Genetic distances within and among species in monophyletic lineages of Parmeliaceae (Ascomycota) as a tool for taxon delimitation

Del-Prado, Ruth; Cubas, Paloma; Lumbsch, H. Thorsten; Divakar, Pradeep K.; Blanco, Óscar; Paz, Guillermo Amo de; Molina, Marı́a; Crespo, Ana

doi:10.1016/j.ympev.2010.04.014

Cited by 79 publications

(101 citation statements)

References 54 publications

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“…However, recent large scale molecular phylogenetic analyses aimed at resolving generic boundaries in the family Parmeliaceae recovered members of the group as a strongly supported clade sister to a clade containing representatives of the genus Parmotrema A. Massal. (Crespo et al 2010). These results indicate that the group is closely related to Parmotrema and renders the continued classification of Parmelia crozalsiana and its relatives within Canoparmelia untenable.…”

Section: Introductionmentioning

confidence: 92%

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Recognition of the Parmelia crozalsiana group as the genus Crespoa.

Lendemer¹

2012

North Amer. Fun.

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Lendemer, J. C., and B. P. Hodkinson. 2012 Abstract: Recent molecular phylogenetic analyses of the lichen family Parmeliaceae have revealed that the members of the Parmelia crozalsiana group form a sister clade to one containing members of the genus Parmotrema. The four species in this group were classified first in Parmelia, then Pseudoparmelia, and later Canoparmelia. Recently, the classification of this group was resolved by placing the species in the newly-described Parmotrema subg. Crespoa. This placement was justified by an absence of characters from the fungal reproductive structures distinguishing members of the group from those classified in Parmotrema subg. Parmotrema. As this classification obfuscates a morphologically and phylogenetically discrete group of foliose macrolichens that has always been recognized as distinct from Parmotrema s. str., we here recognize the group as the genus Crespoa. A discussion of taxonomic rank assignment based on character-types that are preconceived as diagnostic is also provided.

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Section: Introductionmentioning

confidence: 92%

“…The Parmelia crozalsiana group represents a well-supported monophyletic clade within the foliose macrolichen family Parmeliaceae (Crespo et al 2010). Its constituent taxa are characterized by a combination of vegetative thalline morphology and characters of both sexual and asexual fungal reproductive structures (Hawksworth 2011;Hale 1976).…”

Section: Introductionmentioning

confidence: 99%

Recognition of the Parmelia crozalsiana group as the genus Crespoa.

Lendemer¹

2012

North Amer. Fun.

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“…In a smaller number of environmental studies, ITS has been used combined with LSU (24,25). ITS is also used in some fungi for providing an indication of delimitation by a measure of the genetic distances (26). However, phylogenetic approaches are also being used to identify taxonomic units in environmental sampling of fungi (27) and are often more effective in comparison (28).…”

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confidence: 99%

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Schoch

Seifert

Huhndorf

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative proteincoding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter-and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.DNA barcoding | fungal biodiversity T he absence of a universally accepted DNA barcode for Fungi, the second most speciose eukaryotic kingdom (1, 2), is a serious limitation for multitaxon ecological and biodiversity studies. DNA barcoding uses standardized 500-to 800-bp sequences to identify species of all eukaryotic kingdoms using primers that are applicable for the broadest possible taxonomic group. Reference barcodes must be derived from expertly identified vouchers deposited in biological collections with online metadata and validated by available online sequence chromatograms. Interspecific variation should exceed intraspecific variation (the barcode gap), and barcoding is optimal when a sequence is constant and unique to one species (3, 4). Ideally, the barcode locus would be the same for all kingdoms. A region of the mitochondrial gene encoding the cytochrome c oxidase subunit 1 (CO1) is the barcode for animals (3, 4) and the default marker adopted by the Consortium for the Barcode of Life for all groups of organisms, including fungi (5). In Oomycota, part of the kingdom Stramenopila historically studied by mycologists, the de facto barcode internal transcribed spacer (ITS) region is suitable for identification, but the default CO1 marker is more reliable in a few clades of closely related species (6)...

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“…Indeed, cryptic speciation may be hidden under a single epithet as an impressive variation in the barcode ITS has been detected between an accession retrieved from GenBank (material collected in Costa Rica) and our collection from Réunion: 14 bp substitutions plus 1 indel in ITS1 and 17 plus 1 indel in ITS2. Although no detailed study has been conducted on the genetic distances within this genus, the threshold to distinguish species boundaries as highlighted by Del-Prado et al (2010) for several genera in the Parmeliaceae is crossed.…”

Section: Masson 9744056 (H)mentioning

confidence: 99%

Hypotrachyna penduliloba and Remototrachyna pandani, two new species in the hyperdiverse lichen family Parmeliaceae from Réunion in the Mascarene Archipelago

2015

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Extensive exploration of lichen diversity in the tiny and remote tropical island of Réunion (Mascarene Archipelago, Indian Ocean) yielded two new species in the hyperdiverse lichen family Parmeliaceae. Morphological, anatomical and chemical characters and molecular inferences from 3 loci (ITS, nuLSU and mtSSU) strongly support their assignment t o H y p o t r a c h y n a ( s u b g e n u s L o n g i l o b a e ) and Remototrachyna. Hypotrachyna producta is further assigned to H. subgenus Longilobae and is newly reported for Réunion as well as Remototrachyna costaricensis.

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Genetic distances within and among species in monophyletic lineages of Parmeliaceae (Ascomycota) as a tool for taxon delimitation

Cited by 79 publications

References 54 publications

Recognition of the Parmelia crozalsiana group as the genus Crespoa.

Recognition of the Parmelia crozalsiana group as the genus Crespoa.

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Hypotrachyna penduliloba and Remototrachyna pandani, two new species in the hyperdiverse lichen family Parmeliaceae from Réunion in the Mascarene Archipelago

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