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Bogale AT, Braun M, Bernhardt J, Zühlke D, Schiefelbein U, Bog M, Scheidegger C, Zengerer V, Becher D, Grube M, Riedel K, Bengtsson MM. The microbiome of the lichen Lobaria pulmonaria varies according to climate on a subcontinental scale. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13289. [PMID: 38923181 PMCID: PMC11194104 DOI: 10.1111/1758-2229.13289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/03/2024] [Indexed: 06/28/2024]
Abstract
The Lobaria pulmonaria holobiont comprises algal, fungal, cyanobacterial and bacterial components. We investigated L. pulmonaria's bacterial microbiome in the adaptation of this ecologically sensitive lichen species to diverse climatic conditions. Our central hypothesis posited that microbiome composition and functionality aligns with subcontinental-scale (a stretch of ~1100 km) climatic parameters related to temperature and precipitation. We also tested the impact of short-term weather dynamics, sampling season and algal/fungal genotypes on microbiome variation. Metaproteomics provided insights into compositional and functional changes within the microbiome. Climatic variables explained 41.64% of microbiome variation, surpassing the combined influence of local weather and sampling season at 31.63%. Notably, annual mean temperature and temperature seasonality emerged as significant climatic drivers. Microbiome composition correlated with algal, not fungal genotype, suggesting similar environmental recruitment for the algal partner and microbiome. Differential abundance analyses revealed distinct protein compositions in Sub-Atlantic Lowland and Alpine regions, indicating differential microbiome responses to contrasting environmental/climatic conditions. Proteins involved in oxidative and cellular stress were notably different. Our findings highlight microbiome plasticity in adapting to stable climates, with limited responsiveness to short-term fluctuations, offering new insights into climate adaptation in lichen symbiosis.
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Affiliation(s)
| | - Maria Braun
- Institute of MicrobiologyUniversity of GreifswaldGreifswaldGermany
| | - Jörg Bernhardt
- Institute of MicrobiologyUniversity of GreifswaldGreifswaldGermany
| | - Daniela Zühlke
- Institute of MicrobiologyUniversity of GreifswaldGreifswaldGermany
| | - Ulf Schiefelbein
- Landscape EcologyUniversity of Rostock, Botanical GardenRostockGermany
| | - Manuela Bog
- Institute of Botany and Landscape EcologyUniversity of GreifswaldGreifswaldGermany
| | - Christoph Scheidegger
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Veronika Zengerer
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Dörte Becher
- Institute of MicrobiologyUniversity of GreifswaldGreifswaldGermany
| | - Martin Grube
- Karl‐Franzens‐Universität Graz, Institut für BiologieGrazAustria
| | - Katharina Riedel
- Institute of MicrobiologyUniversity of GreifswaldGreifswaldGermany
| | - Mia M. Bengtsson
- Institute of MicrobiologyUniversity of GreifswaldGreifswaldGermany
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Rodríguez‐Arribas C, Martínez I, Aragón G, Zamorano‐Elgueta C, Cavieres L, Prieto M. Specialization patterns in symbiotic associations: A community perspective over spatial scales. Ecol Evol 2023; 13:e10296. [PMID: 37441095 PMCID: PMC10333671 DOI: 10.1002/ece3.10296] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023] Open
Abstract
Specialization, contextualized in a resource axis of an organism niche, is a core concept in ecology. In biotic interactions, specialization can be determined by the range of interacting partners. Evolutionary and ecological factors, in combination with the surveyed scale (spatial, temporal, biological, and/or taxonomic), influence the conception of specialization. This study aimed to assess the specialization patterns and drivers in the lichen symbiosis, considering the interaction between the principal fungus (mycobiont) and the associated Nostoc (cyanobiont), from a community perspective considering different spatial scales. Thus, we determined Nostoc phylogroup richness and composition of lichen communities in 11 Nothofagus pumilio forests across a wide latitudinal gradient in Chile. To measure specialization, cyanobiont richness, Simpson's and d' indices were estimated for 37 mycobiont species in these communities. Potential drivers that might shape Nostoc composition and specialization measures along the environmental gradient were analysed. Limitations in lichen distributional ranges due to the availability of their cyanobionts were studied. Turnover patterns of cyanobionts were identified at multiple spatial scales. The results showed that environmental factors shaped the Nostoc composition of these communities, thus limiting cyanobiont availability to establish the symbiotic association. Besides, specialization changed with the spatial scale and with the metric considered. Cyanolichens were more specialized than cephalolichens when considering partner richness and Simpson's index, whereas the d' index was mostly explained by mycobiont identity. Little evidence of lichen distributional ranges due to the distribution of their cyanobionts was found. Thus, lichens with broad distributional ranges either associated with several cyanobionts or with widely distributed cyanobionts. Comparisons between local and regional scales showed a decreasing degree of specialization at larger scales due to an increase in cyanobiont richness. The results support the context dependency of specialization and how its consideration changes with the metric and the spatial scale considered. Subsequently, we suggest considering the entire community and widening the spatial scale studied as it is crucial to understand factors determining specialization.
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Affiliation(s)
- Clara Rodríguez‐Arribas
- Área de Biodiversidad y Conservación, Research Group of “Ecología, sistemática y evolución de hongos y líquenes (ESEFUNLICH)”, Departamento de Biología, Geología, Física y Química Inorgánica, ESCETUniversidad Rey Juan CarlosMóstolesSpain
| | - Isabel Martínez
- Área de Biodiversidad y Conservación, Research Group of “Ecología, sistemática y evolución de hongos y líquenes (ESEFUNLICH)”, Departamento de Biología, Geología, Física y Química Inorgánica, ESCETUniversidad Rey Juan CarlosMóstolesSpain
| | - Gregorio Aragón
- Área de Biodiversidad y Conservación, Research Group of “Ecología, sistemática y evolución de hongos y líquenes (ESEFUNLICH)”, Departamento de Biología, Geología, Física y Química Inorgánica, ESCETUniversidad Rey Juan CarlosMóstolesSpain
| | - Carlos Zamorano‐Elgueta
- Universidad de AysénCoyhaiqueChile
- CR2‐Center for Climate and Resilience Research (CR)2SantiagoChile
| | - Lohengrin Cavieres
- Departamento de Botánica, Facultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
| | - María Prieto
- Área de Biodiversidad y Conservación, Research Group of “Ecología, sistemática y evolución de hongos y líquenes (ESEFUNLICH)”, Departamento de Biología, Geología, Física y Química Inorgánica, ESCETUniversidad Rey Juan CarlosMóstolesSpain
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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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Allen JL, McMullin RT, Wiersma YF, Scheidegger C. Population genetics and biogeography of the lungwort lichen in North America support distinct Eastern and Western gene pools. AMERICAN JOURNAL OF BOTANY 2021; 108:2416-2424. [PMID: 34634140 DOI: 10.1002/ajb2.1774] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Populations of species with large spatial distributions are shaped by complex forces that differ throughout their ranges. To maintain the genetic diversity of species, genepool-based subsets of widespread species must be considered in conservation assessments. METHODS The population genetics of the lichenized fungus Lobaria pulmonaria and its algal partner, Symbiochloris reticulata, were investigated using microsatellite markers to determine population structure, genetic diversity, and degree of congruency in eastern and western North America. Data loggers measuring temperature and humidity were deployed at selected populations in eastern North America to test for climatic adaptation. To better understand the role Pleistocene glaciations played in shaping population patterns, a North American, range-wide species distribution model was constructed and hindcast to 22,000 years before present and at 500-year time slices from then to the present. RESULTS The presence of two gene pools with minimal admixture was supported, one in the U.S. Pacific Northwest and one in eastern North America. Western populations were significantly more genetically diverse than eastern populations. There was no evidence for climatic adaptation among eastern populations, though there was evidence for range-wide adaptation to evapotranspiration rates. Hindcast distribution models suggest that observed genetic diversity may be due to a drastic Pleistocene range restriction in eastern North America, whereas a substantial coastal refugial area is inferred in the west. CONCLUSIONS Taken together the results show different, complex population histories of L. pulmonaria in eastern and western North America, and suggest that conservation planning for each gene pool should be considered separately.
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Affiliation(s)
- Jessica L Allen
- Eastern Washington University, Biology Department, Cheney, Washington, 99004, USA
- Swiss Federal Institute for Forest, Snow, and Landscape Research WSL, Department of Biodiversity and Conservation Biology, Birmensdorf, 8903, Switzerland
| | - R Troy McMullin
- Canadian Museum of Nature, Research and Collections, Ottawa, Ontario, K1P 6P4, Canada
| | - Yolanda F Wiersma
- Memorial University of Newfoundland and Labrador, Department of Biology, St. John's, Newfoundland and Labrador, A1C 5S7, Canada
| | - Christoph Scheidegger
- Swiss Federal Institute for Forest, Snow, and Landscape Research WSL, Department of Biodiversity and Conservation Biology, Birmensdorf, 8903, Switzerland
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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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Wagner M, Bathke AC, Cary SC, Green TGA, Junker RR, Trutschnig W, Ruprecht U. Myco- and photobiont associations in crustose lichens in the McMurdo Dry Valleys (Antarctica) reveal high differentiation along an elevational gradient. Polar Biol 2020. [DOI: 10.1007/s00300-020-02754-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
AbstractClimatically extreme regions such as the polar deserts of the McMurdo Dry Valleys (78° S) in Continental Antarctica are key areas for a better understanding of changes in ecosystems. Therefore, it is particularly important to analyze and communicate current patterns of biodiversity in these sensitive areas, where precipitation mostly occurs in form of snow and liquid water is rare. Humidity provided by dew, clouds, and fog are the main water sources, especially for rock-dwelling crustose lichens as one of the most common vegetation-forming organisms. We investigated the diversity and interaction specificity of myco-/photobiont associations of 232 crustose lichen specimens, collected along an elevational gradient (171–959 m a.s.l.) within the McMurdo Dry Valleys. The mycobiont species and photobiont OTUs were identified by using three markers each (nrITS, mtSSU, RPB1, and nrITS, psbJ-L, COX2). Elevation, positively associated with water availability, turned out to be the key factor explaining most of the distribution patterns of the mycobionts. Pairwise comparisons showed Lecidea cancriformis and Rhizoplaca macleanii to be significantly more common at higher elevations and Carbonea vorticosa and Lecidea polypycnidophora at lower elevations. Lichen photobionts were dominated by the globally distributed Trebouxia OTU, Tr_A02 which occurred at all habitats. Network specialization resulting from myco-/photobiont bipartite network structure varied with elevation and associated abiotic factors. Along an elevational gradient, the spatial distribution, diversity, and genetic variability of the lichen symbionts appear to be mainly influenced by improved water relations at higher altitudes.
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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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Oh SY, Woo JJ, Hur JS. Distribution of Foliicolous Lichen Strigula and Genetic Structure of S. multiformis on Jeju Island, South Korea. Microorganisms 2019; 7:E430. [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] [Grants] [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 Strigula multiformis 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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Affiliation(s)
- Seung-Yoon Oh
- Korean Lichen Research Institute, Sunchon National University, 255 Jungang-Ro, Suncheon 57922, Korea.
| | - Jung-Jae Woo
- Korean Lichen Research Institute, Sunchon National University, 255 Jungang-Ro, Suncheon 57922, Korea.
- Division of Forest Biodiversity, Korea National Arboretum, 415 Gwangneungsumok-ro, Pocheon 11186, Korea.
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, 255 Jungang-Ro, Suncheon 57922, Korea.
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Devkota S, Chaudhary RP, Werth S, Scheidegger C. Genetic diversity and structure of the epiphytic foliose lichen Lobaria pindarensis in the Himalayas depends on elevation. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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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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Abstract
This paper provides an overview of bioclimatic models applied to lichen species, supporting their potential use in this context as indicators of climate change risk. First, it provides a brief summary of climate change risk, pointing to the relevance of lichens as a topic area. Second, it reviews the past use of lichen bioclimatic models, applied for a range of purposes with respect to baseline climate, and the application of data sources, statistical methods, model extents and resolution and choice of predictor variables. Third, it explores additional challenges to the use of lichen bioclimatic models, including: 1. The assumption of climatically controlled lichen distributions, 2. The projection to climate change scenarios, and 3. The issue of nonanalogue climates and model transferability. Fourth, the paper provides a reminder that bioclimatic models estimate change in the extent or range of a species suitable climate space, and that an outcome will be determined by vulnerability responses, including potential for migration, adaptation, and acclimation, within the context of landscape habitat quality. The degree of exposure to climate change, estimated using bioclimatic models, can help to inform an understanding of whether vulnerability responses are sufficient for species resilience. Fifth, the paper draws conclusions based on its overview, highlighting the relevance of bioclimatic models to conservation, support received from observational data, and pointing the way towards mechanistic approaches that align with field-scale climate change experiments.
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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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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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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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16
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Strong specificity and network modularity at a very fine phylogenetic scale in the lichen genus Peltigera. Oecologia 2018; 187:767-782. [PMID: 29761320 DOI: 10.1007/s00442-018-4159-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 05/03/2018] [Indexed: 10/16/2022]
Abstract
Identifying the drivers and evolutionary consequences of species interactions is a major goal of community ecology. Network-based analyses can provide mathematical tools to detect non-random patterns of interactions, and potentially help predicting the consequences of such patterns on evolutionary dynamics of symbiotic systems. Here, we characterize the structure of a lichen network at a very fine phylogenetic scale, by identifying the photosynthetic partners (i.e., cyanobacteria of the genus Nostoc) of lichenized fungi belonging to a monophyletic section of a single genus (i.e., section Polydactylon of the genus Peltigera), worldwide. Even at such a fine phylogenetic scale, we found that interactions were highly modular and anti-nested, indicating strong preferences in interactions. When considering local Peltigera communities, i.e., datasets at small spatial scales with only a slightly broader phylogenetic range, interactions remained modular but were asymmetric, with generalist Nostoc partners interacting with specialized Peltigera species. This asymmetry was not detected with our global spatial scale dataset. We discuss these results in the light of lichen community assembly, and explore how such interaction patterns may influence coevolution in lichens and the evolutionary stability of the mutualism in general.
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17
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Dal Grande F, Rolshausen G, Divakar PK, Crespo A, Otte J, Schleuning M, Schmitt I. Environment and host identity structure communities of green algal symbionts in lichens. THE NEW PHYTOLOGIST 2018; 217:277-289. [PMID: 28892165 DOI: 10.1111/nph.14770] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
An understanding of how biotic interactions shape species' distributions is central to predicting host-symbiont responses under climate change. Switches to locally adapted algae have been proposed to be an adaptive strategy of lichen-forming fungi to cope with environmental change. However, it is unclear how lichen photobionts respond to environmental gradients, and whether they play a role in determining the fungal host's upper and lower elevational limits. Deep-coverage Illumina DNA metabarcoding was used to track changes in the community composition of Trebouxia algae associated with two phylogenetically closely related, but ecologically divergent fungal hosts along a steep altitudinal gradient in the Mediterranean region. We detected the presence of multiple Trebouxia species in the majority of thalli. Both altitude and host genetic identity were strong predictors of photobiont community assembly in these two species. The predominantly clonally dispersing fungus showed stronger altitudinal structuring of photobiont communities than the sexually reproducing host. Elevation ranges of the host were not limited by the lack of compatible photobionts. Our study sheds light on the processes guiding the formation and distribution of specific fungal-algal combinations in the lichen symbiosis. The effect of environmental filtering acting on both symbiotic partners appears to shape the distribution of lichens.
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Affiliation(s)
- Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Pradeep K Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Matthias Schleuning
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany
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18
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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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Leavitt SD, Kraichak E, Vondrak J, Nelsen MP, Sohrabi M, Perez-Ortega S, St Clair LL, Lumbsch HT. Cryptic diversity and symbiont interactions in rock-posy lichens. Mol Phylogenet Evol 2016; 99:261-274. [DOI: 10.1016/j.ympev.2016.03.030] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 11/24/2022]
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20
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Cornejo C, Scheidegger C. Multi-gene phylogeny of the genus Lobaria: Evidence of species-pair and allopatric cryptic speciation in East Asia. AMERICAN JOURNAL OF BOTANY 2015; 102:2058-2073. [PMID: 26672013 DOI: 10.3732/ajb.1500207] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 10/13/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Accurate species delimitation has critical implications for ecological and conservation studies. The lichen genus Lobaria is widely distributed in old-growth forests. Particularly in East Asia, this genus includes many rare and poorly known taxa that are circumscribed as morpho- or chemospecies, as well as species-pairs. METHODS To critically examine the relationships between species identified via morphological and chemical criteria, phylogenetic species recognition (PSR) was applied to the genus Lobaria. Morphological and chemical patterns of 87 individuals were examined and three independent nuclear loci were sequenced. The East Asian L. meridionalis-group was additionally studied using split decomposition and haplotype network analysis. KEY RESULTS The genus Lobaria and most of its species were strongly supported statistically. Split decomposition and haplotype networks suggest complex evolutionary histories of species within the East Asian L. meridionalis-group. CONCLUSIONS Phylogenetic analyses confirmed the monophyly of the genus Lobaria, including L. anomala. Within Lobaria, three major clades were found. These clades associate with different photobionts and comprise 18 known species and 5 undescribed species. Several chemical compounds were found to be neither stable nor invariant characters. Some taxa of the L. meridionalis-group appear to be monophyletic but remain as allopatric cryptic species. In three clades, this study found evidence for diversification processes between isidiate and nonisidiate specimens (species-pair). These findings are discussed in the context of evolutionary hypotheses for speciation processes.
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Affiliation(s)
- Carolina Cornejo
- Swiss Federal Research Institute WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Christoph Scheidegger
- Swiss Federal Research Institute WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland
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21
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Leavitt SD, Kraichak E, Nelsen MP, Altermann S, Divakar PK, Alors D, Esslinger TL, Crespo A, Lumbsch T. Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen‐forming family Parmeliaceae (Ascomycota). Mol Ecol 2015; 24:3779-97. [DOI: 10.1111/mec.13271] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 06/04/2015] [Accepted: 06/10/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Steven D. Leavitt
- Committee on Evolutionary Biology University of Chicago Chicago IL USA
- Science & Education The Field Museum Chicago IL USA
| | - Ekaphan Kraichak
- Science & Education The Field Museum Chicago IL USA
- Department of Botany Faculty of Science Kasetsart University Bangkok Thailand
| | - Matthew P. Nelsen
- Geological and Environmental Sciences Stanford University Stanford CA USA
| | | | - Pradeep K. Divakar
- Departamento de Biología Vegetal II Facultad de Farmacia Universidad Complutense de Madrid Madrid Spain
| | - David Alors
- Departamento de Biología Vegetal II Facultad de Farmacia Universidad Complutense de Madrid Madrid Spain
| | | | - Ana Crespo
- Departamento de Biología Vegetal II Facultad de Farmacia Universidad Complutense de Madrid Madrid Spain
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22
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Otálora MAG, Belinchón R, Prieto M, Aragón G, Izquierdo P, Martínez I. The threatened epiphytic lichen Lobaria pulmonaria in the Iberian Peninsula: genetic diversity and structure across a latitudinal gradient. Fungal Biol 2015; 119:802-11. [PMID: 26321729 DOI: 10.1016/j.funbio.2015.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 03/11/2015] [Accepted: 05/14/2015] [Indexed: 10/23/2022]
Abstract
The current genetic diversity and structure of a species plays a marked role in the species' future response to environmental changes. Identification of the factors that might ensure the long-term viability of populations along its distribution area is therefore important for conserving biodiversity. In this work, infraspecific genetic diversity and structure of the threatened lichen Lobaria pulmonaria was investigated along a latitudinal gradient, spanning the Spanish latitudinal range of L. pulmonaria. Eighteen populations in Northern, Central, and Southern Spain were analysed using six specific fungal microsatellites of L. pulmonaria. Genetic diversity indices were calculated and compared among populations. Genetic differentiation was assessed using AMOVA and Bayesian methods. Additionally, a redundancy analysis was used to estimate the relative importance of environmental factors on the genetic variation among populations. Annual precipitation was the only factor affecting the genetic diversity probably through its influence on population and thallus size of L. pulmonaria, and significantly higher levels of genetic diversity were detected in southern populations. Isolation by distance was not significant, being environmental variables most important factors controlling genetic variation in L. pulmonaria populations.
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Affiliation(s)
- Mónica A G Otálora
- Biology and Geology Department, Rey Juan Carlos University, 28933 Móstoles, Madrid, Spain
| | - Rocío Belinchón
- Biology and Geology Department, Rey Juan Carlos University, 28933 Móstoles, Madrid, Spain
| | - María Prieto
- Biology and Geology Department, Rey Juan Carlos University, 28933 Móstoles, Madrid, Spain
| | - Gregorio Aragón
- Biology and Geology Department, Rey Juan Carlos University, 28933 Móstoles, Madrid, Spain
| | - Patricia Izquierdo
- Biology and Geology Department, Rey Juan Carlos University, 28933 Móstoles, Madrid, Spain
| | - Isabel Martínez
- Biology and Geology Department, Rey Juan Carlos University, 28933 Móstoles, Madrid, Spain.
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