Phylogenetic relations of European shrubby taxa of the genus<i>Usnea</i>

Saag, Lauri; Tõrra, Tiiu; Saag, Andres; Del-Prado, Ruth; Randlane, Tiina

doi:10.1017/s0024282911000375

Cited by 19 publications

(32 citation statements)

References 64 publications

(88 reference statements)

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“…The genus is recognized by a fruticose thallus with an elastic central cord in the medulla (Fig. 14) (Randlane et al 2009, Clerc 2011a, 2011b, Saag et al 2011). Much of the species taxonomy is poorly known due to the enormous morphological and chemical infraspecific variation.…”

Section: The Usneoid Cladementioning

confidence: 99%

A review of the lichen family Parmeliaceae – history, phylogeny and current taxonomy

Thell

Crespo

Divakar

et al. 2012

Nordic Journal of Botany

121

117

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The largest family of lichen‐forming fungi, the Parmeliaceae, is reviewed. It includes 79 genera in current use and ca 2726 species, a large majority of which belong to one of five main clades: the parmelioid, cetrarioid, usneoid, alectorioid and hypogymnioid. However, 21 genera are positioned outside these clades, and four genera in current use still lack DNA‐ data. The family has been shown to be monophyletic and the generic classification is relatively well‐settled compared with other lecanoralean families. Each clade and its genera are presented here with the latest results from phylogenetic analyses and current taxonomy. In addition, a historical outline of the family and its most prominent researchers is provided.

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Section: The Usneoid Cladementioning

confidence: 99%

A review of the lichen family Parmeliaceae – history, phylogeny and current taxonomy

Thell

Crespo

Divakar

et al. 2012

Nordic Journal of Botany

121

117

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“…S1). Finally, DB22671 fell at the base of a complex formed by U. fulvoreagens (Räsänen) Räsänen, U. glabrescens and U. pacificana, without support, close to a basal grade of specimens originally identified as U. diplotypus Vain., U. glabrescens and U. substerilis, all from Europe (Kelly et al 2011;Saag et al 2011), but relabeled U. pacificana (Mark et al 2016;Lücking et al 2020c). Phylogenetically, the Colombian sample would therefore be identified as U. aff.…”

Section: Querymentioning

confidence: 99%

“…In a detailed analysis of all available ITS barcoding data for this hyperdiverse genus (in the definition by Lücking et al 2017a), Lücking et al (2020c) demonstrated numerous shortcomings in sequence data pertaining to Usnea: first and foremost taxonomic and geographic gaps, but also substantial issues with sequence identifications and voucher information. In addition, species identification in Usnea is challenging, as many presumably widespread taxa represent complexes of partly unrelated lineages and much work remains to be done to fully resolve the taxonomy of this genus (Seymour et al 2007;Wirtz et al 2008Wirtz et al , 2012Lumbsch & Wirtz 2011;Saag et al 2011;Shen et al 2012;Truong & Clerc 2012Truong et al 2013a, b;Clerc 2016;Mark et al 2016;Gerlach et al 2017Gerlach et al , 2019Gerlach et al , 2020Clerc & Otte 2018;Grewe et al 2018;Lagostina et al 2018;Dorey et al 2019;Temu et al 2019;Lücking et al 2020c).…”

Section: Introductionmentioning

confidence: 99%

Testing DNA barcoding in Usnea (Parmeliaceae) in Colombia using the internal transcribed spacer (ITS)

Moncada¹,

Sipman²,

Lücking³

2020

Plant and Fungal Systematics

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We tested the functionality of ITS-based DNA barcoding in lichen fungi using Colombian samples of the genus Usnea as an example. New ITS sequences were generated for 15 samples from five localities in two different ecoregions, representing varying morphologies and medullary chemistries. We employed five strategies to identify the samples: (1) BLASTn on the NCBI BLAST site with the original identifications of the best matching reference sequences; (2) as previous, but with revised identifications of the reference sequences based on a separately published revision of ITS sequences published for the genus; (3) local BLASTn in BioEdit using a separately published, revised and curated set of ITS reference sequences for the genus; (4) multiple alignment based phylogenetic analysis within the framework of all available ITS sequences for Usnea s.str.; and (5) integrative taxonomy, combining molecular phylogeny and comparative analysis of phenotype and chemical data. Using the latter approach as reference, we found that NCBI BLASTn with original identifications performed poorly, resulting in an identification success rate of only 7% (a single sample). NCBI BLASTn with revised identifications more than tripled identification success (23%), but was still unsatisfactory. Local BLASTn in BioEdit using the revised, curated reference data further doubled identification success (47%), but remained inadequate. Multiple alignment-based phylogenetic analysis achieved an identification success rate of 80% compared to the result from integrative taxonomy. Based on these results, we conclude that ITS-based DNA barcoding of the genus Usnea under the current circumstances performs poorly, but can be substantially improved using three strategies: (1) update identifications of reference sequences in primary repositories such as GenBank or alternatively use a curated reference data set; (2) perform local BLAST with a curated reference data set focusing on the target genus only, combined with multiple alignment-based phylogenetic analysis as a verification step; and (3) close substantial geographic and taxonomic gaps in the existing reference data. Our analyses suggest that if a near-complete reference data set with correct identifications existed for the genus, then standard BLAST approaches could achieve high levels of identification success close to 100%. As part of our DNA barcoding exercise, which generated the first 15 ITS sequences for Colombian samples of the genus Usnea, we confirm the presence of U. aranea and U. wasmuthii in Colombia and we report for the first time U. tenuicorticata for the country.

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“…From these numbers, it is evident that recognizing species boundaries in lichenized fungi is still in a state of flux, and finding and applying the appropriate character sets and analytical tools appears to be one of the greatest challenges to empirical species delimitation (Crespo and Perez‐Ortega, 2009; Lumbsch and Leavitt, 2011). Parmeliaceae (Lecanorales), the largest family of lichen‐forming fungi with about 2700 species and 80 genera (Thell et al, 2012; Saag et al, 2013), has been an object of intensive phylogenetic studies during the last decade (e.g., Blanco et al, 2006; Crespo et al, 2007, 2010; Del‐Prado et al, 2010; Saag et al, 2011; Leavitt et al, 2013a–c). The genus Vulpicida J.‐E.…”

Section: Currently Accepted Vulpicida Species Their Character Statesmentioning

confidence: 99%

Species delimitation in the lichenized fungal genus Vulpicida (Parmeliaceae, Ascomycota) using gene concatenation and coalescent‐based species tree approaches

Mark

Saag

Randlane

2014

American J of Botany

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Phylogenetic relations of European shrubby taxa of the genusUsnea

Cited by 19 publications

References 64 publications

A review of the lichen family Parmeliaceae – history, phylogeny and current taxonomy

A review of the lichen family Parmeliaceae – history, phylogeny and current taxonomy

Testing DNA barcoding in Usnea (Parmeliaceae) in Colombia using the internal transcribed spacer (ITS)

Species delimitation in the lichenized fungal genus Vulpicida (Parmeliaceae, Ascomycota) using gene concatenation and coalescent‐based species tree approaches

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