Pub Date : 2020-12-29DOI: 10.35535/pfsyst-2020-0028
A. Spielmann, M. Marcelli
The species of Parmotrema with salazinic acid were revised, based on the types of the accepted names, as well as their synonyms. Descriptions for 66 species are given and the synonymy, chemistry, distribution and taxonomic affinities of each species discussed. Three new species are described: Parmotrema austromaculatum sp. nov., P. bifidum sp. nov. and P. clercianum sp. nov. One new combination in Parmelinella is made, P. afrocetrata comb. nov., as well as 13 new combinations in Parmotrema: P. acanthifolium comb. nov., P. concors comb. nov., P. foliolosum comb. nov., P. granulare comb. nov., P. lividotessellatum comb. nov., P. magnum comb. nov., P. maximum comb. nov., P. nudum comb. nov., P. petropoliense comb. nov., P. radiatum comb. nov., P. reterimulosum comb. nov., P. sieberi comb. nov. and P. warmingii comb. nov. One new name, Parmotrema elixii nom. nov. is proposed for Rimelia pustulata. Two lectotypifications are made: Parmotrema erubescens and P. ruminatum. Twelve taxa remain without definite status and are included in the nomina inquirenda.
{"title":"Type studies on Parmotrema (Parmeliaceae, Ascomycota) with salazinic acid","authors":"A. Spielmann, M. Marcelli","doi":"10.35535/pfsyst-2020-0028","DOIUrl":"https://doi.org/10.35535/pfsyst-2020-0028","url":null,"abstract":"The species of Parmotrema with salazinic acid were revised, based on the types of the accepted names, as well as their synonyms. Descriptions for 66 species are given and the synonymy, chemistry, distribution and taxonomic affinities of each species discussed. Three new species are described: Parmotrema austromaculatum sp. nov., P. bifidum sp. nov. and P. clercianum sp. nov. One new combination in Parmelinella is made, P. afrocetrata comb. nov., as well as 13 new combinations in Parmotrema: P. acanthifolium comb. nov., P. concors comb. nov., P. foliolosum comb. nov., P. granulare comb. nov., P. lividotessellatum comb. nov., P. magnum comb. nov., P. maximum comb. nov., P. nudum comb. nov., P. petropoliense comb. nov., P. radiatum comb. nov., P. reterimulosum comb. nov., P. sieberi comb. nov. and P. warmingii comb. nov. One new name, Parmotrema elixii nom. nov. is proposed for Rimelia pustulata. Two lectotypifications are made: Parmotrema erubescens and P. ruminatum. Twelve taxa remain without definite status and are included in the nomina inquirenda.","PeriodicalId":52151,"journal":{"name":"Plant and Fungal Systematics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45914087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-12-29DOI: 10.35535/pfsyst-2020-0024
Alice Gerlach, R. M. Silveira, C. Rojas, P. Clerc
This study is a reassessment of the Usnea cornuta aggregate diversity mainly in Brazil. Based on previous multi-locus species delimitation analyses using the multispecies coalescent model (MSC), we carried out a posteriori morphological and anatomical studies. The following corticolous new species are described: Usnea arianae with norstictic or fatty or lobaric acids, convex and efflorescent soralia and a lax medulla; U. flabelliformis with protocetraric acid, fan-shaped main branches and a high medulla/cortex ratio; U. rubropallens with protocetraric acid and a faint orange cortical/subcortical pigment; U. stipitata with constictic acid, stipitate soralia and a high medulla/cortex ratio; and U. tenuicorticata with protocetraric acid, a thin cortex and a high medulla/cortex ratio. The newly described species were found to occur so far only in the Americas, except U. arianae which shows an amphi-atlantic distribution in Europe and on the American continent. Seven species already described belonging to the U. cornuta aggr. in Brazil are further treated here: Usnea boomiana with caperatic acid and large, concave soralia, new to South America; U. brasiliensis with protocetraric acid, minute and irregular soralia; U. cornuta with mainly salazinic acid and minute soralia fusing into consoralia; U. macaronesica (syn. nov.: U. subglabrata) with barbatic acid, large excavate soralia and a lax medulla; Usnea subpectinata, a so far european species resurrected from the U. cornuta synonymy, with stictic acid and numerous isidiofibrils, new to South America; and U. trachyclada with thamnolic acid and K+ bright yellow stipitate soralia. Full descriptions with morphological, anatomical and chemical features, geographical distributions, and illustrations are provided for each species along with an identification key.
{"title":"Naming and describing the diversity in the Usnea cornuta aggregate (lichenized Ascomycota, Parmeliaceae) focusing on Brazilian specimens","authors":"Alice Gerlach, R. M. Silveira, C. Rojas, P. Clerc","doi":"10.35535/pfsyst-2020-0024","DOIUrl":"https://doi.org/10.35535/pfsyst-2020-0024","url":null,"abstract":"This study is a reassessment of the Usnea cornuta aggregate diversity mainly in Brazil. Based on previous multi-locus species delimitation analyses using the multispecies coalescent model (MSC), we carried out a posteriori morphological and anatomical studies. The following corticolous new species are described: Usnea arianae with norstictic or fatty or lobaric acids, convex and efflorescent soralia and a lax medulla; U. flabelliformis with protocetraric acid, fan-shaped main branches and a high medulla/cortex ratio; U. rubropallens with protocetraric acid and a faint orange cortical/subcortical pigment; U. stipitata with constictic acid, stipitate soralia and a high medulla/cortex ratio; and U. tenuicorticata with protocetraric acid, a thin cortex and a high medulla/cortex ratio. The newly described species were found to occur so far only in the Americas, except U. arianae which shows an amphi-atlantic distribution in Europe and on the American continent. Seven species already described belonging to the U. cornuta aggr. in Brazil are further treated here: Usnea boomiana with caperatic acid and large, concave soralia, new to South America; U. brasiliensis with protocetraric acid, minute and irregular soralia; U. cornuta with mainly salazinic acid and minute soralia fusing into consoralia; U. macaronesica (syn. nov.: U. subglabrata) with barbatic acid, large excavate soralia and a lax medulla; Usnea subpectinata, a so far european species resurrected from the U. cornuta synonymy, with stictic acid and numerous isidiofibrils, new to South America; and U. trachyclada with thamnolic acid and K+ bright yellow stipitate soralia. Full descriptions with morphological, anatomical and chemical features, geographical distributions, and illustrations are provided for each species along with an identification key.","PeriodicalId":52151,"journal":{"name":"Plant and Fungal Systematics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43263696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-12-29DOI: 10.35535/pfsyst-2020-0020
Alice Gerlach, D. Rodrigues, J. M. Rodríguez, Carlos Enrique Mondaca Rojas, Stella G. Temu, G. Kantvilas
Philippe Clerc was born on April 26, 1955, in Lausanne, Switzerland. He was as an undergraduate at the University of Geneva when he stumbled upon an article in the newspaper Tribune of Geneva about lichens and air pollution that first sparked his interest in lichens. To learn more, he went to Professor G. Turian, who was cited in the article and who loaned him a few books and a microscope, saying ‘First you have to know the species’. So a lichen taxonomist was born! His first academic work dealt with the application of lichens as bioindicators of air pollution in the Wallis region of Switzerland (Clerc & Roh 1979a, b). He obtained his master’s degree in Biology under Prof. Turian’s supervision in 1979. Philippe found his career path through the opportunity to work as a research assistant in the Department of Cryptogamy at the University of Bern under Prof. Klaus Ammann. The Eduard Frey (1888–1974) lichen collection had been acquired recently by the University and, in this collection, Philippe started to study the genus Usnea (the popular ‘old man’s beard’ lichen), which would become his main scientific interest for the next four decades. His first step was to visit Lublin (Poland) to study the collection of the Polish botanist and lichenologist, Józef Motyka (1900–1984), who had published a world monograph of the genus (Motyka 1936–38). The taxonomy and classification of Usnea appeared chaotic at that time and the genus was renowned as one of the most difficult to identify to species level due to its wide phenotypic plasticity and seeming over-abundance of names (as many as 1243). As Philippe later reflected: ‘the first two years of my thesis were completely in the shadows’, but he persisted and gradually dismantled and refined the taxonomy of Usnea. His first publications about the genus were soon published (Clerc 1984a, b) and, at the same time, he also obtained his secondary education certificate (Biology section, under Prof. M. Villard). He was awarded his PhD − ‘Taxonomy and systematics of the genus Usnea in Europe – Preliminary studies towards a monograph’ − in 1986 under the supervision of Professor K. Ammann. After acquiring his doctorate, he moved with his family to the USA to take up a Postdoctoral Research Fellowship at Duke University (North Carolina, USA) under Professors William L. Culberson and Rytas Vilgalys. This was an opportunity to study molecular biology and he became a pioneer in the molecular systematics of Parmeliaceae (1990–1993). He spent 15 months there (1988−1989). Returning to Bern, he started his career, funded by a National Foundation Research Fellowship, which enabled him to continue his project on the molecular systematics of the Parmeliaceae s.l. (lichenized Ascomycetes) that he began during his tenure as a post-doctoral researcher. The molecular era in the classification of lichens was just beginning, and this enabled the elucidation of the biological nature of lichen chimeras (or photosymbiodemes). It was estab
{"title":"A tribute to Philippe Clerc: an eminent and multitalented lichenologist in Switzerland","authors":"Alice Gerlach, D. Rodrigues, J. M. Rodríguez, Carlos Enrique Mondaca Rojas, Stella G. Temu, G. Kantvilas","doi":"10.35535/pfsyst-2020-0020","DOIUrl":"https://doi.org/10.35535/pfsyst-2020-0020","url":null,"abstract":"Philippe Clerc was born on April 26, 1955, in Lausanne, Switzerland. He was as an undergraduate at the University of Geneva when he stumbled upon an article in the newspaper Tribune of Geneva about lichens and air pollution that first sparked his interest in lichens. To learn more, he went to Professor G. Turian, who was cited in the article and who loaned him a few books and a microscope, saying ‘First you have to know the species’. So a lichen taxonomist was born! His first academic work dealt with the application of lichens as bioindicators of air pollution in the Wallis region of Switzerland (Clerc & Roh 1979a, b). He obtained his master’s degree in Biology under Prof. Turian’s supervision in 1979. Philippe found his career path through the opportunity to work as a research assistant in the Department of Cryptogamy at the University of Bern under Prof. Klaus Ammann. The Eduard Frey (1888–1974) lichen collection had been acquired recently by the University and, in this collection, Philippe started to study the genus Usnea (the popular ‘old man’s beard’ lichen), which would become his main scientific interest for the next four decades. His first step was to visit Lublin (Poland) to study the collection of the Polish botanist and lichenologist, Józef Motyka (1900–1984), who had published a world monograph of the genus (Motyka 1936–38). The taxonomy and classification of Usnea appeared chaotic at that time and the genus was renowned as one of the most difficult to identify to species level due to its wide phenotypic plasticity and seeming over-abundance of names (as many as 1243). As Philippe later reflected: ‘the first two years of my thesis were completely in the shadows’, but he persisted and gradually dismantled and refined the taxonomy of Usnea. His first publications about the genus were soon published (Clerc 1984a, b) and, at the same time, he also obtained his secondary education certificate (Biology section, under Prof. M. Villard). He was awarded his PhD − ‘Taxonomy and systematics of the genus Usnea in Europe – Preliminary studies towards a monograph’ − in 1986 under the supervision of Professor K. Ammann. After acquiring his doctorate, he moved with his family to the USA to take up a Postdoctoral Research Fellowship at Duke University (North Carolina, USA) under Professors William L. Culberson and Rytas Vilgalys. This was an opportunity to study molecular biology and he became a pioneer in the molecular systematics of Parmeliaceae (1990–1993). He spent 15 months there (1988−1989). Returning to Bern, he started his career, funded by a National Foundation Research Fellowship, which enabled him to continue his project on the molecular systematics of the Parmeliaceae s.l. (lichenized Ascomycetes) that he began during his tenure as a post-doctoral researcher. The molecular era in the classification of lichens was just beginning, and this enabled the elucidation of the biological nature of lichen chimeras (or photosymbiodemes). It was estab","PeriodicalId":52151,"journal":{"name":"Plant and Fungal Systematics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42954938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-12-29DOI: 10.35535/pfsyst-2020-0033
A. Tsurykau, P. Bely, U. Arup
Molecular analyses of the recently described Xanthoria polessica collected from the type locality and of the Australian species X. coomae were used to determine whether these taxa are distinct species or fall within the wide phenotypic variation of the well-known and cosmopolitan X. parietina. Our results clearly indicate that both taxa should be considered as synonyms of X. parietina since the infraspecific morphological range is accommodated by the observed variation in the thallus and lobe size, their color, position of apothecia, the shape of ascospores, and width of ascospore septum.
{"title":"Molecular phylogenetic analyses reveal two new synonyms of Xanthoria parietina","authors":"A. Tsurykau, P. Bely, U. Arup","doi":"10.35535/pfsyst-2020-0033","DOIUrl":"https://doi.org/10.35535/pfsyst-2020-0033","url":null,"abstract":"Molecular analyses of the recently described Xanthoria polessica collected from the type locality and of the Australian species X. coomae were used to determine whether these taxa are distinct species or fall within the wide phenotypic variation of the well-known and cosmopolitan X. parietina. Our results clearly indicate that both taxa should be considered as synonyms of X. parietina since the infraspecific morphological range is accommodated by the observed variation in the thallus and lobe size, their color, position of apothecia, the shape of ascospores, and width of ascospore septum.","PeriodicalId":52151,"journal":{"name":"Plant and Fungal Systematics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49565394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-12-29DOI: 10.35535/pfsyst-2020-0023
Y. Ohmura
Phylogenetic relationships between Usnea nipparensis and U. sinensis, caperatic acid containing Usnea species, were examined based on ITS rDNA, and the phylogenetic position of U. nipparensis was inferred based on multi-locus gene analysis using ITS rDNA, nuLSU, and MCM7. Although U. nipparensis and U. sinensis have a sorediate and an esorediate shrubby thallus, respectively, and in general look quite different, other detailed morphological and chemical features are similar. Analysis of the ITS rDNA sequences suggests their close relationship, but also confirms the independence of both species, and that they most likely form a ‘species pair’ based on morphological, chemical and molecular phylogenetic data. Phylogenetic trees based on both multi-locus gene and ITS rDNA alone strongly support that U. nipparensis and U. angulata belong to the same clade.
{"title":"Usnea nipparensis and U. sinensis form a ‘species pair ’ presuming morphological, chemical and molecular phylogenetic data","authors":"Y. Ohmura","doi":"10.35535/pfsyst-2020-0023","DOIUrl":"https://doi.org/10.35535/pfsyst-2020-0023","url":null,"abstract":"Phylogenetic relationships between Usnea nipparensis and U. sinensis, caperatic acid containing Usnea species, were examined based on ITS rDNA, and the phylogenetic position of U. nipparensis was inferred based on multi-locus gene analysis using ITS rDNA, nuLSU, and MCM7. Although U. nipparensis and U. sinensis have a sorediate and an esorediate shrubby thallus, respectively, and in general look quite different, other detailed morphological and chemical features are similar. Analysis of the ITS rDNA sequences suggests their close relationship, but also confirms the independence of both species, and that they most likely form a ‘species pair’ based on morphological, chemical and molecular phylogenetic data. Phylogenetic trees based on both multi-locus gene and ITS rDNA alone strongly support that U. nipparensis and U. angulata belong to the same clade.","PeriodicalId":52151,"journal":{"name":"Plant and Fungal Systematics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42536043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-12-29DOI: 10.35535/pfsyst-2020-0032
B. McCune, U. Arup, O. Breuss, Elisa Di Meglio, Joseph Di Meglio, T. L. Esslinger, J. Miadlikowska, Amy E. Miller, R. Rosentreter, Matthias Schultz, J. Sheard, T. Tønsberg, James Walton
We inventoried lichens in Kenai Fjords National Park in Alaska, USA We assembled the known information on occurrence and ecology of lichens in this park by combining field, herbarium, and literature studies. Our results provide baseline data on lichen occurrence that may be used in resource condition assessments, vulnerability assessments, long-term ecological monitoring, and resource management. We report a total of 616 taxa of lichenized fungi from the Park, plus an additional five subspecies and three varieties, all of which are new additions to the National Park Service database for this park unit. An additional five species of nonlichenized lichenicolous fungi are reported here. Eight non-lichenized fungi that are traditionally treated with lichens are also included, most of these associated with bark of particular host species. Four taxa new to North America are reported here (Arctomia delicatula var. acutior, Aspicilia dudinensis, Myriospora myochroa, and Ochrolechia bahusiensis), along with 44 species new to Alaska. Numerous species have been confirmed using ITS barcoding sequences. Also several records assigned to the genus level are reported, many of those are likely new species.
{"title":"Biodiversity and ecology of lichens of Kenai Fjords National Park, Alaska","authors":"B. McCune, U. Arup, O. Breuss, Elisa Di Meglio, Joseph Di Meglio, T. L. Esslinger, J. Miadlikowska, Amy E. Miller, R. Rosentreter, Matthias Schultz, J. Sheard, T. Tønsberg, James Walton","doi":"10.35535/pfsyst-2020-0032","DOIUrl":"https://doi.org/10.35535/pfsyst-2020-0032","url":null,"abstract":"We inventoried lichens in Kenai Fjords National Park in Alaska, USA We assembled the known information on occurrence and ecology of lichens in this park by combining field, herbarium, and literature studies. Our results provide baseline data on lichen occurrence that may be used in resource condition assessments, vulnerability assessments, long-term ecological monitoring, and resource management. We report a total of 616 taxa of lichenized fungi from the Park, plus an additional five subspecies and three varieties, all of which are new additions to the National Park Service database for this park unit. An additional five species of nonlichenized lichenicolous fungi are reported here. Eight non-lichenized fungi that are traditionally treated with lichens are also included, most of these associated with bark of particular host species. Four taxa new to North America are reported here (Arctomia delicatula var. acutior, Aspicilia dudinensis, Myriospora myochroa, and Ochrolechia bahusiensis), along with 44 species new to Alaska. Numerous species have been confirmed using ITS barcoding sequences. Also several records assigned to the genus level are reported, many of those are likely new species.","PeriodicalId":52151,"journal":{"name":"Plant and Fungal Systematics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48163984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-12-29DOI: 10.35535/pfsyst-2020-0031
R. Lücking, B. Moncada, H. Sipman, Priscylla Bezerra Sobreira, C. Viñas, J. Gutiérrez, T. Flynn
The new genus Saxiloba is described with the two species S. firmula from the Caribbean and S. hawaiiensis from Hawaii. Saxiloba is characterized by a unique, placodioid thallus forming distinct lobes, growing on rock in shaded to exposed situations with a trentepohlioid photobiont and a fenestrate thallus anatomy with distinct surface lines. The material is often sterile, but Porina-like perithecia and ascospores had previously been described for the Caribbean taxon and were here confirmed for both species. Molecular sequence data also confirmed placement of this lineage in Porinaceae. Its position within that family supports the notion that Porinaceae should be subdivided into a larger number of genera than proposed in previous classification attempts. Compared to other Porinaceae, Saxiloba exhibits a unique morphology and anatomy that recalls taxa in the related family Graphidaceae and it substantially expands the known phenotypic variation within Porinaceae. The two recognized species are similar in overall morphology but, apart from their disjunct distribution and different substrate ecology, differ in lobe configuration, color and disposition of the crystal clusters and resulting surface patterns.
{"title":"Saxiloba: a new genus of placodioid lichens from the Caribbean and Hawaii shakes up the Porinaceae tree (lichenized Ascomycota: Gyalectales)","authors":"R. Lücking, B. Moncada, H. Sipman, Priscylla Bezerra Sobreira, C. Viñas, J. Gutiérrez, T. Flynn","doi":"10.35535/pfsyst-2020-0031","DOIUrl":"https://doi.org/10.35535/pfsyst-2020-0031","url":null,"abstract":"The new genus Saxiloba is described with the two species S. firmula from the Caribbean and S. hawaiiensis from Hawaii. Saxiloba is characterized by a unique, placodioid thallus forming distinct lobes, growing on rock in shaded to exposed situations with a trentepohlioid photobiont and a fenestrate thallus anatomy with distinct surface lines. The material is often sterile, but Porina-like perithecia and ascospores had previously been described for the Caribbean taxon and were here confirmed for both species. Molecular sequence data also confirmed placement of this lineage in Porinaceae. Its position within that family supports the notion that Porinaceae should be subdivided into a larger number of genera than proposed in previous classification attempts. Compared to other Porinaceae, Saxiloba exhibits a unique morphology and anatomy that recalls taxa in the related family Graphidaceae and it substantially expands the known phenotypic variation within Porinaceae. The two recognized species are similar in overall morphology but, apart from their disjunct distribution and different substrate ecology, differ in lobe configuration, color and disposition of the crystal clusters and resulting surface patterns.","PeriodicalId":52151,"journal":{"name":"Plant and Fungal Systematics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49458638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-12-29DOI: 10.35535/pfsyst-2020-0026
B. Moncada, H. Sipman, R. Lücking
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.
{"title":"Testing DNA barcoding in Usnea (Parmeliaceae) in Colombia using the internal transcribed spacer (ITS)","authors":"B. Moncada, H. Sipman, R. Lücking","doi":"10.35535/pfsyst-2020-0026","DOIUrl":"https://doi.org/10.35535/pfsyst-2020-0026","url":null,"abstract":"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.","PeriodicalId":52151,"journal":{"name":"Plant and Fungal Systematics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45156723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-12-29DOI: 10.35535/pfsyst-2020-0025
R. Lücking, M. R. Nadel, Elena Araujo, Alice Gerlach
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 RAD
{"title":"Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS?","authors":"R. Lücking, M. R. Nadel, Elena Araujo, Alice Gerlach","doi":"10.35535/pfsyst-2020-0025","DOIUrl":"https://doi.org/10.35535/pfsyst-2020-0025","url":null,"abstract":"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 RAD","PeriodicalId":52151,"journal":{"name":"Plant and Fungal Systematics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43370856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-12-29DOI: 10.35535/pfsyst-2020-0022
G. Kantvilas
Two species of Mazosia occur in Tasmania: the foliicolous, pantropical M. phyllosema and M. corticola, here described as new to science. The new species is characterised by a corticolous thallus containing psoromic acid and three-septate ascospores, 17–27 × 4–6.5 μm; it occurs in Tasmanian and Victoria.
{"title":"A new species of Mazosia (lichenised Ascomycetes: Roccellaceae) from Tasmania","authors":"G. Kantvilas","doi":"10.35535/pfsyst-2020-0022","DOIUrl":"https://doi.org/10.35535/pfsyst-2020-0022","url":null,"abstract":"Two species of Mazosia occur in Tasmania: the foliicolous, pantropical M. phyllosema and M. corticola, here described as new to science. The new species is characterised by a corticolous thallus containing psoromic acid and three-septate ascospores, 17–27 × 4–6.5 μm; it occurs in Tasmanian and Victoria.","PeriodicalId":52151,"journal":{"name":"Plant and Fungal Systematics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48535444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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