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Barcenas-Peña A, Divakar PK, Crespo A, Nuñez-Zapata J, Lumbsch HT, Grewe F. Reference-Based Restriction-Site-Associated DNA Sequencing Data Are Useful for Species Delineation in a Recently Diverged Asexually Reproducing Species Complex (Parmeliaceae, Ascomycota). J Fungi (Basel) 2023; 9:1180. [PMID: 38132781 PMCID: PMC10744373 DOI: 10.3390/jof9121180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Cryptic species are common in lichen-forming fungi and have been reported from different genera in the most speciose family, Parmeliaceae. Herein, we address species delimitation in a group of mainly asexually reproducing Parmelina species. The morphologically distinct P. pastillifera was previously found nested within a morphologically circumscribed P. tiliacea based on several loci. However, these studies demonstrated a relatively high genetic diversity within P. tiliacea sensu lato. Here, we revisit the species delimitation in the group by analyzing single-nucleotide polymorphisms (SNPs) through genome-wide assessment using Restriction-Site-Associated sequencing and population genomic methods. Our data support previous studies and provide further insight into the phylogenetic relationships of the four clades found within the complex. Based on the evidence suggesting a lack of gene flow among the clades, we recognize the four clades as distinct species, P. pastillifera and P. tiliacea sensu stricto, and two new species, P. clandestina sp. nov. and P. mediterranea sp. nov.
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Affiliation(s)
- Alejandrina Barcenas-Peña
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL 60605, USA; (H.T.L.); (F.G.)
| | - Pradeep K. Divakar
- Department of Pharmacology, Pharmacognosy and Botany (DU Botany), Faculty of Pharmacy, Plaza de Ramón y Cajal s/n, Universidad Complutense, 28040 Madrid, Spain; (P.K.D.); (A.C.); (J.N.-Z.)
| | - Ana Crespo
- Department of Pharmacology, Pharmacognosy and Botany (DU Botany), Faculty of Pharmacy, Plaza de Ramón y Cajal s/n, Universidad Complutense, 28040 Madrid, Spain; (P.K.D.); (A.C.); (J.N.-Z.)
| | - Jano Nuñez-Zapata
- Department of Pharmacology, Pharmacognosy and Botany (DU Botany), Faculty of Pharmacy, Plaza de Ramón y Cajal s/n, Universidad Complutense, 28040 Madrid, Spain; (P.K.D.); (A.C.); (J.N.-Z.)
| | - H. Thorsten Lumbsch
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL 60605, USA; (H.T.L.); (F.G.)
| | - Felix Grewe
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL 60605, USA; (H.T.L.); (F.G.)
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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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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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Alors D, Grande FD, Cubas P, Crespo A, Schmitt I, Molina MC, Divakar PK. Panmixia and dispersal from the Mediterranean Basin to Macaronesian Islands of a macrolichen species. Sci Rep 2017; 7:40879. [PMID: 28102303 PMCID: PMC5244402 DOI: 10.1038/srep40879] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/12/2016] [Indexed: 02/04/2023] Open
Abstract
The Mediterranean region, comprising the Mediterranean Basin and the Macaronesian Islands, represents a center of diversification for many organisms. The genetic structure and connectivity of mainland and island microbial populations has been poorly explored, in particular in the case of symbiotic fungi. Here we investigated genetic diversity and spatial structure of the obligate outcrossing lichen-forming fungus Parmelina carporrhizans in the Mediterranean region. Using eight microsatellite and mating-type markers we showed that fungal populations are highly diverse but lack spatial structure. This is likely due to high connectivity and long distance dispersal of fungal spores. Consistent with low levels of linkage disequilibrium and lack of clonality, we detected both mating-type idiomorphs in all populations. Furthermore we showed that the Macaronesian Islands are the result of colonization from the Mediterranean Basin. The unidirectional gene flow, though, seemed not to be sufficient to counterbalance the effects of drift, resulting in comparatively allelic poor peripheral populations. Our study is the first to shed light on the high connectivity and lack of population structure in natural populations of a strictly sexual lichen fungus. Our data further support the view of the Macaronesian Islands as the end of the colonization road for this symbiotic ascomycete.
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Affiliation(s)
- David Alors
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Paloma Cubas
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe Universität, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany
| | - M. Carmen Molina
- Departamento de Biología y Geología, Física y Química Inorgánica (Área de Biodiversidad y Conservación), ESCET, Universidad Rey Juan Carlos, Móstoles, 28933 Madrid, Spain
| | - Pradeep K. Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
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Turbo-taxonomy to assemble a megadiverse lichen genus: seventy new species of Cora (Basidiomycota: Agaricales: Hygrophoraceae), honouring David Leslie Hawksworth’s seventieth birthday. FUNGAL DIVERS 2016. [DOI: 10.1007/s13225-016-0374-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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