1
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White KH, Keepers K, Kane N, Lendemer JC. Discovery of New Genomic Configuration of Mating-Type Loci in the Largest Lineage of Lichen-Forming Fungi. Genome Biol Evol 2024; 16:evae094. [PMID: 38686438 PMCID: PMC11126327 DOI: 10.1093/gbe/evae094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
The genetic architecture of mating-type loci in lichen-forming fungi has been characterized in very few taxa. Despite the limited data, and in contrast to all other major fungal lineages, arrangements that have both mating-type alleles in a single haploid genome have been hypothesized to be absent from the largest lineage of lichen-forming fungi, the Lecanoromycetes. We report the discovery of both mating-type alleles from the haploid genomes of three species within this group. Our results demonstrate that Lecanoromycetes are not an outlier among Ascomycetes.
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Affiliation(s)
- Kristin H White
- Department of Ecology and Evolution, University of Colorado, Boulder, CO 80309, USA
| | - Kyle Keepers
- Department of Ecology and Evolution, University of Colorado, Boulder, CO 80309, USA
| | - Nolan Kane
- Department of Ecology and Evolution, University of Colorado, Boulder, CO 80309, USA
| | - James C Lendemer
- Department of Botany, Research and Collections, CEC 3148, The New York State Museum, Albany, NY 12230, USA
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2
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Leavitt SD, DeBolt A, McQuhae E, Allen JL. Genomic Resources for the First Federally Endangered Lichen: The Florida Perforate Cladonia ( Cladonia perforata). J Fungi (Basel) 2023; 9:698. [PMID: 37504687 PMCID: PMC10381751 DOI: 10.3390/jof9070698] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/29/2023] Open
Abstract
Thirty years after its designation as a federally endangered species, the Florida Perforate Cladonia (FPC) remains imperiled in isolated populations in the Florida scrub in the southeastern USA. For threatened and endangered species, such as FPC, reference genomes provide critical insight into genomic diversity, local adaptations, landscape-level genetics, and phylogenomics. Using high-throughput sequencing, we assemble the first draft nuclear and mitochondrial genomes for the FPC mycobiont-Cladonia perforata. We also assess genetic diversity within and among populations in southeastern Florida using genome-scale data and investigate diversity across the entire nuclear ribosomal cistron, including the standard DNA barcoding marker for fungi. The draft nuclear genome spanned 33.6 Mb, and the complete, circular mitochondrial genome was 59 Kb. We also generated the first chloroplast genome, to our knowledge, for the photobiont genus associated with FPC, an undescribed Asterochloris species. We inferred the presence of multiple, distinct mycobiont parental genotypes (genets) occurring at local scales in southeastern Florida, and strikingly, no genets were shared among even the closest sample sites. All sampled thalli shared identical mitochondrial genomes, while the nuclear ribosomal cistron showed limited variability-highlighting the genetic resolution provided by nuclear genome-scale datasets. The genomic resources generated here provide critical resources for informed conservation efforts for the FPC.
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Affiliation(s)
- Steven D Leavitt
- M.L. Bean Life Science Museum and Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Ann DeBolt
- Department of Biology, Boise State University, Boise, ID 83725, USA
| | - Ethan McQuhae
- Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Jessica L Allen
- Department of Biology, Eastern Washington University, Cheney, WA 99004, USA
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3
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Alonso-García M, Pino-Bodas R, Villarreal A JC. Co-dispersal of symbionts in the lichen Cladonia stellaris inferred from genomic data. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2022.101165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Núñez-Torres OP, Almeida-Secaira RI. Genética cuantitativa: principios de la crianza en la producción pecuaria. JOURNAL OF THE SELVA ANDINA ANIMAL SCIENCE 2022. [DOI: 10.36610/j.jsaas.2022.090100023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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5
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Núñez-Torres OP, Almeida-Secaira RI. Quantitative genetics: principles of farming in livestock production. JOURNAL OF THE SELVA ANDINA ANIMAL SCIENCE 2022. [DOI: 10.36610/j.jsaas.2022.090100023x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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6
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Boluda CG, Rico VJ, Naciri Y, Hawksworth DL, Scheidegger C. Phylogeographic reconstructions can be biased by ancestral shared alleles: The case of the polymorphic lichen Bryoria fuscescens in Europe and North Africa. Mol Ecol 2021; 30:4845-4865. [PMID: 34252241 DOI: 10.1111/mec.16078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 06/21/2021] [Accepted: 06/29/2021] [Indexed: 11/26/2022]
Abstract
Large phylogeographic studies on lichens are scarce, and none involves a single species within which different lineages show fixed alternative dispersal strategies. We investigated Bryoria fuscescens (including B. capillaris) in Europe and western North Africa by phenotypically characterizing 1400 specimens from 64 populations and genotyping them with 14 microsatellites. We studied population structure and genetic diversity at the local and continental scales, discussed the post-glacial phylogeography, and compared dispersal capacities of phenotypes with and without soralia. Our main hypothesis is that the estimated phylogeography, migration routes, and dispersal capacities may be strongly biased by ancestral shared alleles. Scandinavia is genetically the richest area, followed by the Iberian Peninsula, the Carpathians, and the Alps. Three gene pools were detected: two partially linked to phenotypic characteristics, and the third one genetically related to the American sister species B. pseudofuscescens. The comparison of one gene pool producing soredia and one not, suggested both as panmictic, with similar levels of isolation by distance (IBD). The migration routes were estimated to span from north to south, in disagreement with the assessed glacial refugia. The presence of ancestral shared alleles in distant populations can explain the similar IBD levels found in both gene pools while producing a false signal of panmixia, and also biasing the phylogeographic reconstruction. The incomplete lineage sorting recorded for DNA sequence loci also supports this hypothesis. Consequently, the high diversity in Scandinavia may rather come from recent immigration into northern populations than from an in situ diversification. Similar patterns of ancestral shared polymorphism may bias the phylogeographical reconstruction of other lichen species.
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Affiliation(s)
- Carlos G Boluda
- Departamento de Farmacología, Farmacognosia y Botánica (U.D. Botánica), Facultad de Farmacia, Universidad Complutense, Madrid, Spain.,Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.,Laboratoire de Systématique Végétale et Biodiversité, Conservatoire et Jardin botaniques and Université de Genève, Chambésy, Switzerland
| | - Víctor J Rico
- Departamento de Farmacología, Farmacognosia y Botánica (U.D. Botánica), Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - Yamama Naciri
- Laboratoire de Systématique Végétale et Biodiversité, Conservatoire et Jardin botaniques and Université de Genève, Chambésy, Switzerland
| | - David L Hawksworth
- Department of Life Sciences, The Natural History Museum, London, UK.,Comparative Fungal Biology, Royal Botanic Gardens, Kew, UK
| | - Christoph Scheidegger
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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7
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Werth S, Meidl P, Scheidegger C. Deep divergence between island populations in lichenized fungi. Sci Rep 2021; 11:7428. [PMID: 33795714 PMCID: PMC8016866 DOI: 10.1038/s41598-021-86448-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/10/2021] [Indexed: 11/17/2022] Open
Abstract
Macaronesia is characterized by a high degree of endemism and represents a noteworthy system to study the evolutionary history of populations and species. Here, we compare the population-genetic structure in three lichen-forming fungi, the widespread Lobaria pulmonaria and two Macaronesian endemics, L. immixta and L. macaronesica, based on microsatellites. We utilize population genetic approaches to explore population subdivision and evolutionary history of these taxa on the Canary Islands, Madeira, Azores, and the western Iberian Peninsula. A common feature in all species was the deep divergence between populations on the Azores, a pattern expected by the large geographic distance among islands. For both endemic species, there was a major split between archipelagos. In contrast, in the widespread L. pulmonaria, divergent individuals were distributed across multiple archipelagos, suggesting a complex evolutionary history involving repeated migration between islands and mainland.
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Affiliation(s)
- Silke Werth
- Systematic Botany and Mycology, Ludwig-Maximilians Universität München, Menzingerstraße 67, 80638, Munich, Germany.
- Department of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland.
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland.
| | - Peter Meidl
- Systematic Botany and Mycology, Ludwig-Maximilians Universität München, Menzingerstraße 67, 80638, Munich, Germany
| | - Christoph Scheidegger
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
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8
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Alonso-García M, Grewe F, Payette S, Villarreal A JC. Population genomics of a reindeer lichen species from North American lichen woodlands. AMERICAN JOURNAL OF BOTANY 2021; 108:159-171. [PMID: 33512730 DOI: 10.1002/ajb2.1601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/28/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Lichens are one of the main structural components of plant communities in the North American boreal biome. They play a pivotal role in lichen woodlands, a large ecosystem situated north of the closed-crown forest zone, and south of the forest-tundra zone. In Eastern Canada (Quebec), there is a remnant LW found 500 km south of its usual distribution range, in the Parc National des Grands-Jardins, originated mainly because of wildfires. We inferred the origin of the lichen Cladonia stellaris from this LW and assessed its genetic diversity in a postfire succession. METHODS We genotyped 122 individuals collected across a latitudinal gradient in Quebec. Using the software Stacks, we compared four different approaches of locus selection and single-nucleotide polymorphism calling. We identified the best fitting approach to investigate population structure and estimate genetic diversity of C. stellaris. RESULTS Populations in southern Quebec are not genetically different from those of northern LWs. The species consists of at least four phylogenetic lineages with elevated levels of genetic diversity and low co-ancestry. In Parc National des Grands-Jardins, we reported high values of genetic diversity not related with time since fire disturbance and low genetic differentiation among populations with different fire histories. CONCLUSIONS This first population genomic study of C. stellaris is an important step forward to understand the origin and biogeographic patterns of lichen woodlands in North America. Our findings also contribute to the understanding of the effect of postfire succession on the genetic structure of the species.
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Affiliation(s)
- Marta Alonso-García
- Département de Biologie, Université Laval, Québec, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Felix Grewe
- The Field Museum, Grainger Bioinformatics Center, 1400 South Lake Shore Drive, Chicago, 60605, USA
| | - Serge Payette
- Département de Biologie, Université Laval, Québec, G1V 0A6, Canada
| | - Juan Carlos Villarreal A
- Département de Biologie, Université Laval, Québec, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, EH3 5LR, Scotland, UK
- Smithsonian Tropical Research Institute, Panama City, Panama
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9
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Axenic culture and biosynthesis of secondary compounds in lichen symbiotic fungi, the Parmeliaceae. Symbiosis 2020. [DOI: 10.1007/s13199-020-00719-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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10
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Multidisciplinary approach to describe Trebouxia diversity within lichenized fungi Buellia zoharyi from the Canary Islands. Symbiosis 2020. [DOI: 10.1007/s13199-020-00722-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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11
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Cladonia subturgida (Cladoniaceae, Lecanoromycetes), an overlooked, but common species in the Mediterranean region. Symbiosis 2020. [DOI: 10.1007/s13199-020-00688-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractCladonia subturgida is a Mediterranean species that has been overlooked. Apparently it was restricted to the Iberian Peninsula and Canary Islands. However, during the study of the genus Cladonia in the Mediterranean region, new populations from 44 localities were found in: south France, Sardinia, south Italian peninsula, Crete and continental Greece. Distribution models based on MaxEnt, GLM, GAM and MARS algorithms were used to estimate the potential distribution of C. subturgida. Sicily, Corsica and the north of Africa were regions with suitable climatic conditions for C. subturgida where it has not been reported yet. The climatic variables with greatest relative influence in the C. subturgida distribution were the Precipitation of Warmest Quarter and the Annual Precipitation. Additionally, the ITS rDNA region was used to study the genetic variation of this species across its distribution area. Eleven haplotypes were found, one of them widely distributed through its geographical range. AMOVA analyses indicated lack of geographical structure.
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12
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Mainland and island populations of Mussaenda kwangtungensis differ in their phyllosphere fungal community composition and network structure. Sci Rep 2020; 10:952. [PMID: 31969602 PMCID: PMC6976661 DOI: 10.1038/s41598-020-57622-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 01/03/2020] [Indexed: 01/12/2023] Open
Abstract
We compared community composition and co-occurrence patterns of phyllosphere fungi between island and mainland populations within a single plant species (Mussaenda kwangtungensis) using high-throughput sequencing technology. We then used 11 microsatellite loci for host genotyping. The island populations differed significantly from their mainland counterparts in phyllosphere fungal community structure. Topological features of co-occurrence network showed geographic patterns wherein fungal assemblages were less complex, but more modular in island regions than mainland ones. Moreover, fungal interactions and community composition were strongly influenced by the genetic differentiation of host plants. This study may advance our understanding of assembly principles and ecological interactions of phyllosphere fungal communities, as well as improve our ability to optimize fungal utilization for the benefit of people.
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13
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Liu F, Chen S, Ferreira MA, Chang R, Sayari M, Kanzi AM, Wingfield BD, Wingfield MJ, Pizarro D, Crespo A, Divakar PK, de Beer ZW, Duong TA. Draft genome sequences of five Calonectria species from Eucalyptus plantations in China, Celoporthe dispersa, Sporothrix phasma and Alectoria sarmentosa. IMA Fungus 2019; 10:22. [PMID: 32647626 PMCID: PMC7325655 DOI: 10.1186/s43008-019-0023-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/11/2019] [Indexed: 12/31/2022] Open
Abstract
Draft genome sequences of five Calonectria species [including Calonectria aciculata, C. crousiana, C. fujianensis, C. honghensis and C. pseudoturangicola], Celoporthe dispersa, Sporothrix phasma and Alectoria sarmentosa are presented. Species of Calonectria are the causal agents of Eucalyptus leaf blight disease, threatening the growth and sustainability of Eucalyptus plantations in China. Celoporthe dispersa is the causal agent of stem canker in native Syzygium cordatum and exotic Tibouchina granulosa in South Africa. Sporothrix phasma was first discovered in the infructescences of Protea laurifolia and Protea neriifolia in South Africa. Alectoria sarmentosa is fruticose lichen belongs to the alectorioid clade of the family Parmeliaceae. The availability of these genome sequences will facilitate future studies on the systematics, population genetics, and genomics of these fungi.
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Affiliation(s)
- Feifei Liu
- State Key Laboratory of Tree Genetics and Breeding (SKLTGB), Chinese Academy of Forestry (CAF), Haidian District, Beijing, 100091 China.,China Eucalypt Research Centre (CERC), Chinese Academy of Forestry (CAF), ZhanJiang, 524022 GuangDong Province China.,Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
| | - Shuaifei Chen
- State Key Laboratory of Tree Genetics and Breeding (SKLTGB), Chinese Academy of Forestry (CAF), Haidian District, Beijing, 100091 China.,China Eucalypt Research Centre (CERC), Chinese Academy of Forestry (CAF), ZhanJiang, 524022 GuangDong Province China.,Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
| | - Maria A Ferreira
- Department of Plant Pathology, Universidade Federal de Lavras (Federal University of Lavras), Postal Box 3037, Lavras, 37200-000 Brazil
| | - Runlei Chang
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
| | - Mohammad Sayari
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
| | - Aquillah M Kanzi
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
| | - David Pizarro
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Ana Crespo
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Pradeep K Divakar
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Z Wilhelm de Beer
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
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14
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Fačkovcová Z, Slovák M, Vďačný P, Melichárková A, Zozomová-Lihová J, Guttová A. Spatio-temporal formation of the genetic diversity in the Mediterranean dwelling lichen during the Neogene and Quaternary epochs. Mol Phylogenet Evol 2019; 144:106704. [PMID: 31821879 DOI: 10.1016/j.ympev.2019.106704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 10/14/2019] [Accepted: 12/06/2019] [Indexed: 01/06/2023]
Abstract
Genetic patterns of lichenized fungi often display a mosaic-like and difficult to interpret structure blurring their evolutionary history. The genetic diversity and phylogeographic pattern of a mycobiont of the predominantly Mediterranean dwelling lichen Solenopsora candicans were investigated on the base of extensive sampling (361 individuals, 77 populations) across its entire distribution range. We tested whether the genetic pattern of S. candicans mirrors paleoclimatic and paleogeological events in the Mediterranean and adjacent regions. The divergence time estimates indicated a Tertiary origin for S. candicans, with formation of intraspecific diversity initiated in the Late Miocene. The distribution of the most divergent haplotypes, mostly of a pre-Pleistocene origin, was restricted to the eastern or western extremities of the Mediterranean exhibiting Kiermack disjunction. The population genetic diversity analyses indicated multiple diversity centres and refugia for S. candicans across the entire Mediterranean Basin. While the south Mediterranean regions harboured both the Tertiary and Quaternary born diversity, conforming to the 'cumulative refugia' paradigm, the Apennine and Balkan Peninsulas in the north hosted mostly younger Pleistocene haplotypes and lineages. The recent population expansion of S. candicans might have occurred in the middle Pleistocene with a population burst in the Apennine and Balkan peninsulas. The presence of unique haplotypes in Central Europe indicates the existence of extra-Mediterranean microrefugia. This study presents the first comprehensive lichen phylogeography from the Mediterranean region and simultaneously reports for the first time the glacial survival of a warm-adapted lichen in the temperate zone.
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Affiliation(s)
- Zuzana Fačkovcová
- Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84523 Bratislava, Slovakia.
| | - Marek Slovák
- Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84523 Bratislava, Slovakia; Department of Botany, Charles University, Benátská 2, 12801 Prague, Czech Republic
| | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Andrea Melichárková
- Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84523 Bratislava, Slovakia
| | - Judita Zozomová-Lihová
- Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84523 Bratislava, Slovakia
| | - Anna Guttová
- Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84523 Bratislava, Slovakia
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15
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Distribution of Foliicolous Lichen Strigula and Genetic Structure of S. multiformis on Jeju Island, South Korea. Microorganisms 2019; 7:microorganisms7100430. [PMID: 31658641 PMCID: PMC6843442 DOI: 10.3390/microorganisms7100430] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 10/02/2019] [Accepted: 10/08/2019] [Indexed: 11/23/2022] Open
Abstract
Strigula is a pantropic foliicolous lichen living on the leaf surfaces of evergreen broadleaf plants. In South Korea, Strigula is the only genus of foliicolous lichen recorded from Jeju Island. Several Strigula species have been recorded, but the ecology of Strigula in South Korea has been largely unexplored. This study examined the distribution and genetic structure of Strigula on Jeju Island. The distribution was surveyed and the influence of environmental factors (e.g., elevation, forest availability, and bioclimate) on the distribution was analyzed using a species distribution modeling analysis. In addition, the genetic variations and differentiation of Strigulamultiformis populations were analyzed using two nuclear ribosomal regions. The distribution of Strigula was largely restricted to a small portion of forest on Jeju Island, and the forest availability was the most important factor in the prediction of potential habitats. The genetic diversity and differentiation of the S. multiformis population were found to be high and were divided according to geography. On the other hand, geographic and environmental distance did not explain the population differentiation. Distribution and population genetic analysis suggested that the available habitat and genetic exchange of Strigula on Jeju Island are limited by the lack of available forest in the lowlands.
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16
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Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T. Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 2019; 58:27-45. [PMID: 31534414 PMCID: PMC6731264 DOI: 10.3897/mycokeys.58.36557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 07/11/2019] [Indexed: 11/23/2022] Open
Abstract
Understanding the distribution of genetic patterns and structure is an essential target in population genetics and, thereby, important for conservation genetics. The main aim of our study was to investigate the population genetics of Usnea subfloridana, a widespread lichenised fungus, focusing on a comparison of genetic variation of its populations amongst three geographically remote and disconnected regions, in order to determine relationships amongst environmental data, variation in lichen secondary chemistry and microsatellite data in genotyped populations. In all, 928 Usnea thalli from 17 populations were genotyped using seven specific fungal microsatellite markers. Different measures of genetic diversity (allelic richness, private allelic richness, Nei's unbiased genetic diversity and clonal diversity) were calculated and compared between lichen populations. Our results revealed a low genetic differentiation of U. subfloridana populations amongst three distant areas in Estonia and also a high level of gene flow. The results support suggestion of the long-range vegetative dispersal of subpendulous U. subfloridana via symbiotic propagules (soralia, isidia or fragments of thalli). Our study has also provided evidence that environmental variables, including mean annual temperature and geographical longitude, shape the genetic structure of U. subfloridana populations in Estonia. Additionally, a weak but statistically significant correlation between lichen chemotypes and microsatellite allele distribution was found in genotyped specimens.
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Affiliation(s)
- Polina Degtjarenko
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, SwitzerlandBiodiversity and Conservation Biology, Swiss Federal Research InstituteBirmensdorfSwitzerland
- Department of Botany, University of Tartu, Lai 40, 51005, Tartu, EstoniaUniversity of TartuTartuEstonia
| | - Inga Jüriado
- Department of Botany, University of Tartu, Lai 40, 51005, Tartu, EstoniaUniversity of TartuTartuEstonia
| | - Tiina Mandel
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, SwitzerlandBiodiversity and Conservation Biology, Swiss Federal Research InstituteBirmensdorfSwitzerland
- Department of Botany, University of Tartu, Lai 40, 51005, Tartu, EstoniaUniversity of TartuTartuEstonia
| | - Tiiu Tõrra
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, SwitzerlandBiodiversity and Conservation Biology, Swiss Federal Research InstituteBirmensdorfSwitzerland
- Department of Botany, University of Tartu, Lai 40, 51005, Tartu, EstoniaUniversity of TartuTartuEstonia
| | - Andres Saag
- Department of Botany, University of Tartu, Lai 40, 51005, Tartu, EstoniaUniversity of TartuTartuEstonia
| | - Christoph Scheidegger
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, SwitzerlandBiodiversity and Conservation Biology, Swiss Federal Research InstituteBirmensdorfSwitzerland
| | - Tiina Randlane
- Department of Botany, University of Tartu, Lai 40, 51005, Tartu, EstoniaUniversity of TartuTartuEstonia
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Pizarro D, Dal Grande F, Leavitt SD, Dyer PS, Schmitt I, Crespo A, Thorsten Lumbsch H, Divakar PK. Whole-Genome Sequence Data Uncover Widespread Heterothallism in the Largest Group of Lichen-Forming Fungi. Genome Biol Evol 2019; 11:721-730. [PMID: 30715356 PMCID: PMC6414310 DOI: 10.1093/gbe/evz027] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2019] [Indexed: 12/20/2022] Open
Abstract
Fungal reproduction is regulated by the mating-type (MAT1) locus, which typically comprises two idiomorphic genes. The presence of one or both allelic variants at the locus determines the reproductive strategy in fungi—homothallism versus heterothallism. It has been hypothesized that self-fertility via homothallism is widespread in lichen-forming fungi. To test this hypothesis, we characterized the MAT1 locus of 41 genomes of lichen-forming fungi representing a wide range of growth forms and reproductive strategies in the class Lecanoromycetes, the largest group of lichen-forming fungi. Our results show the complete lack of genetic homothallism suggesting that lichens evolved from a heterothallic ancestor. We argue that this may be related to the symbiotic lifestyle of these fungi, and may be a key innovation that has contributed to the accelerated diversification rates in this fungal group.
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Affiliation(s)
- David Pizarro
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Spain
| | - Francesco Dal Grande
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität and Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Steven Don Leavitt
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, Provo, Utah
| | | | - Imke Schmitt
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität and Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Ana Crespo
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Spain
| | | | - Pradeep Kumar Divakar
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Spain
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18
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Belinchón R, Ellis CJ, Yahr R. Climate-woodland effects on population genetics for two congeneric lichens with contrasting reproductive strategies. FEMS Microbiol Ecol 2018; 94:5069390. [PMID: 30107505 DOI: 10.1093/femsec/fiy159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/09/2018] [Indexed: 01/08/2023] Open
Abstract
Genetic variation is expected to be influenced by the interaction between reproductive mode and dispersal traits on the one hand and environmental and habitat setting affecting establishment success on the other. We evaluated how environmental/habitat setting affects population genetic variation (i.e. variation in genetic diversity and structure) when regulated by contrasting dispersal traits. We used fungus-specific microsatellite markers to examine genetic diversity and structure of two closely related epiphytic lichen fungi that differ in their primary reproductive mode: Nephroma laevigatum (sexually reproducing, n = 191, 10 microsatellites) and N. parile (asexually reproducing, n = 182, 12 microsatellites), along a steep climatic gradient in Scotland. Despite their reproductive differences, we found a high proportion of clones in both species and a background pattern of genetic structure related to climatic gradients. We also demonstrated that woodland connectivity, rather than geographic distance, explained genetic diversity in both species. Environmental/habitat setting, modulated by the reproductive mode of the species, affects genetic diversity and structure, but the putative dissimilarity in their reproductive mode is less important than has been previously assumed. We reinforce the importance of protecting highly connected populations, positioned along a gradient capturing the segregation of gene pool differences in response to climatic variation.
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Affiliation(s)
- Rocío Belinchón
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, EH3 5LR, Edinburgh, UK
| | | | - Rebecca Yahr
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, EH3 5LR, Edinburgh, UK
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19
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Lagostina E, Dal Grande F, Andreev M, Printzen C. The use of microsatellite markers for species delimitation in Antarctic Usnea subgenus Neuropogon. Mycologia 2018; 110:1047-1057. [DOI: 10.1080/00275514.2018.1512304] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Elisa Lagostina
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, D-60325 Frankfurt/Main, Germany
- Fachbereich 15 Biowissenschaften, Biozentrum, Campus Riedberg, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Mikhail Andreev
- Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popov St. 2, Saint Petersburg 197376, Russia
| | - Christian Printzen
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, D-60325 Frankfurt/Main, Germany
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20
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Allen JL, McKenzie SK, Sleith RS, Alter SE. First genome-wide analysis of the endangered, endemic lichen Cetradonia linearis reveals isolation by distance and strong population structure. AMERICAN JOURNAL OF BOTANY 2018; 105:1556-1567. [PMID: 30157288 DOI: 10.1002/ajb2.1150] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/14/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Lichenized fungi are evolutionarily diverse and ecologically important, but little is known about the processes that drive their diversification and genetic differentiation. Distributions are often assumed to be wholly shaped by ecological requirements rather than dispersal limitations. Furthermore, although asexual and sexual reproductive structures are observable, the lack of information about recombination rates makes inferences about reproductive strategies difficult. We investigated the population genomics of Cetradonia linearis, a federally endangered lichen in the southern Appalachians of eastern North America, to test the relative contributions of environmental and geographic distance in shaping genetic structure, and to characterize the mating system and genome-wide recombination. METHODS Whole-genome shotgun sequencing was conducted to generate data for 32 individuals of C. linearis. A reference genome was assembled, and reads from all samples were aligned to generate a set of single-nucleotide polymorphisms for further analyses. KEY RESULTS We found evidence for low rates of recombination and for isolation by distance, but not for isolation by environment. The species is putatively unisexual, given that only one mating-type locus was found. Hindcast species distribution models and the distribution of genetic diversity support C. linearis having a larger range during the Last Glacial Maximum in the southern portion of its current extent. CONCLUSIONS Our findings contribute to the understanding of factors that shape genetic diversity in C. linearis and in fungi more broadly. Because all populations are highly genetically differentiated, the extirpation of any population would mean the loss of unique genetic diversity; therefore, our results support the continued conservation of this species.
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Affiliation(s)
- Jessica L Allen
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York, 10458, USA
- The Graduate Center, City University of New York, 365 5th Avenue, New York, New York, 10016, USA
| | - Sean K McKenzie
- Rockefeller University, 1230 York Avenue, New York, New York, 10065, USA
| | - Robin S Sleith
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York, 10458, USA
- The Graduate Center, City University of New York, 365 5th Avenue, New York, New York, 10016, USA
| | - S Elizabeth Alter
- The Graduate Center, City University of New York, 365 5th Avenue, New York, New York, 10016, USA
- Biology Department, York College, 94-20 Guy R Brewer Blvd., Jamaica, New York, 11451, USA
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21
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Degtjarenko P, Tõrra T, Mandel T, Marmor L, Saag A, Scheidegger C, Randlane T. Unconstrained gene flow between populations of a widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia. Fungal Biol 2018; 122:731-737. [DOI: 10.1016/j.funbio.2018.03.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/27/2018] [Accepted: 03/27/2018] [Indexed: 01/17/2023]
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22
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Meiser A, Otte J, Schmitt I, Grande FD. Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi. Sci Rep 2017; 7:14881. [PMID: 29097759 PMCID: PMC5668418 DOI: 10.1038/s41598-017-14576-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/12/2017] [Indexed: 01/07/2023] Open
Abstract
The metagenome skimming approach, i.e. low coverage shotgun sequencing of multi-species assemblages and subsequent reconstruction of individual genomes, is increasingly used for in-depth genomic characterization of ecological communities. This approach is a promising tool for reconstructing genomes of facultative symbionts, such as lichen-forming fungi, from metagenomic reads. However, no study has so far tested accuracy and completeness of assemblies based on metagenomic sequences compared to assemblies based on pure culture strains of lichenized fungi. Here we assembled the genomes of Evernia prunastri and Pseudevernia furfuracea based on metagenomic sequences derived from whole lichen thalli. We extracted fungal contigs using two different taxonomic binning methods, and performed gene prediction on the fungal contig subsets. We then assessed quality and completeness of the metagenome-based assemblies using genome assemblies as reference which are based on pure culture strains of the two fungal species. Our comparison showed that we were able to reconstruct fungal genomes from uncultured lichen thalli, and also cover most of the gene space (86-90%). Metagenome skimming will facilitate genome mining, comparative (phylo)genomics, and population genetics of lichen-forming fungi by circumventing the time-consuming, sometimes unfeasible, step of aposymbiotic cultivation.
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Affiliation(s)
- Anjuli Meiser
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany
| | - Imke Schmitt
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany.
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany.
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany.
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23
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Ronnås C, Werth S, Ovaskainen O, Várkonyi G, Scheidegger C, Snäll T. Discovery of long-distance gamete dispersal in a lichen-forming ascomycete. THE NEW PHYTOLOGIST 2017; 216:216-226. [PMID: 28782804 PMCID: PMC5655791 DOI: 10.1111/nph.14714] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/16/2017] [Indexed: 06/01/2023]
Abstract
Accurate estimates of gamete and offspring dispersal range are required for the understanding and prediction of spatial population dynamics and species persistence. Little is known about gamete dispersal in fungi, especially in lichen-forming ascomycetes. Here, we estimate the dispersal functions of clonal propagules, gametes and ascospores of the epiphytic lichen Lobaria pulmonaria. We use hierarchical Bayesian parentage analysis, which integrates genetic and ecological information from multiannual colonization and dispersal source data collected in a large, old-growth forest landscape. The effective dispersal range of gametes is several hundred metres to kilometres from potential paternal individuals. By contrast, clonal propagules disperse only tens of metres, and ascospores disperse over several thousand metres. Our study reveals the dispersal distances of individual reproductive units; clonal propagules, gametes and ascospores, which is of great importance for a thorough understanding of the spatial dynamics of ascomycetes. Sexual reproduction occurs between distant individuals. However, whereas gametes and ascospores disperse over long distances, the overall rate of colonization of trees is low. Hence, establishment is the limiting factor for the colonization of new host trees by the lichen in old-growth landscapes.
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Affiliation(s)
- Cecilia Ronnås
- Swedish Species Information CentreSwedish University of Agricultural SciencesBox 7007UppsalaS‐75007Sweden
| | - Silke Werth
- Institute of Plant SciencesUniversity of GrazHolteigasse 6Graz8010Austria
| | - Otso Ovaskainen
- Department of BiosciencesUniversity of HelsinkiPO Box 65HelsinkiFI‐00014Finland
- Centre for Biodiversity DynamicsDepartment of BiologyNorwegian University of Science and TechnologyTrondheimN‐7491Norway
| | - Gergely Várkonyi
- Friendship Park Research CentreFinnish Environment Institute SYKELentiirantie 342BKuhmoFI‐88900Finland
| | - Christoph Scheidegger
- Swiss Federal Institute for ForestSnow and Landscape ResearchWSLZürcherstr. 111BirmensdorfCH‐8903Switzerland
| | - Tord Snäll
- Swedish Species Information CentreSwedish University of Agricultural SciencesBox 7007UppsalaS‐75007Sweden
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