OLICH: A reference library of DNA barcodes for Nordic lichens

Marthinsen, Gunnhild; Rui, Siri; Timdal, Einar

doi:10.3897/bdj.7.e36252

Cited by 32 publications

(26 citation statements)

References 44 publications

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“…Further, both subfarinacea ecomorphotypes are sympatric along the northern coasts of Norway. These results are consistent with the library of DNA barcodes for Nordic countries ( Marthinsen et al 2019 ). (4) Two very variable groups, both producing evernic acid and not resolved as sister taxa: one includes the corticolous R. fastigiata , almost always fertile, usually forming densely tufted and richly branched, pulvinate thalli, but quite variable in size of thalli and lobes and especially in the spur-shaped lobe at the base of apothecia; and the saxicolous R. breviuscula , with fertile, densely tufted and branched, pulvinate thalli.…”

Section: Discussionsupporting

confidence: 89%

The fruticose genera in the Ramalinaceae (Ascomycota, Lecanoromycetes): their diversity and evolutionary history

Spjut¹,

Simon²,

Guissard³

et al. 2020

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We present phylogenetic analyses of the fruticose Ramalinaceae based on extensive collections from many parts of the world, with a special focus on the Vizcaíno deserts in north-western Mexico and the coastal desert in Namibia. We generate a four-locus DNA sequence dataset for accessions of Ramalina and two additional loci for Niebla and Vermilacinia. Four genera are strongly supported: the subcosmopolitan Ramalina, the new genus Namibialina endemic to SW Africa, and a duo formed by Niebla and Vermilacinia, endemic to the New World except the sorediate V. zebrina that disjunctly occurs in Namibia. The latter three genera are restricted to coastal desert and chaparral where vegetation depends on moisture from ocean fog. Ramalina is subcosmopolitan and much more diverse in its ecology. We show that Ramalina and its sister genus Namibialina diverged from each other at c. 48 Myrs, whereas Vermilacinia and Niebla split at c. 30 Myrs. The phylogeny of the fruticose genera remains unresolved to their ancestral crustose genera. Species delimitation within Namibialina and Ramalina is rather straightforward. The phylogeny and taxonomy of Vermilacinia are fully resolved, except for the two youngest clades of corticolous taxa, and support current taxonomy, including four new taxa described here. Secondary metabolite variation in Niebla generally coincides with major clades which are comprised of species complexes with still unresolved phylogenetic relationships. A micro-endemism pattern of allopatric species is strongly suspected for both genera, except for the corticolous taxa within Vermilacinia. Both Niebla and saxicolous Vermilacinia have chemotypes unique to species clades that are largely endemic to the Vizcaíno deserts. The following new taxa are described: Namibialinagen. nov. with N. melanothrix (comb. nov.) as type species, a single new species of Ramalina (R. krogiae) and four new species of Vermilacinia (V. breviloba, V. lacunosa, V. pustulata and V. reticulata). The new combination V. granulans is introduced. Two epithets are re-introduced for European Ramalina species: R. crispans (= R. peruviana auct. eur.) and R. rosacea (= R. bourgeana auct. p.p). A lectotype is designated for Vermilacinia procera. A key to saxicolous species of Vermilacinia is presented.

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Section: Discussionsupporting

confidence: 89%

The fruticose genera in the Ramalinaceae (Ascomycota, Lecanoromycetes): their diversity and evolutionary history

Spjut¹,

Simon²,

Guissard³

et al. 2020

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“…Phylogenetic inference for Usnea flammea, forming a well-supported clade of several accessions from Macaronesia and western Europe (Kelly et al 2011;Saag et al 2011;Schoch et al 2012;Gerlach et al 2019a;Marthinsen et al 2019), was well in line with its type originating from Portugal (Stirton 1881). The situation was the opposite for U. flavocardia, described from Chile (Räsänen 1936), but all ITS accessions originating from Europe and North America (Kelly et al 2011;Saag et al 2011;Schoch et al 2014;Millanes et al 2014;Araujo 2016).…”

Section: Usnea Subgenus Neuropogon New Zealand Cladesupporting

confidence: 62%

“…The mycobiont-photobiont studies focused exclusively on New Zealand (Buckley et al 2014;Rafat et al 2015) and Antarctica (Park et al 2014(Park et al , 2015. The third major group of accessions (11%) originated from floristic and (meta-)barcoding surveys (Hur et al 2005;Kim et al 2006;Kelly et al 2011;Orock et al 2012;Schoch et al 2012;Šoun et al 2015;Mark et al 2016b;Jaouen et al 2019;Lendemer et al 2019;Marthinsen et al 2019).…”

Section: Metadata Diversitymentioning

confidence: 99%

“…Broader DNA barcoding studies also included data on Usnea or in part focused on the latter, particularly in New Zealand (Kelly et al 2011), but also Switzerland (Mark et al 2016b), Norway (Marthinsen et al 2019), and Cameroon (Orock et al 2012). A large amount of ITS data was generated for analyses of mycobiont-photobiont associations of Usnea lichens and their corresponding ecology and morphology in New Zealand and Antarctica (Rafat 2014;Buckley et al 2014;Cao et al 2015Cao et al , 2018Park et al 2015;Rafat et al 2015).…”

Section: Introductionmentioning

confidence: 99%

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Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS?

Lücking¹,

Nadel²,

Araújo³

et al. 2020

Plant and Fungal Systematics

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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.

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“…In addition, the relationships among Hispidopannaria, Phormopsora, and Pannaria were changed by including or excluding specific taxa of the Pannariaceae or related taxa (data not shown), a conclusion which is valid also for other genera represented in the phylograms. Different phylogenetic markers have been used in recent phylogenetic studies on Pannariaceae, and this, as well as marker incongruence, may have led to variable and instable phylogenies of the family (Ekman and Jørgensen 2002;Passo et al 2008;Wedin et al 2009;Elvebakk et al 2010Elvebakk et al , 2016Ekman et al 2014;Magain and Sérusiaux 2014;Lendemer et al 2017;Fryday et al 2017;Park et al 2018;Marthinsen et al 2019). The conclusion from comparing the application of single phylogenetic markers in the present study ( Fig.…”

Section: Discussionmentioning

confidence: 99%

Hispidopannaria and Phormopsora, two new and small, but evolutionary old Pannariaceae lichen genera from southern South America

2020

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Based on phylogenetic analyses of the ITS, nuclear large subunit rRNA, mitochondrial small subunit rRNA, and MCM7 genes, species previously treated as Pannaria hispidula and P. isabellina are shown to represent two new Pannariaceae genera, Hispidopannaria and Phormospsora. Each genus forms monophyletic clades, both in multilocus phylogeny and in single gene phylogenies. In the multilocus phylogeny, both genera together formed a monophyletic clade as a sister group to the genus Pannaria, whereas this monophyly was not maintained in single gene phylogenies. Hispidopannaria differs from Pannaria in having large, geotropically arranged, hispid squamules, IKI+ internal ascus structures, and perispores with irregular pulvinate verrucae and apical extensions. The southern South American, TLC-negative species H. hispidula is generitype and is concentrated to trunks in the evergreen Nothofagus forests of south-central Chile. Psoroma dasycladum, a similar endemic species from the Juan Fernández Archipelago, is also transferred to Hispidopannaria. Phormopsora is monospecific and is the only member of Pannariaceae which contains norstictic and connorstictic acids. Its thallus of large, branched squamules with large, foliose cephalodia and its bullate perispores with long-apiculate apical extensions also separate it from Pannaria. Its species, Phormopsora isabellina, has a similar distribution as H. hispidula on the South American mainland, but is more widespread. The position of these two small genera as a sister group to the large and diverse genus Pannaria, indicates a long period of slow evolutionary rate, with the island endemic Hispidopannaria dasyclada as an exception. Reproductive isolation and photobiont specialization are partly suggested to explain their slow evolution and lack of surviving speciation.

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OLICH: A reference library of DNA barcodes for Nordic lichens

Cited by 32 publications

References 44 publications

The fruticose genera in the Ramalinaceae (Ascomycota, Lecanoromycetes): their diversity and evolutionary history

The fruticose genera in the Ramalinaceae (Ascomycota, Lecanoromycetes): their diversity and evolutionary history

Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS?

Hispidopannaria and Phormopsora, two new and small, but evolutionary old Pannariaceae lichen genera from southern South America

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