Fig 1
Molecular phylogeny of alectorioid lichens focusing on Bryoria and Sulcaria. Strict consensus obtained from TNT analysis based on a combined ITS, Mcm7 and GAPDH data set. Bootstrap values b50% obtained from TNT analysis are shown above nodes and BPP values b90% obtained from Bayesian analysis are shown below nodes. Five Bryoria sections and positions of B. pseudocapillaris and B. spiralifera are indicated in coloured boxes.
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Bryoria pseudocapillaris and B. spiralifera are currently treated as members of Bryoria section Implexae although conspicuous, long and depressed pseudocyphellae characterizing both species resemble those found in the genus Sulcaria. Both genera belong in Parmeliaceae and form an alectorioid group together with Alectoria, Gowardia and Pseudephebe....
Citations
... The first five markers were selected based on our previous studies of the genus Bryoria (i.e. Velmala et al. 2009Velmala et al. , 2014Myllys et al. 2011Myllys et al. , 2014Myllys et al. , 2016. The Tsr1 region has been shown to have potential in resolving clades at both higher and lower taxonomic levels within the Parmeliaceae Widhelm et al. 2016). ...
In recent years, the genus Bryoria ( Parmeliaceae , Lecanoromycetes ) has been the subject of considerable phylogenetic scrutiny. Here we used information on six gene regions, three nuclear protein-coding markers ( Mcm 7, GAPDH and Tsr 1), two nuclear ribosomal markers (ITS and IGS) and a partial mitochondrial small subunit (mtSSU), to examine infrageneric relationships in the genus and to assess species delimitation in the Bryoria bicolor / B . tenuis group in section Divaricatae . For this purpose, phylogenetic analyses and several of the available algorithms for species delimitation (ASAP, GMYC single, GMYC multiple and bPTP) were employed. We also estimated divergence times for the genus using *BEAST. Our phylogenetic analyses based on the combined data set of six gene loci support the monophyly of sections Americanae , Divaricatae and Implexae , while section Bryoria is polyphyletic and groups in two clades. Species from Bryoria clade 1 are placed in an emended section Americanae . Our study reveals that section Divaricatae is young ( c . 5 My) and is undergoing diversification, especially in South-East Asia and western North America. Separate phylogenetic analyses of section Divaricatae using ITS produced a topology congruent with the current species concepts. However, the remaining gene regions produced poorly resolved phylogenetic trees and the different species delimitation methods also generated highly inconsistent results, congruent with other studies that highlight the difficulty of species delimitation in groups with recent and rapid radiation. Based on our results, we describe the new species B . ahtiana sp. nov., characterized by its bicolorous, caespitose, widely divergent thallus, conspicuously thickening main stems, well-developed secondary branches, and rather sparse third-order branchlets. Another new lineage, referred to here as B . tenuis s. lat., is restricted to western North America and may represent a new species recently diverged from B . tenuis s. str., though further work is needed.
... or within Parmeliaceae (Wedin et al. 1999;Ohmura 2002;Articus 2004;Ohmura & Kanda 2004;Wirtz et al. 2006;Arup et al. 2007). Usnea sequences were also generated as outgroups for other taxa (LaGreca 1999;Thell et al. 2002;Schmull et al. 2011;Myllys et al. 2014). ...
... Usnea hirta is one of the presumably most widespread species in the genus with reports from all major areas in North and South America, Europe, Africa, Asia, and Oceania (Mies 1989;Halonen et al. 1998;Elix & McCarthy 1998Fos & Clerc 2000;Calvelo & Liberatore 2002;Articus et al. 2002;Bjerke et al. 2006;Clerc 2007;Randlane et al. 2009;Kelly et al. 2011;Saag et al. 2011;Shrestha et al. 2012;Noer et al. 2013;Santiago et al. 2013;Myllys et al. 2014;Burkin & Kononenko 2015;Shukla et al. 2015;Herrera-Campos 2016;Paliya et al. 2016;Gagarina et al. 2017;Galinato et al. 2017Galinato et al. , 2018Bungartz et al. 2018;Esslinger 2019). All accessions in this strongly supported clade were from Europe (Articus et al. 2002;Kelly et al. 2011;Saag et al. 2011;Millanes et al. 2014;Araujo 2016). ...
We present an exhaustive analysis of the ITS barcoding marker in the genus Usnea s.lat., separated into Dolichousnea, Eumitria, and Usnea including the subgenus Neuropogon, analyzing 1,751 accessions. We found only a few low-quality accessions, whereas information on voucher specimens and accuracy and precision of identifications was of subpar quality for many accessions. We provide an updated voucher table, alignment and phylogenetic tree to facilitate DNA barcoding of Usnea, either locally or through curated databases such as UNITE. Taxonomic and geographic coverage was moderate: while Dolichousnea and subgenus Neuropogon were well-represented among ITS data, sampling for Eumitria and Usnea s.str. was sparse and biased towards certain lineages and geographic regions, such as Antarctica, Europe, and South America. North America, Africa, Asia and Oceania were undersampled. A peculiar situation arose with New Zealand, represented by a large amount of ITS accessions from across both major islands, but most of them left unidentified. The species pair Usnea antarctica vs. U. aurantiacoatra was the most sampled clade, including numerous ITS accessions from taxonomic and ecological studies. However, published analyses of highly resolved microsatellite and RADseq markers showed that ITS was not able to properly resolve the two species present in this complex. While lack of resolution appears to be an issue with ITS in recently evolving species complexes, we did not find evidence for gene duplication (paralogs) or hybridization for this marker. Comparison with other markers demonstrated that particularly IGS and RPB1 are useful to complement ITS-based phylogenies. Both IGS and RPB1 provided better backbone resolution and support than ITS; while IGS also showed better resolution and support at species level, RPB1 was less resolved and delineated for larger species complexes. The nuLSU was of limited use, providing neither resolution nor backbone support. The other three commonly employed protein-coding markers, TUB2, RPB2, and MCM7, showed variable evidence of possible gene duplication and paralog formation, particularly in the MCM7, and these markers should be used with care, especially in multimarker coalescence approaches. A substantial challenge was provided by difficult morphospecies that did not form coherent clades with ITS or other markers, suggesting various levels of cryptic speciation, the most notorious example being the U. cornuta complex. In these cases, the available data suggest that multimarker approaches using ITS, IGS and RPB1 help to assess distinct lineages. Overall, ITS was found to be a good first approximation to assess species delimitation and recognition in Usnea s.lat., as long as the data are carefully analyzed, and reference sequences are critically assessed and not taken at face value. In difficult groups, we recommend IGS as a secondary barcode marker, with the option to employ more resource-intensive approaches, such as RADseq, in species complexes involving so-called species pairs or other cases of disparate morphology not reflected in the ITS or IGS. Attempts should be made to close taxonomic and geographic gaps especially for the latter two markers, in particular in Eumitria and Usnea s.str. and in the highly diverse areas of North America and Central America, Africa, Asia, and Oceania.
... Based on the small collection made by the author, the first lichens, Cladonia and Lepraria spp., reported from the western part of the Arasbaran area, appear in Ahti & Sohrabi (2006) and Sohrabi & Orange (2006), respectively. Additional data on parmelioid lichens from Arasbaran were reported by Sohrabi & Alstrup, (2007) and , and further records from there referred to in Seaward et al. (2008); Seaward et al. (2004); Myllys et al. (2011);Myllys et al. (2014); Velmala et al. (2014); Boluda et al. (2015); Valadbeigi, Nordin, et al. (2011);Valadbeigi, Sipman, et al. (2011). ...
Based on revision of 533 herbarium specimens and literature review, 227 lichenized and 36 lichenicolous fungi belonging to 115 genera and 52 families (including 8 "incertae sedis" taxa) are reported from Arasbaran UNESCO-MAB Biosphere Reserve. In addition, 103 taxa are reported for the first time from Arasbaran. Of these nineteen lichenized fungi and two lichenicolous fungi were not known from Iran before, the lichenized fungi Aspicilia pavimentans,Bryobilimbia hypnorumCaloplaca phaeothamnos,Cetreliamonachorum,Circinaria elmorei, Cladonia borealis, L. populicola, Lecidea auriculata, Pertusaria flavicans, P. pluripuncta, P. pseudocorallina, P. xanthoplaca, Phaeophyscia poeltii, Rinodina trachytica,Scytinium aragonii, Usnea glabrata, Varicellaria lactea, Xanthocarpia tominii, and the lichenicolous fungi Rosellinula haplospora and Telogalla olivieri. ITS rDNA was used to confirm the identity ofLecidea auriculata. The history of floristic study and the diversity of lichen species in the region are briefly discussed.
... It is one of a few similar hypermaritime fruticose lichens. The species pair, Bryoria spiralifera and B. pseudocapillaris, were found to be conspecific (Myllys et al. 2014) differing only chemically. Furthermore they were synonmized and moved to the genus Sulcaria. ...
... Each taxon from the reconstructed species tree was assigned with a geographic state of New World, Old World, or widespread. Species distributions were obtained from selected literature (Esslinger, 1980;Wu & Wang, 1992;Chen, 1996;Myllys & al., 2014). We subsequently used the likelihood ratio test and the Akaike information criterion (AIC) for model comparisons. ...
Lineages with broad, intercontinental distributions can provide insight into factors that influence diversity across both temporal and geographic scales. Lichens are well known for distinct biogeographic distribution patterns, including a high number of lineages with intercontinental distributions. The lichen-forming fungal genus Oropogon, from one of the largest families of lichen-forming ascomycetes, Parmeliaceae, occurs in both Asia and the Neotropics. How this genus obtained this disjunct distribution is not currently known. To better understand factors shaping diversity in Oropogon, we (i) estimated the timing of diversification of major clades within this genus; (ii) inferred the historical biogeography of Oropogon; and (iii) identified factors that potentially affected the distribution and evolution of this genus. Our results suggest that the genus originally radiated during the early Miocene, with subsequent diversification events occurring during the middle Miocene. Ancestral area reconstructions for Oropogon suggest that the genus was either widespread with subsequent separate diversification in Asia and America or originated in the New World (America), with subsequent migration to Asia. We hypothesize that the Mi-1 glaciation impacted diversification of Oropogon species in Asia, and that the rise of major mountain ranges, such as the Himalayas, helped promote diversification in Oropogon in the Old World.
... More recently, Bryoria has been subject to ongoing re-evaluation using molecular methods (Velmala et al. 2009Myllys et al. 2011Myllys et al. , 2014. While these studies have contributed to a deeper understanding of relationships in the genus, the taxonomy of Bryoria is still hardly settled. ...
... We generated 27 ITS sequences and 29 Mcm7 sequences from 29 specimens. The rest of the sequence data were obtained from the National Center for Biotechnology Information (NCBI) database (http:// www.ncbi.nlm.nih.gov) and originated mostly from our previous studies (i.e., Myllys et al. 2011Myllys et al. , 2014. Our DNA sequences of the ITS regions and a partial Mcm7 gene region were aligned separately with MUSCLE v.3.8.31 (Edgar 2004) using EMBL-EBI's freely available web service (http://www.ebi.ac.uk/Tools/msa/ muscle/). ...
... As a result, the two subclades previously recognized in this section must now be kept separate and are referred to here as section Bryoria clade 1 and section Bryoria clade 2. Bryoria clade 1 also includes a monotypic section Americanae and forms an unsupported sister group with B. fremontii, while Bryoria clade 2 is most closely related to section Implexae. The non-monophyly most probably stems from the different combination of the gene regions used: inMyllys et al. (2014) section Bryoria was paraphyletic in the tree obtained from ITS+Mcm7 data, while in the ITS+GAPDH+FIG. 1. Phylogenetic position of Bryoria alaskana sp. nov. ...
Two new species of Bryoria are described based on morphology, chemistry and molecular phylogeny (ITS and Mcm7). Both species belong in section Bryoria, which was resolved as a polyphyletic group in the ITS+Mcm7 phylogeny. Bryoria alaskana belongs to a clade restricted to South-East Asia and north-west North America, and is so far known from south-east Alaska and the Sino-Himalayan Mountains. This highly variable species is most reliably recognized by its pendent, esorediate thallus, its production of fumarprotocetraric acid, and the combination of isotomic branching, abundant, whitish, predominantly fusiform pseudocyphellae, and sparse, short perpendicular side branches. Black emorient patches are lacking. Bryoria irwinii is endemic to north-west North America and is closely related to B. araucana from South America, B. poeltii from South-East Asia, as well as B. nadvornikiana and B. trichodes, both widely distributed in the Northern Hemisphere. It is a subpendent, esorediate species recognized by its predominantly anisotomic branching, olivaceous hue, black emorient patches, conspicuous pale brownish, fusiform pseudocyphellae, and numerous perpendicular, more or less basally constricted, side branches.
... Despite the substantial resources that have been devoted to using molecular data to resolve outstanding questions of generic circumscription and species delimitation in the Parmeliaceae Buaruang et al. 2015;de Paz et al. 2010ade Paz et al. , 2010bDel-Prado et al. 2010Divakar et al. 2010Divakar et al. , 2013Elix et al. 2010;Lendemer and Hodkinson 2010;Mark et al. 2012;Nelson et al. 2012;Nelsen et al. 2013;Leavitt et al. 2014;Lendemer and Ruiz 2015;Saag et al. 2014), and more specifically the related fruticose genus Bryoria Velmala et al. 2014), Alectoria has not been the direct subject of such a study. Nonetheless, recent molecular studies of Bryoria and Parmeliaceae have included samples of Alectoria and recovered results that strongly suggested further study was needed (Halonen et al. 2009;Myllys et al. 2014). ...
... Feuerer and Thell s.n. (HBG), Austria To examine the relationships within Alectoria, individual datasets were constructed for each of the three genes, with taxon sampling across the genus and with Gowardia nigricans used as an outgroup following the methods of Miadlikowska et al. (2014), Myllys et al. (2014), and Halonen et al. (2009). The datasets were assembled in Mesquite 3.03 (Maddison and Maddison 2015) by downloading the following from GenBank to supplement the newly generated sequences: all ITS, Mcm7, and mtSSU sequences tagged with "Alectoria" and "Gowardia nigricans" returned from an NCBI Nucleotide search on 7 August 2015. ...
... The results of our molecular phylogenetic analyses, despite employing an expanded taxon sampling, largely do not support the current taxonomic delineations of species within Alectoria that have been based on morphological and chemical characters. This supports the findings of previous studies (Halonen et al. 2009;Myllys et al. 2014) that have recovered similar results using a more limited sampling both taxonomically and geographically. However, our molecular analysis sheds considerable new light on this distinctive group of macrolichens and suggests substantial avenues for further search. ...
Alectoria is a genus of fruticose lichen characterised by the presence of usnic acid and conspicuous raised pseudocyphellae. This genus is particularly diverse and abundant in montane, boreal, and Arctic regions of North America. Because intermediate forms have been reported for several species of Alectoria on the continent, it has been suggested that these species were initially delimited based on the extremes of morphological gradients. Here, we use the results of molecular phylogenetic analyses of two nuclear genes, ITS and Mcm7, with 48 representatives of 9 taxa to examine the delineation of 5 taxa that have been previously shown to be related to, or confused with, A. sarmentosa: A. fallacina, A. imshaugii, A. sarmentosa var. sorediosa, A. sarmentosa subsp. vexillifera, and A. vancouverensis. Alectoria fallacina was found to be well-supported and distantly related to A. sarmentosa. Conversely, the other four taxa were recovered as a single monophyletic group with little internal structure, which did not support the presently defined morphological species. A provisional taxonomic treatment is proposed pending more detailed study at the population level. Alectoria sarmentosa var. sorediosa is recognized at the species level, which necessitates the new combination: A. sorediosa. An updated key to the North American species of Alectoria is also provided.
... Bryoria Brodo & D. Hawksw. is the largest genus in the alectorioid clade of the family Parmeliaceae (Divakar et al. 2015), which inhabits temperate to alpine regions worldwide. It has been comprehensively studied in North America and northern Europe (Brodo & Hawksworth 1977;Myllys et al. 2011a); however, morphological simplicity and chemical variability make its taxonomy difficult, and recent molecular data have resulted in several changes (Velmala et al. 2009Myllys et al. 2014). Recent studies have discovered additional new species in Bryoria from east-central Asia (Myllys et al. 2011b;Jørgensen et al. 2012), southern South America and the Antarctic (Olech & Bystrek 2004;Fryday & Øvstedal 2012). ...
Bryoria araucana
sp. nov. is described from Chile on the basis of morphological, chemical and molecular data. It has a grey to dark greyish brown pendent thallus with the base usually black, branching angles mainly obtuse, terminal branches with few lateral branchlets acutely inserted, fumarprotocetraric acid, and often protocetraric and confumarprotocetraric acids. It is morphologically similar to the Northern Hemisphere
B. trichodes
, but lacks soralia and has inconspicuous concolorous or slightly darker pseudocyphellae.
Bryoria glabra
is also reported for the first time from the Southern Hemisphere. New phylogenetic data based on ITS, mtSSU and
MCM7
analyses suggest that
Bryoria
sect.
Bryoria
is polyphyletic and needs revision.
... My assumption was correct, these two Bryoria species were clearly grouped with the two Sulcaria species, which were all distant from any other species of Bryoria. Other researchers have since found the same results (Myllys et al. 2014). They lumped the two Bryoria species into one, Sulcaria spiralifera. ...
... Amber, formed by the hardened resin of trees, is famous for its ability to capture ancient life and preserves even soft-bodied microorganisms in cellular and ultrastructural fidelity. Several well-preserved lichens have been described from [35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50] Ma old Baltic and 16 Ma old Dominican amber (for age estimation, see [7][8]), and identified as representatives of extant genera [9][10][11][12]. These rare lichen fossils have served as minimum age constraints in several recent studies assessing the evolutionary history of the Lecanoromycetes [13][14][15]. ...
... The monophyletic lineage of alectorioid lichens presently includes five genera of which three produce fruticose, often pendent and beard-like thalli: Alectoria, Bryoria, and Sulcaria [24,33,35]. Alectoria is a genus of seven species presently recognized with Northern Hemisphere or bipolar distribution, while Bryoria consists of 30-40 mainly circumboreal species, and Sulcaria contains six species restricted to either Asia or North America [35][36][37][38]. Typically, Alectoria produce raised and elongate fusiform to ovoid pseudocyphellae [39] that remotely resemble the slightly raised cracks observed in the cross section of the fossil thallus from Bitterfeld amber (Fig 3E). ...
... On the other hand, several species of Bryoria produce relatively inconspicuous, linear pseudocyphellae [40] that are similar to the linear pseudocyphella observed on the branch surface of the Bitterfeld fossil ( Fig 3G). In most species of Sulcaria pseudocyphellae form conspicuous, long, and spiraling grooves [36,41]. ...
One of the most important issues in molecular dating studies concerns the incorporation of
reliable fossil taxa into the phylogenies reconstructed from DNA sequence variation in extant
taxa. Lichens are symbiotic associations between fungi and algae and/or cyanobacteria.
Several lichen fossils have been used as minimum age constraints in recent studies
concerning the diversification of the Ascomycota. Recent evolutionary studies of Lecanoromycetes,
an almost exclusively lichen-forming class in the Ascomycota, have utilized the
Eocene amber inclusion Alectoria succinic as a minimum age constraint. However, a re-investigation
of the type material revealed that this inclusion in fact represents poorly preserved
plant remains, most probably of a root. Consequently, this fossil cannot be used as
evidence of the presence of the genus Alectoria (Parmeliaceae, Lecanorales) or any other
lichens in the Paleogene. However, newly discovered inclusions from Paleogene Baltic and
Bitterfeld amber verify that alectorioid morphologies in lichens were in existence by the Paleogene.
The new fossils represent either a lineage within the alectorioid group or belong to
the genus Oropogon.
