B. Moncada, J. A. Mercado‐Díaz, Clifford W. Smith, F. Bungartz, E. Sérusiaux, H. Lumbsch, R. Lücking
Abstract: Sticta is a subcosmopolitan genus most diverse in the tropics. Traditionally, many taxa were considered to be widespread and morphologically variable, following broadly circumscribed morphodemes. Among these is the S. weigelii morphodeme, characterized by a cyanobacterial photobiont and rather narrow, flabellate to truncate or tapering lobes producing predominantly marginal isidia. Molecular phylogenetic analyses focusing on the ITS fungal barcoding marker revealed that this morphodeme represents several species, some of which are only distantly related to each other. Here we describe two species and one subspecies of this morphodeme as new to science, based on analysis of 400 specimens, for 344 of which we generated ITS barcoding data. The two new species, S. andina and S. scabrosa, are broadly distributed in the Neotropics and also found in Hawaii, where the latter is represented by the new subspecies, S. scabrosa subsp. hawaiiensis; in the case of S. andina, the species is also found in the Azores. Sticta andina exhibits high phenotypic variation and reticulate genetic diversification, whereas the phenotypically rather uniform S. scabrosa contains two main haplotypes, one restricted to Hawaii. Sticta andina occurs in well-preserved montane to andine forests and paramos, whereas the two subspecies of S. scabrosa are found in tropical lowland to lower montane forests, tolerating disturbance and extending into anthropogenic habitats. Citation: Moncada B., Mercado-Díaz J. A., Smith C. W., Bungartz F., Sérusiaux E., Lumbsch H. T. & Lücking R. 2021: Two new common, previously unrecognized species in the Sticta weigelii morphodeme (Ascomycota: Peltigeraceae). – Willdenowia 51: 35–45. Version of record first published online on 24 February 2021 ahead of inclusion in April 2021 issue.
摘要:刺花属是热带地区分布最广的亚世界性属。传统上，许多分类群被认为是广泛分布和形态可变的，遵循广泛限定的形态。其中有S. weigelii morphodeme，其特征是一个蓝藻光生物和相当狭窄，扇形到截形或渐尖的裂片，主要产生边缘isidia。对ITS真菌条形码标记的分子系统发育分析表明，该形态组代表了多个物种，其中一些物种彼此之间只有远亲关系。在这里，我们根据对400个标本的分析，将该形态亚种描述为科学上的新物种，其中344个标本我们生成了ITS条形码数据。这两个新种，S. andina和S. scabrosa，广泛分布于新热带地区，在夏威夷也有发现，后者以S. scabrosa亚种为代表。hawaiiensis;以S. andina为例，该物种也在亚速尔群岛发现。花楸表现出高度的表型变异和网状遗传多样化，而花楸则表现出表型相当均匀的两种主要单倍型，其中一种仅限于夏威夷。麻刺藓发生在保存完好的山地到山地森林和山地森林中，而麻刺藓的两个亚种则分布在热带低地到低山地森林中，它们能忍受干扰并扩展到人为栖息地。引用本文:Moncada B.， Mercado-Díaz J. A.， Smith C. W.， Bungartz F.， s rusiaux E.， Lumbsch H. T.和l cking R. 2021:一种新发现的未被发现的刺麻属植物(子囊菌科:刺麻科)。- willdewia 51: 35-45。记录版本于2021年2月24日首次在网上发布，并于2021年4月被收录。
{"title":"Two new common, previously unrecognized species in the Sticta weigelii morphodeme (Ascomycota: Peltigeraceae)","authors":"B. Moncada, J. A. Mercado‐Díaz, Clifford W. Smith, F. Bungartz, E. Sérusiaux, H. Lumbsch, R. Lücking","doi":"10.3372/wi.51.51103","DOIUrl":"https://doi.org/10.3372/wi.51.51103","url":null,"abstract":"Abstract: Sticta is a subcosmopolitan genus most diverse in the tropics. Traditionally, many taxa were considered to be widespread and morphologically variable, following broadly circumscribed morphodemes. Among these is the S. weigelii morphodeme, characterized by a cyanobacterial photobiont and rather narrow, flabellate to truncate or tapering lobes producing predominantly marginal isidia. Molecular phylogenetic analyses focusing on the ITS fungal barcoding marker revealed that this morphodeme represents several species, some of which are only distantly related to each other. Here we describe two species and one subspecies of this morphodeme as new to science, based on analysis of 400 specimens, for 344 of which we generated ITS barcoding data. The two new species, S. andina and S. scabrosa, are broadly distributed in the Neotropics and also found in Hawaii, where the latter is represented by the new subspecies, S. scabrosa subsp. hawaiiensis; in the case of S. andina, the species is also found in the Azores. Sticta andina exhibits high phenotypic variation and reticulate genetic diversification, whereas the phenotypically rather uniform S. scabrosa contains two main haplotypes, one restricted to Hawaii. Sticta andina occurs in well-preserved montane to andine forests and paramos, whereas the two subspecies of S. scabrosa are found in tropical lowland to lower montane forests, tolerating disturbance and extending into anthropogenic habitats. Citation: Moncada B., Mercado-Díaz J. A., Smith C. W., Bungartz F., Sérusiaux E., Lumbsch H. T. & Lücking R. 2021: Two new common, previously unrecognized species in the Sticta weigelii morphodeme (Ascomycota: Peltigeraceae). – Willdenowia 51: 35–45. Version of record first published online on 24 February 2021 ahead of inclusion in April 2021 issue.","PeriodicalId":48969,"journal":{"name":"Willdenowia","volume":"51 1","pages":"35 - 45"},"PeriodicalIF":1.9,"publicationDate":"2021-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47832087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Callmander, R. Vogt, Anna Donatelli, S. Buerki, C. Nepi
Abstract: Otto Warburg (1859–1938) had a great interest in tropical botany. He travelled in South-East Asia and the South Pacific between 1885 and 1889 and brought back a considerable collection of plant specimens from this expedition later donated to the Royal Botanical Museum in Berlin. Warburg published the first comprehensive monograph on the family Pandanaceae in 1900 in the third issue of Das Pflanzenreich established and edited by Adolf Engler (1844–1930). The aim of this article is to clarify the taxonomy, nomenclature and typification of Warburg's contributions to the Pandanaceae. Considerable parts of Warburg's original material was destroyed in Berlin during World War II but duplicates survived, shared by Engler and Warburg with Ugolino Martelli (1860–1934). Martelli was an expert on the family and he assembled a precious herbarium of Pandanaceae that was later donated to the Museo di Storia Naturale dell'Università degli Studi di Firenze. Warburg published 86 new names in Pandanaceae between 1898 and 1909 (five new sections, 69 new species, five new varieties, two new combinations and five replacement names). A complete review of the material extant in B and FI led to the conclusion that 38 names needed a nomenclatural act: 34 lectotypes, three neotypes and one epitype are designated here. Twenty new synonyms are also proposed. One Freycinetia name and six Pandanus names are considered as incertae sedis. A total of 21 names published by Warburg are accepted: 11 in Freycinetia and ten in Pandanus. In addition, four names published in Pandanus by Warburg serve as the basionyms of accepted names in the genus Benstonea. Citation: Callmander M. W., Vogt R., Donatelli A., Buerki S. & Nepi C. 2021: Otto Warburg and his contributions to the screw pine family (Pandanaceae). – Willdenowia 51: 5–31. Version of record first published online on 15 February 2021 ahead of inclusion in April 2021 issue.
{"title":"Otto Warburg and his contributions to the screw pine family (Pandanaceae)","authors":"M. Callmander, R. Vogt, Anna Donatelli, S. Buerki, C. Nepi","doi":"10.3372/wi.51.51101","DOIUrl":"https://doi.org/10.3372/wi.51.51101","url":null,"abstract":"Abstract: Otto Warburg (1859–1938) had a great interest in tropical botany. He travelled in South-East Asia and the South Pacific between 1885 and 1889 and brought back a considerable collection of plant specimens from this expedition later donated to the Royal Botanical Museum in Berlin. Warburg published the first comprehensive monograph on the family Pandanaceae in 1900 in the third issue of Das Pflanzenreich established and edited by Adolf Engler (1844–1930). The aim of this article is to clarify the taxonomy, nomenclature and typification of Warburg's contributions to the Pandanaceae. Considerable parts of Warburg's original material was destroyed in Berlin during World War II but duplicates survived, shared by Engler and Warburg with Ugolino Martelli (1860–1934). Martelli was an expert on the family and he assembled a precious herbarium of Pandanaceae that was later donated to the Museo di Storia Naturale dell'Università degli Studi di Firenze. Warburg published 86 new names in Pandanaceae between 1898 and 1909 (five new sections, 69 new species, five new varieties, two new combinations and five replacement names). A complete review of the material extant in B and FI led to the conclusion that 38 names needed a nomenclatural act: 34 lectotypes, three neotypes and one epitype are designated here. Twenty new synonyms are also proposed. One Freycinetia name and six Pandanus names are considered as incertae sedis. A total of 21 names published by Warburg are accepted: 11 in Freycinetia and ten in Pandanus. In addition, four names published in Pandanus by Warburg serve as the basionyms of accepted names in the genus Benstonea. Citation: Callmander M. W., Vogt R., Donatelli A., Buerki S. & Nepi C. 2021: Otto Warburg and his contributions to the screw pine family (Pandanaceae). – Willdenowia 51: 5–31. Version of record first published online on 15 February 2021 ahead of inclusion in April 2021 issue.","PeriodicalId":48969,"journal":{"name":"Willdenowia","volume":"51 1","pages":"5 - 31"},"PeriodicalIF":1.9,"publicationDate":"2021-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48685683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Van de Vijver B., Tudesque L. & Ector L. (ed.), Diatom taxonomy and ecology. From France to the sub-Antarctic islands. Celebrating the work and life of Prof. Dr. René Le Cohu on the occasion of his 80th birthday. – Nova Hedwigia Beiheft 146. – Stuttgart: J. Cramer in Borntraeger Science Publishers, 2017. – ISBN 978-3-443-51068-8. – 17 × 24 cm, 780 g, 325 pp., 1210 figures, 24 tables, softback. – Price: EUR 139.00. – Available at https://www.schweizerbart.de/papers/nova_suppl/list/146#issue Citation: Mora D. 2021: Book review: Van de Vijver B., Tudesque L. & Ector L. (ed.), Diatom taxonomy and ecology. From France to the sub-Antarctic islands. Celebrating the work and life of Prof. Dr. René Le Cohu on the occasion of his 80th birthday. – Willdenowia 51: 33–34. Version of record first published online on 15 February 2021 ahead of inclusion in April 2021 issue.
Van de Vijver B.，Tudesque L.和Ector L.（编辑），硅藻分类学和生态学。从法国到亚南极群岛。在勒内·勒科胡教授博士80岁生日之际庆祝他的工作和生活Nova Hedwigia Beiheft 146.–斯图加特：J.Cramer在博恩特雷格科学出版社，2017年ISBN 978-3-443-51068-817×24厘米，780克，325页，1210幅，24张桌子，软背价格：139.00欧元可在https://www.schweizerbart.de/papers/nova_suppl/list/146#issue引文：Mora D.2021：书评：Van de Vijver B.，Tudesque L.&Ector L.（编辑），硅藻分类学与生态学。从法国到亚南极群岛。在勒内·勒科胡教授博士80岁生日之际庆祝他的工作和生活Willdenowia 51:33-34。该记录的版本于2021年2月15日首次在线发布，随后将于2021年4月出版。
{"title":"Book review: Van de Vijver B., Tudesque L. & Ector L. (ed.), Diatom taxonomy and ecology. From France to the sub-Antarctic islands. Celebrating the work and life of Prof. Dr. René Le Cohu on the occasion of his 80th birthday","authors":"Demetrio Mora","doi":"10.3372/wi.51.51102","DOIUrl":"https://doi.org/10.3372/wi.51.51102","url":null,"abstract":"Van de Vijver B., Tudesque L. & Ector L. (ed.), Diatom taxonomy and ecology. From France to the sub-Antarctic islands. Celebrating the work and life of Prof. Dr. René Le Cohu on the occasion of his 80th birthday. – Nova Hedwigia Beiheft 146. – Stuttgart: J. Cramer in Borntraeger Science Publishers, 2017. – ISBN 978-3-443-51068-8. – 17 × 24 cm, 780 g, 325 pp., 1210 figures, 24 tables, softback. – Price: EUR 139.00. – Available at https://www.schweizerbart.de/papers/nova_suppl/list/146#issue Citation: Mora D. 2021: Book review: Van de Vijver B., Tudesque L. & Ector L. (ed.), Diatom taxonomy and ecology. From France to the sub-Antarctic islands. Celebrating the work and life of Prof. Dr. René Le Cohu on the occasion of his 80th birthday. – Willdenowia 51: 33–34. Version of record first published online on 15 February 2021 ahead of inclusion in April 2021 issue.","PeriodicalId":48969,"journal":{"name":"Willdenowia","volume":"51 1","pages":"33 - 34"},"PeriodicalIF":1.9,"publicationDate":"2021-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45040192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Index to typifications of names in Willdenowia 50(3)","authors":"","doi":"10.3372/wi.50.50306","DOIUrl":"https://doi.org/10.3372/wi.50.50306","url":null,"abstract":"","PeriodicalId":48969,"journal":{"name":"Willdenowia","volume":"50 1","pages":"560 - 560"},"PeriodicalIF":1.9,"publicationDate":"2020-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41530029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Index to new names and combinations appearing in Willdenowia 50(3)","authors":"","doi":"10.3372/wi.50.50305","DOIUrl":"https://doi.org/10.3372/wi.50.50305","url":null,"abstract":"","PeriodicalId":48969,"journal":{"name":"Willdenowia","volume":"50 1","pages":"559 - 559"},"PeriodicalIF":1.9,"publicationDate":"2020-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47376882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract: The botanical exploration of Albania in its modern sense started in the mid-nineteenth century with the collections and publications of A. Grisebach, E. Weiss and C. Grimus von Grimburg, who followed the road from Prizren to Shkoder or were active in the hinterland of the harbours on the Adriatic Sea. In the late nineteenth and early twentieth centuries, A. Baldacci, N. Košanin and I. Dörfler laid the foundations of the floristic knowledge of Albania, focusing their attention on northern Albania and the coastal regions. A considerable amount of collecting was undertaken during the First World War by people commissioned by or active for the foreign powers occupying the country, with the major results published by A. Hayek in Vienna and S. Jávorka in Budapest. In the interwar period, F. Markgraf concentrated his floristic research on central Albania, although his work remained uncompleted. Even during the Second World War, collecting and publishing on the flora of Albania did not come to a stop. However, in the mid-twentieth century considerable areas of Albania remained totally unknown botanically, in particular in the southern part of the country. This contribution gives a detailed and critical overview of the botanical exploration of Albania from 1839 until 1945 with emphasis on the collecting routes, the widely scattered herbarium record and the interdependence of field work and the political (and military) situation in the country. Citation: Lack H. W. & Barina Z. 2020: The early botanical exploration of Albania (1839–1945). – Willdenowia 50: 519–558. Version of record first published online on 17 December 2020 ahead of inclusion in December 2020 issue.
摘要：阿尔巴尼亚现代意义上的植物探索始于19世纪中期，由A.Grisebah、E.Weiss和C.Grimus von Grimburg收集和出版，他们沿着普里兹伦到什科德的道路，或活跃在亚得里亚海港口腹地。19世纪末和20世纪初，A.Baldacci、N.Košanin和I.Dörfler奠定了阿尔巴尼亚植物区系知识的基础，他们将注意力集中在阿尔巴尼亚北部和沿海地区。第一次世界大战期间，占领该国的外国势力委托或为其活动的人进行了大量的收集，主要成果由A.Hayek在维也纳和S.Jávorka在布达佩斯发表。在两次世界大战期间，F.Markgraf将他的植物区系研究集中在阿尔巴尼亚中部，尽管他的工作仍未完成。即使在第二次世界大战期间，阿尔巴尼亚植物群的收集和出版也没有停止。然而，在二十世纪中期，阿尔巴尼亚的相当一部分地区在植物学上仍然完全不为人知，尤其是在该国南部。这篇文章详细而批判性地概述了1839年至1945年阿尔巴尼亚的植物探索，重点介绍了采集路线、广泛分布的植物标本馆记录以及实地工作与该国政治（和军事）局势的相互依存性。引文：Lack H.W.&Barina Z.2020：阿尔巴尼亚的早期植物学探索（1839–1945）Willdenowia 50:519–558。该记录的版本于2020年12月17日首次在线发布，随后将收录在2020年12月刊中。
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Abstract: Eocene Baltic amber forms the largest amber deposit worldwide; however, its source vegetation and climate are much debated. Representatives of the oak family (Fagaceae) were abundant in the Baltic amber source area based on numerous inclusions of staminate inflorescences or individual florets, previously assigned to Castanea and Quercus. However, the actual generic and infrageneric diversity of Fagaceae from Baltic amber remained unknown. Using flower characteristics and section-diagnostic in situ pollen of staminate inflorescences and detached floret inclusions, we describe 18 fossil-species of Fagaceae making this family by far the most diverse plant family preserved in Baltic amber. We substantiate the occurrence of the Castaneoideae, Quercoideae (Quercus sect. Cyclobalanopsis/Lobatae; Q. sect. Lobatae; Q. sect. Protobalanus), Trigonobalanoideae and the extinct genus Eotrigonobalanus. Among the 18 fossil-species, six are described as new: Q. aimeeana, Q. casparyi, Q. multipilosa, E. campanulata, E. conwentzii, E. longianthera; and one new combination is published: Q. brachyandra (≡ Castanea brachyandra). In addition, a lectotype is designated for the name Quercites meyerianus and neotypes are designated for the names Castanea inclusa and Quercus longistaminea (≡ C. longistaminea). Members of the Fagaceae probably inhabited azonal and zonal vegetation types of the amber source area, including bottomland flood-plains and stream banks (Q. sect. Lobatae), dry habitats (Q. sect. Lobatae, Q. sect. Protobalanus), peaty soils, riparian and swamp forests (Castanopsis, Eotrigonobalanus), as well as mixed mesophytic forests (castaneoids, Quercoideae, trigonobalanoids). Affinities to extant North American and E to SE Asian floras support the recent notion that late Eocene Baltic amber (38–34 Ma) was formed in a warm-temperate climate. Citation: Sadowski E.-M., Schmidt A. R. & Denk T. 2020: Staminate inflorescences with in situ pollen from Eocene Baltic amber reveal high diversity in Fagaceae (oak family). – Willdenowia 50: 405–517. doi: https://doi.org/10.3372/wi.50.50303 Version of record first published online on 1 December 2020 ahead of inclusion in December 2020 issue.
{"title":"Staminate inflorescences with in situ pollen from Eocene Baltic amber reveal high diversity in Fagaceae (oak family)","authors":"Eva‐Maria Sadowski, A. Schmidt, T. Denk","doi":"10.3372/wi.50.50303","DOIUrl":"https://doi.org/10.3372/wi.50.50303","url":null,"abstract":"Abstract: Eocene Baltic amber forms the largest amber deposit worldwide; however, its source vegetation and climate are much debated. Representatives of the oak family (Fagaceae) were abundant in the Baltic amber source area based on numerous inclusions of staminate inflorescences or individual florets, previously assigned to Castanea and Quercus. However, the actual generic and infrageneric diversity of Fagaceae from Baltic amber remained unknown. Using flower characteristics and section-diagnostic in situ pollen of staminate inflorescences and detached floret inclusions, we describe 18 fossil-species of Fagaceae making this family by far the most diverse plant family preserved in Baltic amber. We substantiate the occurrence of the Castaneoideae, Quercoideae (Quercus sect. Cyclobalanopsis/Lobatae; Q. sect. Lobatae; Q. sect. Protobalanus), Trigonobalanoideae and the extinct genus Eotrigonobalanus. Among the 18 fossil-species, six are described as new: Q. aimeeana, Q. casparyi, Q. multipilosa, E. campanulata, E. conwentzii, E. longianthera; and one new combination is published: Q. brachyandra (≡ Castanea brachyandra). In addition, a lectotype is designated for the name Quercites meyerianus and neotypes are designated for the names Castanea inclusa and Quercus longistaminea (≡ C. longistaminea). Members of the Fagaceae probably inhabited azonal and zonal vegetation types of the amber source area, including bottomland flood-plains and stream banks (Q. sect. Lobatae), dry habitats (Q. sect. Lobatae, Q. sect. Protobalanus), peaty soils, riparian and swamp forests (Castanopsis, Eotrigonobalanus), as well as mixed mesophytic forests (castaneoids, Quercoideae, trigonobalanoids). Affinities to extant North American and E to SE Asian floras support the recent notion that late Eocene Baltic amber (38–34 Ma) was formed in a warm-temperate climate. Citation: Sadowski E.-M., Schmidt A. R. & Denk T. 2020: Staminate inflorescences with in situ pollen from Eocene Baltic amber reveal high diversity in Fagaceae (oak family). – Willdenowia 50: 405–517. doi: https://doi.org/10.3372/wi.50.50303 Version of record first published online on 1 December 2020 ahead of inclusion in December 2020 issue.","PeriodicalId":48969,"journal":{"name":"Willdenowia","volume":"50 1","pages":"405 - 517"},"PeriodicalIF":1.9,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47934960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
R. Lücking, B. Truong, Dang Thi Thu Huong, Ngoc Han Le, Q. D. Nguyen, Van Dat Nguyen, E. Raab-Straube, S. Bollendorff, K. Govers, Vanessa Di Vincenzo
Abstract: DNA barcoding using the nuclear internal transcribed spacer (ITS) has become prevalent in surveys of fungal diversity. This approach is, however, associated with numerous caveats, including the desire for speed, rather than accuracy, through the use of automated analytical pipelines, and the shortcomings of reference sequence repositories. Here we use the case of a specimen of the bracket fungus Trametes s.lat. (which includes the common and widespread turkey tail, T. versicolor) to illustrate these problems. The material was collected in Vietnam as part of a biodiversity inventory including DNA barcoding approaches for arthropods, plants and fungi. The ITS barcoding sequence of the query taxon was compared against reference sequences in GenBank and the curated fungal ITS database UNITE, using BLASTn and MegaBLAST, and was subsequently analysed in a multiple alignment-based phylogenetic context through a maximum likelihood tree including related sequences. Our results initially indicated issues with BLAST searches, including the use of pairwise local alignments and sorting through Total score and E value, rather than Percentage identity, as major shortcomings of the DNA barcoding approach. However, after thorough analysis of the results, we concluded that the single most important problem of this approach was incorrect sequence labelling, calling for the implementation of third-party annotations or analogous approaches in primary sequence repositories. In addition, this particular example revealed problems of improper fungal nomenclature, which required reinstatement of the genus name Cubamyces (= Leiotrametes), with three new combinations: C. flavidus, C. lactineus and C. menziesii. The latter was revealed as the correct identification of the query taxon, although the name did not appear among the best BLAST hits. While the best BLAST hits did correspond to the target taxon in terms of sequence data, their label names were misleading or unresolved, including [Fungal endophyte], [Uncultured fungus], Basidiomycota, Trametes cf. cubensis, Lenzites elegans and Geotrichum candidum (an unrelated ascomycetous contaminant). Our study demonstrates that accurate identification of fungi through molecular barcoding is currently not a fast-track approach that can be achieved through automated pipelines. Citation: Lücking R., Truong B. V., Huong D. T. T., Le N. H., Nguyen Q. D., Nguyen V. D., Raab-Straube E. von, Bollendorff S., Govers K. & Di Vincenzo V. 2020: Caveats of fungal barcoding: a case study in Trametes s.lat. (Basidiomycota: Polyporales) in Vietnam reveals multiple issues with mislabelled reference sequences and calls for third-party annotations. – Willdenowia 50: 383–403. doi: https://doi.org/10.3372/wi.50.50302 Version of record first published online on 15 September 2020 ahead of inclusion in December 2020 issue.
摘要:利用核内转录间隔段(ITS)进行DNA条形码技术在真菌多样性调查中已成为一种普遍的方法。然而，这种方法伴随着许多警告，包括对速度的渴望，而不是准确性，通过使用自动化分析管道，以及参考序列存储库的缺点。这里我们以支架真菌Trametes .lat的标本为例。(其中包括常见和广泛分布的火鸡尾巴，T. versicolor)来说明这些问题。这些材料是在越南收集的，作为生物多样性清单的一部分，其中包括节肢动物、植物和真菌的DNA条形码方法。使用BLASTn和MegaBLAST将查询分类单元的ITS条形码序列与GenBank和整理的真菌ITS数据库UNITE中的参考序列进行比较，随后通过包含相关序列的最大似然树在基于多比对的系统发育背景下进行分析。我们的结果最初表明了BLAST搜索的问题，包括使用成对局部比对和通过总分和E值排序，而不是百分比身份，这是DNA条形码方法的主要缺点。然而，经过对结果的彻底分析，我们得出结论，这种方法的一个最重要的问题是不正确的序列标记，需要在主序列存储库中实现第三方注释或类似的方法。此外，这个特殊的例子揭示了真菌命名不当的问题，这需要恢复属名Cubamyces (= Leiotrametes)，用三个新的组合:C. flavidus, C. lactineus和C. menziesii。后者显示为查询分类单元的正确标识，尽管该名称没有出现在最佳BLAST命中。虽然从序列数据来看，BLAST命中的最佳目标分类群确实与目标分类群相对应，但它们的标签名称具有误导性或未确定，包括[真菌内生菌]、[未培养真菌]、担子菌、Trametes cf. cubensis、Lenzites elegans和Geotrichum candidum(一种无关的子囊菌污染物)。我们的研究表明，通过分子条形码准确鉴定真菌目前不是一种可以通过自动化管道实现的快速通道方法。引用本文:l cking R.， Truong b.v V, Huong d.t.t T, Le n.h .， Nguyen Q. D.， Raab-Straube E. von, Bollendorff S.， Govers K.和Di Vincenzo V. 2020:真菌条形码的注意:以真菌为例研究。(担子菌:Polyporales)在越南揭示了与错误标记的参考序列和要求第三方注释的多个问题。-野生动物学报50:383-403。doi: https://doi.org/10.3372/wi.50.50302记录版本于2020年9月15日首次在线发布，随后将被纳入2020年12月号。
{"title":"Caveats of fungal barcoding: a case study in Trametes s.lat. (Basidiomycota: Polyporales) in Vietnam reveals multiple issues with mislabelled reference sequences and calls for third-party annotations","authors":"R. Lücking, B. Truong, Dang Thi Thu Huong, Ngoc Han Le, Q. D. Nguyen, Van Dat Nguyen, E. Raab-Straube, S. Bollendorff, K. Govers, Vanessa Di Vincenzo","doi":"10.3372/wi.50.50302","DOIUrl":"https://doi.org/10.3372/wi.50.50302","url":null,"abstract":"Abstract: DNA barcoding using the nuclear internal transcribed spacer (ITS) has become prevalent in surveys of fungal diversity. This approach is, however, associated with numerous caveats, including the desire for speed, rather than accuracy, through the use of automated analytical pipelines, and the shortcomings of reference sequence repositories. Here we use the case of a specimen of the bracket fungus Trametes s.lat. (which includes the common and widespread turkey tail, T. versicolor) to illustrate these problems. The material was collected in Vietnam as part of a biodiversity inventory including DNA barcoding approaches for arthropods, plants and fungi. The ITS barcoding sequence of the query taxon was compared against reference sequences in GenBank and the curated fungal ITS database UNITE, using BLASTn and MegaBLAST, and was subsequently analysed in a multiple alignment-based phylogenetic context through a maximum likelihood tree including related sequences. Our results initially indicated issues with BLAST searches, including the use of pairwise local alignments and sorting through Total score and E value, rather than Percentage identity, as major shortcomings of the DNA barcoding approach. However, after thorough analysis of the results, we concluded that the single most important problem of this approach was incorrect sequence labelling, calling for the implementation of third-party annotations or analogous approaches in primary sequence repositories. In addition, this particular example revealed problems of improper fungal nomenclature, which required reinstatement of the genus name Cubamyces (= Leiotrametes), with three new combinations: C. flavidus, C. lactineus and C. menziesii. The latter was revealed as the correct identification of the query taxon, although the name did not appear among the best BLAST hits. While the best BLAST hits did correspond to the target taxon in terms of sequence data, their label names were misleading or unresolved, including [Fungal endophyte], [Uncultured fungus], Basidiomycota, Trametes cf. cubensis, Lenzites elegans and Geotrichum candidum (an unrelated ascomycetous contaminant). Our study demonstrates that accurate identification of fungi through molecular barcoding is currently not a fast-track approach that can be achieved through automated pipelines. Citation: Lücking R., Truong B. V., Huong D. T. T., Le N. H., Nguyen Q. D., Nguyen V. D., Raab-Straube E. von, Bollendorff S., Govers K. & Di Vincenzo V. 2020: Caveats of fungal barcoding: a case study in Trametes s.lat. (Basidiomycota: Polyporales) in Vietnam reveals multiple issues with mislabelled reference sequences and calls for third-party annotations. – Willdenowia 50: 383–403. doi: https://doi.org/10.3372/wi.50.50302 Version of record first published online on 15 September 2020 ahead of inclusion in December 2020 issue.","PeriodicalId":48969,"journal":{"name":"Willdenowia","volume":"50 1","pages":"383 - 403"},"PeriodicalIF":1.9,"publicationDate":"2020-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43862537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract: The genus Gomphrena comprises about 120 species in the Americas and 35 in Australia. Previous research revealed that Gossypianthus, Lithophila and Philoxerus are closely related but the monophyly of Gomphrena remained unresolved. Our aim was to clarify phylogenetic relationships in Gomphrena and allies based on a thorough sampling of species and to reconstruct the evolution of morphological characters including C4 photosynthesis, and to explore the disjunction of the Australian taxa. We generated datasets of plastid (matK-trnK, trnL-F, rpl16) and nrITS representing 45 taxa of Gomphrena plus relatives and analysed them with parsimony, likelihood and Bayesian methods. Ancestral states of phenotypic characters were reconstructed with BayesTraits. BEAST was employed for divergence time estimates using an extended Amaranthaceae–Chenopodiaceae dataset to place fossil calibration points. Gossypianthus is closely related to a Gomphrena radiata–G. umbellata–G. tomentosa clade and G. meyeniana, whereas Lithophila and Philoxerus appear as successive sisters of the Australian species of Gomphrena. The majority of Andean species appears in a large clade including annual and perennial species. The Cerrado species Gomphrena mollis and G. rupestris, which are C3, constitute an early-branching lineage, whereas the core Gomphrena clade is C4 and has the inner two sepals strongly compressed as synapomorphy. A major subclade evolved inflorescences with subglobose paracladia in a whorl, supported by pseudanthial leaves. Whereas the core Gomphrena clade started to diversify around 11.4 Ma (8.45–14.5 95% highest posterior density [HPD]) the Australian lineage split at only 4.8 Ma (2.61–7.18 HPD). Our detailed phylogenetic analysis of Gomphrena depicts 10 major lineages including segregate genera. We hypothesize that an adaptation to costal habitats was followed by long-distance dispersal to Australia. We also propose a revised genus concept of Gomphrena including Gossypianthus, Lithophila and Philoxerus, considering that these small segregate genera were based on states of vegetative characters exhibiting adaptations to specific habitats rather than phylogeny and overall morphology. Citation: Ortuño Limarino T. & Borsch Th. 2020: Gomphrena (Amaranthaceae, Gomphrenoideae) diversified as a C4 lineage in the New World tropics with specializations in floral and inflorescence morphology, and an escape to Australia. – Willdenowia 50: 345–381. doi: https://doi.org/10.3372/wi.50.50301 Version of record first published online on 31 August 2020 ahead of inclusion in December 2020 issue.
{"title":"Gomphrena (Amaranthaceae, Gomphrenoideae) diversified as a C4 lineage in the New World tropics with specializations in floral and inflorescence morphology, and an escape to Australia","authors":"Teresa Ortuño Limarino, T. Borsch","doi":"10.3372/wi.50.50301","DOIUrl":"https://doi.org/10.3372/wi.50.50301","url":null,"abstract":"Abstract: The genus Gomphrena comprises about 120 species in the Americas and 35 in Australia. Previous research revealed that Gossypianthus, Lithophila and Philoxerus are closely related but the monophyly of Gomphrena remained unresolved. Our aim was to clarify phylogenetic relationships in Gomphrena and allies based on a thorough sampling of species and to reconstruct the evolution of morphological characters including C4 photosynthesis, and to explore the disjunction of the Australian taxa. We generated datasets of plastid (matK-trnK, trnL-F, rpl16) and nrITS representing 45 taxa of Gomphrena plus relatives and analysed them with parsimony, likelihood and Bayesian methods. Ancestral states of phenotypic characters were reconstructed with BayesTraits. BEAST was employed for divergence time estimates using an extended Amaranthaceae–Chenopodiaceae dataset to place fossil calibration points. Gossypianthus is closely related to a Gomphrena radiata–G. umbellata–G. tomentosa clade and G. meyeniana, whereas Lithophila and Philoxerus appear as successive sisters of the Australian species of Gomphrena. The majority of Andean species appears in a large clade including annual and perennial species. The Cerrado species Gomphrena mollis and G. rupestris, which are C3, constitute an early-branching lineage, whereas the core Gomphrena clade is C4 and has the inner two sepals strongly compressed as synapomorphy. A major subclade evolved inflorescences with subglobose paracladia in a whorl, supported by pseudanthial leaves. Whereas the core Gomphrena clade started to diversify around 11.4 Ma (8.45–14.5 95% highest posterior density [HPD]) the Australian lineage split at only 4.8 Ma (2.61–7.18 HPD). Our detailed phylogenetic analysis of Gomphrena depicts 10 major lineages including segregate genera. We hypothesize that an adaptation to costal habitats was followed by long-distance dispersal to Australia. We also propose a revised genus concept of Gomphrena including Gossypianthus, Lithophila and Philoxerus, considering that these small segregate genera were based on states of vegetative characters exhibiting adaptations to specific habitats rather than phylogeny and overall morphology. Citation: Ortuño Limarino T. & Borsch Th. 2020: Gomphrena (Amaranthaceae, Gomphrenoideae) diversified as a C4 lineage in the New World tropics with specializations in floral and inflorescence morphology, and an escape to Australia. – Willdenowia 50: 345–381. doi: https://doi.org/10.3372/wi.50.50301 Version of record first published online on 31 August 2020 ahead of inclusion in December 2020 issue.","PeriodicalId":48969,"journal":{"name":"Willdenowia","volume":"50 1","pages":"345 - 381"},"PeriodicalIF":1.9,"publicationDate":"2020-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47059427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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