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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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Degtjarenko P, Mark K, Moisejevs R, Himelbrant D, Stepanchikova I, Tsurykau A, Randlane T, Scheidegger C. Low genetic differentiation between apotheciate Usnea florida and sorediate Usnea subfloridana (Parmeliaceae, Ascomycota) based on microsatellite data. Fungal Biol 2020; 124:892-902. [PMID: 32948277 DOI: 10.1016/j.funbio.2020.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 07/15/2020] [Accepted: 07/22/2020] [Indexed: 10/23/2022]
Abstract
Accurate species delimitation has a pivotal role in conservation biology, and it is especially important for threatened species where decisions have political and economic consequences. Finding and applying appropriate character sets and analytical tools to resolve interspecific relationships remains challenging in lichenized fungi. The main aim of our study was to re-assess the species boundaries between Usnea subfloridana and Usnea florida, which have been phylogenetically indistinguishable until now, but are different in reproductive mode and ecological preferences, using fungal-specific simple sequence repeats (SSR), i.e. microsatellite markers. Bayesian clustering analysis, discriminant analysis of principal components (DAPC), minimal spanning network (MSN), and principal component analysis (PCA) failed to separate U. florida and U. subfloridana populations. However, a low significant differentiation between the two taxa was observed across all populations according to AMOVA results. Also, analysis of shared haplotypes and statistical difference in clonal diversity (M) supported the present-day isolation between the apotheciate U. florida and predominantly sorediate U. subfloridana. Our results do not provide a clear support either for the separation of species in this pair or the synonymization of U. florida and U. subfloridana. We suggest that genome-wide data could help resolve the taxonomic question in this species pair.
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Affiliation(s)
- Polina Degtjarenko
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland; Department of Botany, University of Tartu, Lai 40, 51005, Tartu, Estonia; Institute of Life Sciences and Technology, Daugavpils University, Parādes 1a, 5401, Daugavpils, Latvia.
| | - Kristiina Mark
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr.R.Kreutzwaldi 1, 51006, Tartu, Estonia
| | - Rolands Moisejevs
- Institute of Life Sciences and Technology, Daugavpils University, Parādes 1a, 5401, Daugavpils, Latvia
| | - Dmitry Himelbrant
- Department of Botany, St. Petersburg State University, Universitetskaya Emb. 7-9, 199034, St. Petersburg, Russia; Laboratory of Lichenology and Bryology, Komarov Botanical Institute RAS, Professor Popov St. 2, 197376, St. Petersburg, Russia
| | - Irina Stepanchikova
- Department of Botany, St. Petersburg State University, Universitetskaya Emb. 7-9, 199034, St. Petersburg, Russia; Laboratory of Lichenology and Bryology, Komarov Botanical Institute RAS, Professor Popov St. 2, 197376, St. Petersburg, Russia
| | - Andrei Tsurykau
- Department of Biology, F. Skorina Gomel State University, Sovetskaja Str. 104, BY-246019, Gomel, Belarus; Department of Ecology, Botany and Nature Protection, Institute of Natural Sciences, Samara National Research University, Moskovskoye Shosse 34, 443086, Samara, Russia
| | - Tiina Randlane
- Department of Botany, University of Tartu, Lai 40, 51005, Tartu, Estonia
| | - Christoph Scheidegger
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
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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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