chaetophora, U. diplotypus, U. cylindrica) that do not separate genetically or chemically. Current data suggest conspecificity of U. chaetophora, U. diplotypus, and U. cylindrica to U. dasopoga, but better sampling of these morphotypes and reevaluation of U. barbata are needed for official taxonomic changes.
Usnea barbata is also present in the barbata-intermedia-lapponica-substerilis clade, together with fertile U. intermedia, and sorediate U. lapponica and U. substerilis. This aggregate is characterized by thin cortex, lax, and thick medulla, not clearly tapering and often foveolate branches, and salazinic acid as the most common strain (see Table 5 for reference to morphospecies). Our analyses show weak clustering of U. intermedia with U. barbata accessions and separation from U. lapponica and U. substerilis. Conspecificity of U. intermedia and U. barbata is also supported by old herbarium material where U. barbata is more often fertile and very much resembles contemporary collections of U. intermedia (Articus 2004b). Usnea lapponica and U. substerilis are considered similar and closely related in morphological studies, differing primarily in the shape of soralia and production of isidiomorphs (Halonen et al. 1998; Randlane et al. 2009; Clerc 2011). Separation of these species is often difficult as intermediate forms occur. Our study supports the close relationship between the phenotypic species. The species show no clear differentiation in anatomy or secondary chemistry, and are intermixed in a cluster in our genetic analyses. The differences in morphology could be explained with the development of soralia and erosion of isidiomorphs. These findings suggest conspecificity of U. lapponica and U. substerilis, and we propose synonymization of U. substerilis under U. lapponica (see the “Taxonomy” section below).
The analyzed species in sect. Usnea have wide distributional ranges, often occurring across the Northern Hemisphere, but they show a low degree of geographical structure within the phylogeny. Instead, secondary metabolites seem to mostly corroborate the phylogenetic clades recovered from our data (Fig. 1). Lichen secondary chemistry has been suggested as an important systematic character in other lichen-forming fungi (Schmitt and Lumbsch 2004; Elix et al. 2009; Spribille et al. 2011), and also in genus Usnea, it is considered important in species delimitation (Clerc 1998; Truong et al. 2013). However, very high chemotypic variation within morphology-based entities may indicate the need for phylogenetic reevaluation of species boundaries as was demonstrated in Usnea cornuta s. l. (Truong et al. 2013). Our data suggest the need for reevaluation of some chemotypes in species (1) U. glabrescens, (2) U. pacificana, and (3) U. wasmuthii.
Usnea glabrescens as currently circumscribed with four different chemotypes (see Table 5) does not form a monophyletic group in our analyses. A single specimen of U. cf. glabrescens with psoromic acid (WAS_29; Switzerland) clustered in the barbata-intermedia-lapponica-substerilis clade. The specimen was examined carefully to rule out an identification mistake, but the morphology, anatomy, and chemistry were identical with U. glabrescens. The rest of the specimens in this study have chemotypes with norstictic acid and position in the fulvoreagens-glabrescens clade. We suppose that psoromic-acid containing specimens of U. glabrescens could be hybrids.
Usnea pacificana is morphologically similar to U. subfloridana but has a unique chemistry containing baeomycesic, barbatic, and squamatic acids. In our analyses, the single specimen of this species positions in the fulvoreagens-glabrescens clade, in the vicinity of U. glabrescens specimens. Sequence data of five loci from an additional specimen collected from California, USA (PAC_01), support the close relationship between U. pacificana and U. glabrescens showing more than 99 % pairwise similarity over the five loci with analyzed U. glabrescens s. str. accessions (see Online Resource 2 for concatenated gene tree of fulvoreagens-glabrescens clade with additional samples having incomplete data). The Usnea pacificana-specific chemotype with baeomycesic acid may be more widespread in the fulvoreagens-glabrescens clade as it was also found in U. cf. fulvoreagens (USN_01) from Portugal.
Five different chemotypes have been described in Usnea wasmuthii, including chemotypes with barbatic acid, salazinic acid, and thamnolic acid (Table 5). The presence of barbatic acid as the major compound was consistent in our U. wasmuthii samples and might be a useful character in identification of the wasmuthii clade. Salazinic acid occurs widely in many other clades in sect. Usnea, and thamnolic acid is generally restricted to the florida-subfloridana clade. Unusual chemotypes could be the result of several factors, including introgression, hybridization, and contaminations from sample handling or misidentifications.
The phenomenon, where otherwise indistinguishable lichen species differ only in reproduction mode, is known as the species-pair concept, first developed by Poelt (1970). A species-pair includes the “primary,” sexually reproducing species and the “secondary,” vegetatively reproducing species. Several species-pairs have been identified in the genus Usnea (i.e., Usnea florida–U. subfloridana; U. intermedia–U. barbata–U. lapponica; U. aurantiaco-atra–U. antarctica; U. perpusilla–U. sphacelata; U. trachycarpa–U. subantarctica), but phylogenetic studies suggest that many of those should be considered conspecific (Articus et al. 2002; Articus 2004b; Seymour et al. 2007; Saag et al. 2011; Wirtz et al. 2012). Our results are in accordance with previous research and do not support independence of the studied species-pairs.
Usnea florida and U. subfloridana have been considered a species-pair where U. florida is the primary, fertile counterpart and U. subfloridana the sterile, secondary counterpart (Clerc 1984). Previous phylogenetic analyses have demonstrated that they do not form a species-pair but instead a clade in which they are intermixed (Articus et al. 2002; Kelly et al. 2011; Saag et al. 2011). Our analyses support synonymy of U. florida and U. subfloridana; however, we do not propose official taxonomic changes due to conservation reasons caused by ecological requirements of these entities (U. florida preferring old deciduous trees in areas with high humidity is threatened or near threatened in many European countries, while U. subfloridana is less ecologically demanding and widespread).
Halonen et al. (1998) suggested that Usnea rigida (Ach.) Röhl. (now synonymized under U. intermedia) could be regarded as the fertile and primary counterpart in the U. rigida aggregate that includes the sterile and only rarely fertile U. barbata, U. lapponica, and U. substerilis. Later, U. intermedia was proposed as the sexually reproducing counterpart for the sorediate U. lapponica (Saag et al. 2011). Our study suggests conspecificity of U. barbata and U. intermedia, but further studies in the U. barbata species complex are needed before taxonomic consequences could be considered (see also the discussion on this group above).
Usnea thallus anatomy has been used to delimit morphological species (Clerc 1998; Clerc 2011). The parameters of the inner structure of a branch (CMA values) were shown to be informative in identification of monophyletic lineages in genus Usnea (Seymour et al. 2007). This is also supported by our data where species with similar ratios for CMA tend to cluster together (clades with Usnea barbata and related species in Fig. 1b). Usnea barbata is very polymorphic; Randlane et al. (2009) have suggested that it may consist of a collection of intergrading taxa. Indeed, the species is polyphyletic in our study forming two groups different in anatomical features (Fig. 2), but at the same time, these characters are partly overlapping and do not allow separation of intermediate forms or “hybrids” unanimously.
Several distinct lineages that do not correspond to previously described morphological taxa were detected within our data—(1) a new shrubby species Usnea parafloridana, (2) a potential cryptic species within U. fulvoreagens, and (3) a strongly supported subclade of U. subfloridana.
Specimens with distinct morphology and chemistry from Wisconsin (USA) form a monophyletic clade that represents an undescribed species, proposed in this paper as Usnea parafloridana sp. nov. This taxon is characterized by a shrubby thallus, with relatively few and thick branches. The type of soralia is most similar to U. subfloridana—punctiform to enlarged and bearing many short isidiomorphs. It is closely related to U. wasmuthii that, however, differs in its medullary chemistry and soralium morphology. For detailed species description and discussion, see the “Taxonomy” section below.
Usnea fulvoreagens is morphologically and chemically similar to U. glabrescens, and the two species cluster together in genetic analyses (Kelly et al. 2011; Saag et al. 2011). The first species is regarded as a morphotype of U. glabrescens in Clerc (2011). In our study, U. fulvoreagens in the current sense is polyphyletic, forming two strongly supported clades within the fulvoreagens-glabrescens clade, but being distinct from U. glabrescens. Both of these clades include specimens from Europe and North America (see Online Resource 2 for phylogeny with additional samples), have chemotypes with norstictic acid, and are morphologically similar. However, the two clades are genetically different enough to represent cryptic species, confirmed also in BP&P analyses.
Clade subfloridana-1 includes U. subfloridana specimens from North America with thamnolic acid (squamatic acid in other North American specimens); it was clearly distinct in the STACEY species delimitation analysis and was not collapsed with other florida-subfloridana in BP&P. However, more data are needed before any strong conclusions can be made.
Gene congruence and species delimitation in a young species complex
The genus Usnea is considered a hyper-diverse group, showing exceptionally high speciation rates compared with many other genera in the family Parmeliaceae (Kraichak et al. 2015a). The success could be explained by key innovations (Sanderson and Donoghue 1996)—such as a pendulous thallus with a central axis and the production of usnic acid in the cortex to better exploit habitats and protect the photobiont from high radiation (McEvoy et al. 2006; Trest et al. 2015). At the same time, individual groups within the genus Usnea are characterized by low genetic variation and unresolved relationships among species (Lumbsch and Wirtz 2011; Saag et al. 2011; Truong et al. 2013). Our data support the previous findings and show little variation and weak phylogenetic signal in the studied loci (ITS, IGS, beta-tubulin, MCM7, RPB1, RPB2) at this phylogenetic scale. Furthermore, strongly supported conflicts were found between our gene trees. Single-locus gene trees proved insufficient to delimit evolutionary groups in sect. Usnea and some clades (e.g., barbata-intermedia-lapponica-substerilis clade, florida-subfloridana clade) gained significant branch support only in the multi-locus analyses (e.g., barbata-intermedia-lapponica-substerilis clade, florida-subfloridana clade). Even so, it is evident that more genetic markers, preferably in highly variable genome regions, are necessary to construct species trees in young diverging groups. Low support along the “backbone” of sect. Usnea probably reflects rapid diversification. Similar high morphological divergence with low genetic variation was demonstrated in genus Bryoria Brodo & D. Hawksw., section Implexae (Velmala et al. 2014). It is possible that both genera, Bryoria and Usnea, are undergoing the rapid diversification for similar reasons. Both have similar pendant habits in which thalli are minimally attached to the substrate and expand into unoccupied space.
Older species have had time to accumulate apomorphies and gene-tree monophyly, while young species often lack monophyly due to ILS. Few apomorphies compared to synapomorphic mutations and conflicting gene trees make inferring the species tree and delimiting species especially challenging in young species complexes (Saag et al. 2014). By visual comparison, several conflicts were found between our gene trees. However, as the nodal support in individual gene topologies was generally low, most of the conflicts were only weakly supported and were often within delimited clades. These can be explained with weak or conflicting phylogenetic signal that generates trees with short branch lengths and low support values. Considering the low divergence in our loci, it is unclear how much incongruence between genes comes from real conflicting phylogenetic signal versus gene tree estimation error due to mutational homoplasy.
In the presence of ILS and/or hybridization, using the multispecies coalescent model to infer species phylogeny is suggested (Carstens and Knowles 2007; Fujita et al. 2012; Carstens et al. 2013), but these methods require assigning samples a priori to putative lineages (Carstens et al. 2013). Species delimitation in sect. Usnea proved especially difficult, as commonly used models that use gene trees to estimate speciation or branching events and identify putative species based on a threshold (we tested The Generalized Mixed Yule Coalescent, GMYC of Pons et al. 2006; Poisson Tree Processes, PTP of Zhang et al. 2013; and O’Meara’s heuristic method, Brownie of O’Meara et al. 2006) failed to find consensus in the number of species and grouping of specimens over replicates and inferences in our data (analyses not shown). We then applied the recently developed coalescent-based species delimitation method STACEY to estimate the species tree and identify independent evolutionary lineages in our group. This method was more consistent over replications, and the resulting SMC-tree correlated well with the concatenated tree and species tree from *BEAST. Even then, we have remained conservative when identifying putative species for the species validation analyses in BP&P and species tree reconstruction in *BEAST, as the branch supports within clades were low in multi-locus analyses.
Taxonomy
The formal taxonomic changes are made here, as proposed in the “Discussion” section.
Usnea lapponica Vain.
Meddeland. Soc. Fauna Fl. Fenn. 48: 173 (1925) – Usnea sorediifera ssp. lapponica (Vain.) Motyka, Wydaw. Muz. Ślask. Katowicach 3: 23 (1930) – Type: Russia, Murmansk region, Lapponia Imandrae, Lovozero, 1887 Kihlman (H, lectotype designated by Clerc 1987: 494).
Syn. Usnea monstruosa Vain., Wydaw. Muz. Ślask. Katowicach 3: 25 (1930). – Usnea arnoldii Motyka, Lich. Gen. Usnea Monogr. 1: 288 (1936) – Usnea fulvoreagens auct. non (Räsänen) Räsänen
Syn. nov. Usnea substerilis Motyka, Lich. Gen. Usnea Monogr. 1: 257 (1936). – Usnea sorediifera var. substerilis (Motyka) Keissl. (1960). – Type: Italy (“Austria”), Bolzano, Gröden, St. Ulrich, above Unterkoffel, 1899 Arnold, Lich. Exs. no. 1538b (W, lectotype, designated by Motyka 1936: 291).
Usnea parafloridana K. Mark, Will-Wolf & Randlane sp. nov.
Type: USA, Wisconsin, Vilas Co., Trout Lake Conifer Swamp State Natural Area; 46.0135° N, −89.6586° W; 27.08.2011, Susan Will-Wolf WW14807: isolates WW_018 (holotype, TU; Fig. 4a, c, e), WW_023 (isotype 1, WIS), WW_013 (isotype 2, F).
Usnea parafloridana K. Mark, Will-Wolf & Randlane sp. nov. – view of general habit (a, b), soralia with isidiomorphs (c), fibrils (d), soralia (e), and branch anatomy (f). Scale bars 7 mm (a, b), 1.5 mm (c), 2 mm (d), 0.4 mm (e), and 0.3 mm (f). Photographed specimens WW14807 (holotype; a, c, e), WW14858 (b, d), and WW14857 (f)
Morphology: thallus shrubby, up to 3–6 cm long, often with relatively few branches; branching mainly isotomic-dichotomous, divergent; lateral branches not narrowed at point of attachment; basal part distinctly jet black, with few annular cracks; papillae verrucose, numerous on main branches and lesser or absent on lateral branches; fibrils few to numerous; soralia small and punctiform when young, enlarging, becoming close to each other but usually staying delimited when mature, more numerous on terminal branches; isidiomorphs numerous, spinulose, relatively short and thick, both on young and mature soralia; cortex thick (9–15 %); medulla thin (10.5–13 %), dense, not pigmented; central cord thick (60–73 %) and white; apothecia not seen (Fig. 4; colour illustrations in online version). Secondary chemistry: usnic acid in cortex; norstictic acid as a major compound, salazinic acid as an accessory substance (present in most examined specimens) in medulla. Ecology: on branches of Abies balsamea, Larix laricina, Picea mariana, or Pinus strobus in cedar swamp, conifer bog and pine plantation with trees over one-hundred years old. Distribution: currently 15 specimens are known from four localities in Wisconsin, USA. Etymology: the species is morphologically somewhat similar to Usnea subfloridana (both taxa have similar shrubby thalli, black basal parts and delimited soralia with numerous isidiomorphs), which phylogenetically appears conspecific with U. florida. The same root “florida” is used in the epithet of the new taxon to underline this morphological similarity while the prefix “para-” indicates phylogenetic distinctness of the species from U. florida and U. subfloridana.
Other specimens examined: USA, Wisconsin: Trout Lake Conifer Swamp State Natural Area, 46.0135° N, −89.6586° W, 27.08.2011, Susan Will-Wolf WW14801, WW14802, WW14808, WW14811, WW14812, WW14813, Matthew P. Nelsen WW14857, WW14858, WW14862; N of Mud Creek, 45.9289° N, −89.5636° W, 27.08.2011, Susan Will-Wolf WW14820; Papoose Creek Pines State Natural Area, 46.1502° N, −89.8562° W, 27.08.2011, Susan Will-Wolf WW14827; Jyme Lake bog in Kemp Biological Station, 45.8392° N, −89.6714° W, 28.08.2011, Susan Will-Wolf WW14863.
Notes: Usnea parafloridana includes specimens from Wisconsin (USA) with distinct morphology and chemistry; it forms a strongly supported monophyletic clade (see Fig. 1 and Online Resource 3 for concatenated gene tree for all examined specimens). This taxon morphologically resembles most Usnea subfloridana, with delimited soralia bearing numerous isidiomorphs, especially on thin and terminal branches. However, it differs in chemistry; the studied specimens produce norstictic acid often together with salazinic acid (see also Online Resource 4 for TLC plate example), while the dominant depsidones in U. subfloridana are thamnolic and squamatic acids. The rare species Usnea praetervisa (in Eastern Asia, Europe, and North America; Fos and Clerc (2000)) is also morphologically similar to U. subfloridana and includes norstictic acid; it therefore could easily be confused with U. parafloridana. The development of soralia in U. praetervisa is different from U. subfloridana (as described in Clerc (2004)); a photograph of U. praetervisa soralia is provided in Clerc (2007)). U. praetervisa is usually more richly branched and chemotypes with norstictic acid together with connorstictic or stictic acids are known. It is genetically related to U. dasopoga, while U. parafloridana is closely related to U. wasmuthii. The latter has different medullary chemistry and shape of soralia (see Table 5 for detailed morphology and chemistry).
References
Akaike, H. (1974). A new look at the statistical model identification. IEEE Transactions on Automatic Control, 19(6), 716–723.
Articus, K. (2004a). Neuropogon and the phylogeny of Usnea s.l. (Parmeliaceae, Lichenized Ascomycetes). Taxon, 53(4), 925–934.
Articus, K. (2004b). Phylogenetic studies in Usnea (Parmeliaceae) and allied genera (Vol. 931, Acta Universitatis Upsaliensis. Comprehensive summaries of Uppsala Dissertations from the Faculty of Science and Technology). Uppsala: Acta Universitatis Upsaliensis.
Articus, K., Mattsson, J.-E., Tibell, L., Grube, M., & Wedin, M. (2002). Ribosomal DNA and β-tubulin data do not support the separation of the lichens Usnea florida and U. subfloridana as distinct species. Mycological Research, 106(4), 412–418.
Boni, M. F., Posada, D., & Feldman, M. W. (2007). An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics, 176, 1035–1047.
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., et al. (2014). BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology, 10(4), e1003537. doi:10.1371/journal.pcbi.1003537.
Carbone, I., & Kohn, L. M. (1999). A method for designing primer sets for speciation studies in filamentous Ascomycetes. Mycologia, 91(3), 553–556.
Carstens, B. C., & Knowles, L. L. (2007). Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Systematic Biology, 56(3), 400–411.
Carstens, B. C., Pelletier, T. A., Reid, N. M., & Satler, J. D. (2013). How to fail at species delimitation. Molecular Ecology, 22(17), 4369–4383.
Clerc, P. (1984). Contribution à la revision de la systématique des Usnées (Ascomycotina, Usnea) d'Europe. I. Usnea florida (L.) Wigg. emend. Clerc. Cryptogamie. Bryologie and Lichénologie, 5, 333–360.
Clerc, P. (1987). Systematics of the Usnea fragilescens aggregate and its distribution in Scandinavia. Nordic Journal of Botany, 7(4), 479–495.
Clerc, P. (1998). Species concepts in the genus Usnea (lichenized Ascomycetes). The Lichenologist, 30(4–5), 321–340.
Clerc, P. (2004). Notes on the genus Usnea Adanson. II. Bibliotheca Lichenologica, 88, 79–90.
Clerc, P. (2007). Usnea. In T. H. Nash III, C. Gries, & F. Bungartz (Eds.), Lichen flora of the Greater Sonoran Desert Region (Vol. 3) (p. 327). Tempe: Arizona State.
Clerc, P. (2011). Usnea. In A. Thell, & R. Moberg (Eds.), Nordic Lichen Flora 4. (pp. 107–127): Museum of Evolution, Uppsala University.
R Core Team (2014). R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org
Cornejo, C., Chabanenko, S., & Scheidegger, C. (2009). Phylogenetic analysis indicates transitions from vegetative to sexual reproduction in the Lobaria retigera group (Lecanoromycetidae, Ascomycota). The Lichenologist, 41(03), 275–284.
Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9(8), 772–772.
Delport, W., Poon, A. F., Frost, S. D., & Pond, S. L. (2010). Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics, 26, 2455–2457.
Drummond, A. J., Ho, S. Y., Phillips, M. J., & Rambaut, A. (2006). Relaxed phylogenetics and dating with confidence. PLoS Biology, 4(5), e88. doi:10.1371/journal.pbio.0040088.
Drummond, A. J., Suchard, M. A., Xie, D., & Rambaut, A. (2012). Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29(8), 1969–1973.
Edwards, S. V. (2009). Is a new and general theory of molecular systematics emerging? Evolution, 63(1), 1–19.
Edwards, D. L., & Knowles, L. L. (2014). Species detection and individual assignment in species delimitation: can integrative data increase efficacy? Proceedings of the Royal Society B, 281(1777), 20132765. doi:10.1098/rspb.2013.2765.
Elix, J. A., Corush, J., & Lumbsch, H. T. (2009). Triterpene chemosyndromes and subtle morphological characters characterise lineages in the Physcia aipolia group in Australia (Ascomycota). Systematics and Biodiversity, 7(4), 479–487.
Fos, S., & Clerc, P. (2000). The lichen genus Usnea on Quercus suber in Iberian cork-oak forests. The Lichenologist, 32(1), 67–88.
Fujita, M. K., Leaché, A. D., Burbrink, F. T., McGuire, J. A., & Moritz, C. (2012). Coalescent-based species delimitation in an integrative taxonomy. Trends in Ecology & Evolution, 27(9), 480–488.
Gardes, M., & Bruns, T. D. (1993). ITS primers with enhanced specificity for basidiomycetes – application to the identification of mycorrhizae and rusts. Molecular Ecology, 2(2), 113–118.
Giarla, T. C., & Esselstyn, J. A. (2015). The challenges of resolving a rapid, recent radiation: empirical and simulated phylogenomics of Philippine shrews. Systematic Biology. doi:10.1093/sysbio/syv029.
Gibbs, M. J., Armstrong, J. S., & Gibbs, A. J. (2000). Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics, 16, 573–582.
Givnish, T. J. (2015). Adaptive radiation versus ‘radiation’ and ‘explosive diversification’: why conceptual distinctions are fundamental to understanding evolution. New Phytologist, 207(2), 297–303.
Glass, N. L., & Donaldson, G. C. (1995). Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous Ascomycetes. Applied and Environmental Microbiology, 61(4), 1323–1330.
Halonen, P. (2000). Usnea pacificana, sp. nov. and U. wasmuthii (Lichenized Ascomycetes) in Pacific North America. The Bryologist, 103(1), 38–43.
Halonen, P., Clerc, P., Goward, T., Brodo, I. M., & Wulff, K. (1998). Synopsis of the genus Usnea (lichenized Ascomycetes) in British Columbia, Canada. Bryologist, 101, 36–60.
Halonen, P., Myllys, L., Ahti, T., & Petrova, O. V. (1999). The lichen genus Usnea in East Fennoscandia. III. The shrubby species. Annales Botanici Fennici, 36, 235–256.
Heled, J., & Drummond, A. J. (2010). Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution, 27(3), 570–580.
Huelsenbeck, J. P., & Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17(8), 754–755.
Jones, G. R. (2015). STACEY: species delimitation and phylogeny estimation under the multispecies coalescent. doi:10.1101/010199. Preprint in biorxiv.org.
Jones, G., Zeynep, A., & Oxelman, B. (2014). DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. Bioinformatics, 31, 991–998.
Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution, 30(4), 772–780.
Katoh, K., & Toh, H. (2008). Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics, 9(4), 286–298.
Kelly, L. J., Hollingsworth, P. M., Coppins, B. J., Ellis, C. J., Harrold, P., Tosh, J., et al. (2011). DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context. New Phytologist, 191(1), 288–300.
Kimura, M. (1980). A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111–120.
Knowles, L. L., & Kubatko, L. S. (2010). Estimating species trees: practical and theoretical aspects. Hoboken: Wiley-Blackwell.
Kosakovsky Pond, S. L., Posada, D., Gravenor, M. B., Woelk, C. H., & Frost, S. D. W. (2006). GARD: a genetic algorithm for recombination detection. Bioinformatics, 22(24), 3096–3098.
Kraichak, E., Divakar, P. K., Crespo, A., Leavitt, S. D., Nelsen, M. P., Lücking, R., et al. (2015a). A tale of two hyper-diversities: diversification dynamics of the two largest families of lichenized fungi. Scientific Reports, 5, 10028. doi:10.1038/srep10028.
Kraichak, E., Lücking, R., Aptroot, A., Beck, A., Dornes, P., John, V., et al. (2015b). Hidden diversity in the morphologically variable script lichen (Graphis scripta) complex (Ascomycota, Ostropales, Graphidaceae). Organisms Diversity & Evolution, 15(3), 447–458.
Leaché, A. D. (2009). Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus). Systematic Biology, 58(6), 547–559.
Leavitt, S. D., Fankhauser, J. D., Leavitt, D. H., Porter, L. D., Johnson, L. A., & St. Clair, L. L. (2011a). Complex patterns of speciation in cosmopolitan "rock posy" lichens – discovering and delimiting cryptic fungal species in the lichen-forming Rhizoplaca melanophthalma species-complex (Lecanoraceae, Ascomycota). Molecular Phylogenetics and Evolution, 59(3), 587–602.
Leavitt, S. D., Johnson, L., & St. Clair, L. L. (2011b). Species delimitation and evolution in morphologically and chemically diverse communities of the lichen-forming genus Xanthoparmelia (Parmeliaceae, Ascomycota) in western North America. American Journal of Botany, 98(2), 175–188.
Linda in Arcadia. (2013). Usnea dasopoga, a name to be reinstated for U. filipendula, and its orthography. Taxon, 62(3), 604–605.
Lindblom, L., & Ekman, S. (2006). Genetic variation and population differentiation in the lichen-forming ascomycete Xanthoria parietina on the island Storfosna, central Norway. Molecular Ecology, 15(6), 1545–1559.
Liu, Y. L., Whelen, S., & Hall, B. D. (1999). Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Molecular Biology and Evolution, 16, 1799–1808.
Lumbsch, H. T., & Wirtz, N. (2011). Phylogenetic relationships of the neuropogonoid core group in the genus Usnea (Ascomycota: Parmeliaceae). The Lichenologist, 43(6), 553–559.
Lumbsch, H. T., Ahti, T., Altermann, S., Amo De Paz, G., Aptroot, A., Arup, U., et al. (2011). One hundred new species of lichenized fungi: a signature of undiscovered global diversity. Phytotaxa, 18, 1–127.
Madden, T. (2002). The BLAST sequence analysis tool. In J. McEntyre & J. Ostell (Eds.), The NCBI handbook. Bethesda: National Center for Biotechnology Information.
Maddison, W. P. (1997). Gene trees in species trees. Systematic Biology, 46(3), 523–536.
Maddison, W. P., & Maddison, D. R. (2011). Mesquite: a modular system for evolutionary analysis. Version 2.75. http://mesquiteproject.org.
Martin, D., & Rybicki, E. (2000). RDP: detection of recombination amongst aligned sequences. Bioinformatics, 16, 562–563.
Martin, D. P., Posada, D., Crandall, K. A., & Williamson, C. (2005). A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Research and Human Retroviruses, 21, 98–102.
Martin, D. P., Lemey, P., Lott, M., Moulton, V., Posada, D., & Lefeuvre, P. (2010). RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics, 26(19), 2462–2463.
Mason-Gamer, R. J., & Kellogg, E. A. (1996). Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Systematic Biology, 45(4), 524–545.
Matheny, P. B., Liu, Y. J., Ammirati, J. F., & Hall, B. D. (2002). Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe, Agaricales). American Journal of Botany, 89(4), 688–698.
Maynard Smith, J. (1992). Analyzing the mosaic structure of genes. Journal of Molecular Evolution, 34, 126–129.
McCune, B. (2005). Usnea in Pacific Northwest. http://people.oregonstate.edu/~mccuneb/Usnea.PDF Accessed 25 Feb 2015.
McEvoy, M., Nybakken, L., Solhaug, K. A., & Gauslaa, Y. (2006). UV triggers the synthesis of the widely distributed secondary lichen compound usnic acid. Mycological Progress, 5(4), 221–229.
Molina, M. C., Del-Prado, R., Divakar, P. K., Sánchez-Mata, D., & Crespo, A. (2011). Another example of cryptic diversity in lichen-forming fungi: the new species Parmelia mayi (Ascomycota: Parmeliaceae). Organisms Diversity & Evolution, 11(5), 331–342.
Motyka, J. (1936). Lichenum generis Usnea studium monographicum. Pars systematica (2 vol. in 1 bd.). Lublin: Editio et proprietas auctoris.
Ohmura, Y. (2001). Taxonomic study of the genus Usnea (lichenized Ascomycetes) in Japan and Taiwan. Journal of Hattori Botanical Laboratory, 90, 1–96.
Ohmura, Y. (2002). Phylogenetic evaluation of infrageneric groups of the genus Usnea based on ITS regions in rDNA. Journal of Hattori Botanical Laboratory, 92, 231–243.
Ohmura, Y., & Kanda, H. (2004). Taxonomic status of section Neuropogon in the genus Usnea elucidated by morphological comparisons and ITS rDNA sequences. The Lichenologist, 36(3–4), 217–225.
O'Meara, B. C., Ané, C., Sanderson, M. J., & Wainwright, P. C. (2006). Testing for different rates of continuous trait evolution using likelihood. Evolution, 60(5), 922–933.
Orange, A., James, P. W., & White, F. J. (2001). Microchemical methods for the identification of Lichens. London: British Lichen Society.
Padidam, M., Sawyer, S., & Fauquet, C. M. (1999). Possible emergence of new geminiviruses by frequent recombination. Virology, 265, 218–225.
Poelt, J. (1970). Das Konzept der Artenpaare bei den Flechten. Vorträge aus dem Gesamtgebiet der Botanik, Neue Folge, 4, 187–198.
Pons, J., Barraclough, T. G., Gomez-Zurita, J., Cardoso, A., Duran, D. P., Hazell, S., et al. (2006). Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology, 55(4), 595–609.
Posada, D., & Crandall, K. A. (2001). Evaluation of methods for detecting recombination from DNA sequences: computer simulations. PNAS, 98, 13757–13762.
Rambaut, A. (2009). FigTree. Version 1.3.1. http://tree.bio.ed.ac.uk/software/figtree. Edinburgh: Institute of Evolutionary Biology, University of Edinburgh.
Rambaut, A., & Drummond, A. (2007). Tracer. Version 1.4. http://beast.bio.ed.ac.uk.
Rambaut, A., & Drummond, A. (2012a). LogCombiner Version 1.7.2. http://beast.bio.ed.ac.uk.
Rambaut, A., & Drummond, A. (2012b). TreeAnnotator Version 1.7.2. http://beast.bio.ed.ac.uk.
Randlane, T., Tõrra, T., Saag, A., & Saag, L. (2009). Key to European Usnea species. The Diversity of Lichenology: Jubilee Volume, 100(100), 419–462.
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S., et al. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61(3), 539–542.
Saag, L., Tõrra, T., Saag, A., Del-Prado, R., & Randlane, T. (2011). Phylogenetic relations of European shrubby taxa of the genus Usnea. The Lichenologist, 43(05), 427–444.
Saag, L., Mark, K., Saag, A., & Randlane, T. (2014). Species delimitation in the lichenized fungal genus Vulpicida (Parmeliaceae, Ascomycota) using gene concatenation and coalescent-based species tree approaches. American Journal of Botany, 101(12), 2169–2182.
Sanderson, M. J., & Donoghue, M. J. (1996). Reconstructing shifts in diversification rates on phylogenetic trees. Trends in Ecology & Evolution, 11(1), 15–20.
Scherrer, S., Zippler, U., & Honegger, R. (2005). Characterisation of the mating-type locus in the genus Xanthoria (lichen-forming ascomycetes, Lecanoromycetes). Fungal Genetics and Biology, 42(12), 976–988.
Schmitt, I., & Lumbsch, H. T. (2004). Molecular phylogeny of the Pertusariaceae supports secondary chemistry as an important systematic character set in lichen-forming ascomycetes. Molecular Phylogenetics and Evolution, 33(1), 43–55.
Schmitt, I., Crespo, A., Divakar, P. K., Fankhauser, J. D., Herman-Sackett, E., Kalb, K., et al. (2009). New primers for promising single-copy genes in fungal phylogenetics and systematics. Persoonia, 23, 35–40.
Seymour, F. A., Crittenden, P. D., Wirtz, N., Øvstedal, D. O., Dyer, P. S., & Lumbsch, H. T. (2007). Phylogenetic and morphological analysis of Antarctic lichen-forming Usnea species in the group Neuropogon. Antarctic Science, 19(1), 71–82.
Singh, G., Dal Grande, F., Divakar, P. K., Otte, J., Leavitt, S. D., Szczepanska, K., et al. (2015). Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota). PLoS One, 10(5), e0124625. doi:10.1371/journal.pone.0124625.
Sistrom, M., Donnellan, S. C., & Hutchinson, M. N. (2013). Delimiting species in recent radiations with low levels of morphological divergence: a case study in Australian Gehyra geckos. Molecular Phylogenetics and Evolution, 68(1), 135–143.
Spinks, P. Q., Thomson, R. C., Pauly, G. B., Newman, C. E., Mount, G., & Shaffer, H. B. (2013). Misleading phylogenetic inferences based on single-exemplar sampling in the turtle genus Pseudemys. Molecular Phylogenetics and Evolution, 68, 269–281.
Spitzer, M., Wildenhain, J., Rappsilber, J., & Tyers, M. (2014). BoxPlotR: a web tool for generation of box plots. Nature Methods, 11(2), 121–122.
Spribille, T., Klug, B., & Mayrhofer, H. (2011). A phylogenetic analysis of the boreal lichen Mycoblastus sanguinarius (Mycoblastaceae, lichenized Ascomycota) reveals cryptic clades correlated with fatty acid profiles. Molecular Phylogenetics and Evolution, 59(3), 603–614.
Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22(21), 2688–2690.
Stamatakis, A., Hoover, P., & Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML Web servers. Systematic Biology, 57(5), 758–771.
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731–2739.
Tehler, A., & Irestedt, M. (2007). Parallel evolution of lichen growth forms in the family Roccellaceae (Arthoniales, Ascomycota). Cladistics, 23(5), 432–454.
Thell, A., Crespo, A., Divakar, P. K., Kärnefelt, I., Leavitt, S. D., Lumbsch, H. T., et al. (2012). A review of lichen family Parmeliaceae – history, phylogeny and current taxonomy. Nordic Journal of Botany, 30, 641–664.
Tõrra, T., & Randlane, T. (2007). The lichen genus Usnea (lichenized Ascomycetes, Parmeliaceae) in Estonia with a key to the species in the Baltic countries. The Lichenologist, 39, 415–438.
Trest, M. T., Will-Wolf, S., Keuler, R., Shay, N., Hill, K., Studer, A., et al. (2015). Potential impacts of UV exposure on lichen communities: a pilot study of Nothofagus dombeyi trunks in southernmost Chile. Ecosystem Health and Sustainability, 1(4), art14. doi:10.1890/EHS15-0008R1.1.
Truong, C., Divakar, P. K., Yahr, R., Crespo, A., & Clerc, P. (2013). Testing the use of ITS rDNA and protein-coding genes in the generic and species delimitation of the lichen genus Usnea (Parmeliaceae, Ascomycota). Molecular Phylogenetics and Evolution, 68(2), 357–372.
Velmala, S., Myllys, L., Halonen, P., Goward, T., & Ahti, T. (2009). Molecular data show that Bryoria fremontii and B. tortuosa (Parmeliaceae) are conspecific. The Lichenologist, 41(03), 231–242.
Velmala, S., Myllys, L., Goward, T., Holien, H., & Halonen, P. (2014). Taxonomy of Bryoria section Implexae (Parmeliaceae, Lecanoromycetes) in North America and Europe, based on chemical, morphological and molecular data. Annales Botanici Fennici, 51, 345–371.
Wagner, C. E., Keller, I., Wittwer, S., Selz, O. M., Mwaiko, S., Greuter, L., et al. (2013). Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Molecular Ecology, 22(3), 787–798.
Wedin, M., Westberg, M., Crewe, A. T., Tehler, A., & Purvis, O. W. (2009). Species delimitation and evolution of metal bioaccumulation in the lichenized Acarospora smaragdula (Ascomycota, Fungi) complex. Cladistics, 25(2), 161–172.
Weiller, G. F. (1998). Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Molecular Biology and Evolution, 15, 326–335.
White, T. J., Bruns, T., Lee, S., & Taylor, J. W. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, & T. J. White (Eds.), PCR protocols: a guide to methods and applications (pp. 315–322). New York: Academic Press.
Wiens, J. J. (1998). Combining data sets with different phylogenetic histories. Systematic Biology, 47(4), 568–581.
Willis, S. C., Farias, I. P., & Ortí, G. (2013). Multi-locus species tree for the Amazonian peacock basses (Cichlidae: Cichla): emergent phylogenetic signal despite limited nuclear variation. Molecular Phylogenetics and Evolution, 69(3), 479–490.
Wirtz, N., Printzen, C., Sancho, L. G., & Lumbsch, H. T. (2006). The phylogeny and classification of Neuropogon and Usnea (Parmeliaceae, Ascomycota) revisited. Taxon, 55(2), 367–376.
Wirtz, N., Printzen, C., & Lumbsch, H. T. (2008). The delimitation of Antarctic and bipolar species of neuropogonoid Usnea (Ascomycota, Lecanorales): a cohesion approach of species recognition for the Usnea perpusilla complex. Mycological Research, 112, 472–484.
Wirtz, N., Printzen, C., & Lumbsch, H. T. (2012). Using haplotype networks, estimation of gene flow and phenotypic characters to understand species delimitation in fungi of a predominantly Antarctic Usnea group (Ascomycota, Parmeliaceae). Organisms Diversity & Evolution, 12(1), 17–37.
Yang, Z., & Rannala, B. (2010). Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences, 107(20), 9264–9269.
Yang, Z., & Rannala, B. (2014). Unguided species delimitation using DNA sequence data from multiple loci. Molecular Biology and Evolution, 31(12), 3125–3135.
Zhang, J., Kapli, P., Pavlidis, P., & Stamatakis, A. (2013). A general species delimitation method with applications to phylogenetic placements. Bioinformatics, 29(22), 2869–2876.
Acknowledgments
We thank the collectors who provided the specimens used here and anonymous reviewers for useful comments. The study was financially supported by the Estonian Research Council (grants ETF9109 and PUT1017 to TR) and European Union Social Fund through the ESF Doctoral Studies and Internationalisation Programme Activity 6. The molecular work was performed in the DNA Genotyping and Sequencing Core Facility of the Estonian Biocentre and Institute of Molecular and Cell Biology at the University of Tartu (Tartu, Estonia) and in the Pritzker Laboratory for Molecular Systematics at the Field Museum (Chicago, IL, USA). Computationally demanding analyses were carried out in the High Performance Computing Center at the University of Tartu.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Ethical approval
This article does not contain any studies with human participants or animals performed by any of the authors.
Additional information
An erratum to this article is available at http://dx.doi.org/10.1007/s13127-016-0311-5.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Online Resource 1
Fig. S1–S6 Majority rule consensus trees inferred from ML analysis on ITS (Fig. S1), IGS (Fig. S2), beta-tubulin (Fig. S3), MCM7 (Fig. S4), RPB1 (Fig. S5) and RPB2 (Fig. S6) datasets together with nonparametric bootstrap support (BP) and posterior probability (PP) values from Bayesian inference. Above branch is indicated ML bootstrap probabilities (BP) and below Bayesian posterior probability (PP) scores. Branches marked in bold indicate strong support (BP ≥ 70 and PP ≥ 0.95) for specified clade. Scale bar shows the number of substitutions per site (PDF 339 kb)
Online Resource 2
Fig. S7 Majority rule consensus tree of all available Usnea fulvoreagens, U. glabrescens s.str. and U. pacificana sequences (Table 1) with U. silesiaca as an outgroup, based on six concatenated loci, inferred in RAxML. Clade bootsrap probabilites (BP) are given above branch and strongly supported clades (BP ≥ 70 %) are marked in bold. Scale bar shows the number of substitutions per site. In brackets are given specimen code, country, and secondary chemistry. Secondary metabolites in fulvoreagens-glabrescens clade: bar − barbatic acid; BMY − baeomycesic acid; NSTI − norstictic acid; pro − protocetraric acid; SAL − salazinic acid; SQU − squamatic acid; STI-comp − stictic acid complex with connorstictic cryptostictic acids; unid rfcl x − unidentified substance from reference class x. Capital letters denotes major compounds in chemotype, lower case accessory substances (PDF 136 kb)
Online Resource 3
Fig. S8 Majority rule consensus tree of all studied Usnea parafloridana specimens with some representatives from florida-subfloridana and wasmuthii clades, based on six concatenated loci, inferred in RAxML. Clade bootsrap probabilites (BP) are given above branch and strongly supported clades (BP ≥ 70 %) are marked in bold. Scale bar shows the number of substitutions per site. In brackets are given specimen codes and secondary chemistry. Secondary metabolites in U. parafloridana: NSTI − norstictic acid; SAL − salazinic acid; unid rfcl x − unidentified substance from reference class x. Capital letters denotes major compounds in chemotype, lower case accessory substances (PDF 274 kb)
Online Resource 4
Fig. S9 Examples of lichen substances of some studied Usnea specimens, incl. U. parafloridana sp. nov., identified in thin layer chromatography analyses. Secondary metabolites are visualized in solvent system A, after treatment with sulphuric acid and heating (Orange et al. 2001). Identified secondary metabolites: al – alectorialic acid; bar − barbatic acid; bmy − baeomycesic acid; cnsti – connorstictic acid; csti – cryptostictic acid; nsti – norstictic acid; sal – salazinic acid; squ − squamatic acid; sti – stictic acid; tha – thamnolic acid; usn − usnic acid (PDF 1398 kb)
Rights and permissions
About this article
Cite this article
Mark, K., Saag, L., Leavitt, S.D. et al. Evaluation of traditionally circumscribed species in the lichen-forming genus Usnea, section Usnea (Parmeliaceae, Ascomycota) using a six-locus dataset. Org Divers Evol 16, 497–524 (2016). https://doi.org/10.1007/s13127-016-0273-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13127-016-0273-7