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Otero A, Barcenas-Peña A, Lumbsch HT, Grewe F. Reference-Based RADseq Unravels the Evolutionary History of Polar Species in 'the Crux Lichenologorum' Genus Usnea (Parmeliaceae, Ascomycota). J Fungi (Basel) 2023; 9:99. [PMID: 36675920 PMCID: PMC9865703 DOI: 10.3390/jof9010099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/03/2023] [Accepted: 01/08/2023] [Indexed: 01/13/2023] Open
Abstract
Nearly 90% of fungal diversity, one of the most speciose branches in the tree of life, remains undescribed. Lichenized fungi as symbiotic associations are still a challenge for species delimitation, and current species diversity is vastly underestimated. The ongoing democratization of Next-Generation Sequencing is turning the tables. Particularly, reference-based RADseq allows for metagenomic filtering of the symbiont sequence and yields robust phylogenomic trees of closely related species. We implemented reference-based RADseq to disentangle the evolution of neuropogonoid lichens, which inhabit harsh environments and belong to Usnea (Parmeliaceae, Ascomycota), one of the most taxonomically intriguing genera within lichenized fungi. Full taxon coverage of neuropogonoid lichens was sampled for the first time, coupled with phenotype characterizations. More than 20,000 loci of 126 specimens were analyzed through concatenated and coalescent-based methods, including time calibrations. Our analysis addressed the major taxonomic discussions over recent decades. Subsequently, two species are newly described, namely U. aymondiana and U. fibriloides, and three species names are resurrected. The late Miocene and Pliocene-Pleistocene boundary is inferred as the timeframe for neuropogonoid lichen diversification. Ultimately, this study helped fill the gap of fungal diversity by setting a solid backbone phylogeny which raises new questions about which factors may trigger complex evolutionary scenarios.
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Affiliation(s)
- Ana Otero
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Science & Education, The Field Museum, Chicago, IL 60605, USA
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2
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A New Cryptic Lineage in Parmeliaceae (Ascomycota) with Pharmacological Properties. J Fungi (Basel) 2022; 8:jof8080826. [PMID: 36012814 PMCID: PMC9409757 DOI: 10.3390/jof8080826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
We used molecular data to address species delimitation in a species complex of the parmelioid genus Canoparmelia and compare the pharmacological properties of the two clades identified. We used HPLC_DAD_MS chromatography to identify and quantify the secondary substances and used a concatenated data set of three ribosomal markers to infer phylogenetic relationships. Some historical herbarium specimens were also examined. We found two groups that showed distinct pharmacological properties. The phylogenetic study supported the separation of these two groups as distinct lineages, which are here accepted as distinct species: Canoparmelia caroliniana occurring in temperate to tropical ecosystems of a variety of worldwide localities, including America, Macaronesia, south-west Europe and potentially East Africa, whereas the Kenyan populations represent the second group, for which we propose the new species C. kakamegaensis Garrido-Huéscar, Divakar & Kirika. This study highlights the importance of recognizing cryptic species using molecular data, since it can result in detecting lineages with pharmacological properties previously overlooked.
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Kantelinen A, Printzen C, Poczai P, Myllys L. Lichen speciation is sparked by a substrate requirement shift and reproduction mode differentiation. Sci Rep 2022; 12:11048. [PMID: 35773369 PMCID: PMC9247095 DOI: 10.1038/s41598-022-14970-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 06/15/2022] [Indexed: 12/04/2022] Open
Abstract
We show that obligate lignicoles in lichenized Micarea are predominately asexual whereas most facultative lignicoles reproduce sexually. Our phylogenetic analyses (ITS, mtSSU, Mcm7) together with ancestral state reconstruction show that the shift in reproduction mode has evolved independently several times within the group and that facultative and obligate lignicoles are sister species. The analyses support the assumption that the ancestor of these species was a facultative lignicole. We hypothezise that a shift in substrate requirement from bark to wood leads to differentiation in reproduction mode and becomes a driver of speciation. This is the first example of lichenized fungi where reproduction mode is connected to substrate requirement. This is also the first example where such an association is demonstrated to spark lichen speciation. Our main hypothesis is that obligate species on dead wood need to colonize new suitable substrata relatively fast and asexual reproduction is more effective a strategy for successful colonization.
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Affiliation(s)
- Annina Kantelinen
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, 00014, Helsinki, Finland.
| | - Christian Printzen
- Senckenberg Forschungsinstitut und Naturmuseum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Péter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, 00014, Helsinki, Finland.,Museomics Research Group, Viikki Plant Science Centre (ViPS), University of Helsinki, PO Box 65, 00014, Helsinki, Finland
| | - Leena Myllys
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, 00014, Helsinki, Finland
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4
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Interpreting phylogenetic conflict: Hybridization in the most speciose genus of lichen-forming fungi. Mol Phylogenet Evol 2022; 174:107543. [PMID: 35690378 DOI: 10.1016/j.ympev.2022.107543] [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: 06/11/2021] [Revised: 02/06/2022] [Accepted: 05/13/2022] [Indexed: 11/24/2022]
Abstract
While advances in sequencing technologies have been invaluable for understanding evolutionary relationships, increasingly large genomic data sets may result in conflicting evolutionary signals that are often caused by biological processes, including hybridization. Hybridization has been detected in a variety of organisms, influencing evolutionary processes such as generating reproductive barriers and mixing standing genetic variation. Here, we investigate the potential role of hybridization in the diversification of the most speciose genus of lichen-forming fungi, Xanthoparmelia. As Xanthoparmelia is projected to have gone through recent, rapid diversification, this genus is particularly suitable for investigating and interpreting the origins of phylogenomic conflict. Focusing on a clade of Xanthoparmelia largely restricted to the Holarctic region, we used a genome skimming approach to generate 962 single-copy gene regions representing over 2 Mbp of the mycobiont genome. From this genome-scale dataset, we inferred evolutionary relationships using both concatenation and coalescent-based species tree approaches. We also used three independent tests for hybridization. Although different species tree reconstruction methods recovered largely consistent and well-supported trees, there was widespread incongruence among individual gene trees. Despite challenges in differentiating hybridization from ILS in situations of recent rapid radiations, our genome-wide analyses detected multiple potential hybridization events in the Holarctic clade, suggesting one possible source of trait variability in this hyperdiverse genus. This study highlights the value in using a pluralistic approach for characterizing genome-scale conflict, even in groups with well-resolved phylogenies, while highlighting current challenges in detecting the specific impacts of hybridization.
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Senanayake IC, Pem D, Rathnayaka AR, Wijesinghe SN, Tibpromma S, Wanasinghe DN, Phookamsak R, Kularathnage ND, Gomdola D, Harishchandra D, Dissanayake LS, Xiang MM, Ekanayaka AH, McKenzie EHC, Hyde KD, Zhang HX, Xie N. Predicting global numbers of teleomorphic ascomycetes. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00498-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
AbstractSexual reproduction is the basic way to form high genetic diversity and it is beneficial in evolution and speciation of fungi. The global diversity of teleomorphic species in Ascomycota has not been estimated. This paper estimates the species number for sexual ascomycetes based on five different estimation approaches, viz. by numbers of described fungi, by fungus:substrate ratio, by ecological distribution, by meta-DNA barcoding or culture-independent studies and by previous estimates of species in Ascomycota. The assumptions were made with the currently most accepted, “2.2–3.8 million” species estimate and results of previous studies concluding that 90% of the described ascomycetes reproduce sexually. The Catalogue of Life, Species Fungorum and published research were used for data procurement. The average value of teleomorphic species in Ascomycota from all methods is 1.86 million, ranging from 1.37 to 2.56 million. However, only around 83,000 teleomorphic species have been described in Ascomycota and deposited in data repositories. The ratio between described teleomorphic ascomycetes to predicted teleomorphic ascomycetes is 1:22. Therefore, where are the undiscovered teleomorphic ascomycetes? The undescribed species are no doubt to be found in biodiversity hot spots, poorly-studied areas and species complexes. Other poorly studied niches include extremophiles, lichenicolous fungi, human pathogens, marine fungi, and fungicolous fungi. Undescribed species are present in unexamined collections in specimen repositories or incompletely described earlier species. Nomenclatural issues, such as the use of separate names for teleomorph and anamorphs, synonyms, conspecific names, illegitimate and invalid names also affect the number of described species. Interspecies introgression results in new species, while species numbers are reduced by extinctions.
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Barreto Xavier-Leite A, da Silva Cáceres ME, Aptroot A, Moncada B, Lücking R, Tomio Goto B. Phylogenetic revision of the lichenized family Gomphillaceae (Ascomycota: Graphidales) suggests post-K-Pg boundary diversification and phylogenetic signal in asexual reproductive structures. Mol Phylogenet Evol 2022; 168:107380. [PMID: 34999241 DOI: 10.1016/j.ympev.2021.107380] [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: 05/24/2020] [Revised: 08/26/2021] [Accepted: 11/25/2021] [Indexed: 11/26/2022]
Abstract
We present the first broad molecular-phylogenetic revision of the lichenized family Gomphillaceae, based on 408 newly generated sequences of the mitochondrial SSU rDNA and nuclear LSU rDNA, representing 342 OTUs. The phylogenetic analysis of 20 out of the 28 currently accepted genera resulted in 48 clades. Twelve genera were resolved as monophyletic: Actinoplaca, Arthotheliopsis, Bullatina, Caleniopsis, Corticifraga, Gomphillus, Gyalectidium, Gyalidea, Jamesiella, Rolueckia, Rubrotricha, and Taitaia. Two genera resulted paraphyletic, namely Aulaxina (including Caleniopsis) and Asterothyrium (including Linhartia). Six genera were in part highly polyphyletic: Aderkomyces, Calenia, Echinoplaca, Gyalideopsis, Psorotheciopsis, and Tricharia. While ascoma morphology and anatomy has traditionally been considered as main character complex to distinguish genera, our study supported the notion that the characteristic asexual anamorph of Gomphillaceae, the so-called hyphophores, are diagnostic for most of the newly recognized clades. As a result, we recognize 26 new genus-level clades, three of which have names available (Microxyphiomyces, Psathyromyces, Spinomyces) and 23 that will require formal description as new genera. We also tested monophyly for 53 species-level names for which two or more specimens were sequenced: 27 were supported as monophyletic and representing a single species, 13 as monophyletic but with an internal topology suggesting cryptic speciation, four as paraphyletic, and nine as polyphyletic. These data suggest that species richness in the family is higher than indicated by the number of accepted names (currently 425); they also confirm that recently refined species concepts reflect species richness better than the broad concepts applied in Santesson's monograph. A divergence time analysis revealed that foliicolous Gomphillaceae diversified after the K-Pg-boundary and largely during the Miocene, a notion supported by limited data available for other common foliicolous lineages such as Chroodiscus (Graphidaceae), Pilocarpaceae, and Porinaceae. This contradicts recent studies suggesting that only macrofoliose Lecanoromycetes exhibit increased diversification rates in the Cenozoic.
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Affiliation(s)
- Amanda Barreto Xavier-Leite
- Programa de Pós-Graduação em Sistemática e Evolução, CB, Universidade Federal do Rio Grande do Norte, Campus Universitário, 59072-970, Natal, RN, Brazil.
| | - Marcela E da Silva Cáceres
- Departamento de Biociências, Universidade Federal de Sergipe, CEP: 49500-000, Itabaiana, Sergipe, Brazil.
| | - André Aptroot
- Laboratório de Botânica / Liquenologia, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, CEP 79070-900, Campo Grande, Mato Grosso do Sul, Brazil.
| | - Bibiana Moncada
- Universidad Distrital Francisco José de Caldas, Licenciatura en Biología, Cra. 4 No. 26B-54, Torre de Laboratorios, Herbario, Bogotá, Colombia.
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Strasse 6-8, 14195 Berlin, Germany.
| | - Bruno Tomio Goto
- Departamento de Botânica e Zoologia, CB, Universidade Federal do Rio Grande do Norte, Campus Universitário, 59072-970, Natal, RN, Brazil.
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Scur MC, Kitaura MJ, de Paula JB, Spielmann AA, Lorenz AP. Contrasting variation patterns in Austroplaca hookeri and Rusavskia elegans (Teloschistaceae, lichenized Ascomycota) in maritime Antarctica. Polar Biol 2021. [DOI: 10.1007/s00300-021-02976-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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8
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Nelsen MP, Leavitt SD, Heller K, Muggia L, Lumbsch HT. Macroecological diversification and convergence in a clade of keystone symbionts. FEMS Microbiol Ecol 2021; 97:6279059. [PMID: 34014310 DOI: 10.1093/femsec/fiab072] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/18/2021] [Indexed: 11/12/2022] Open
Abstract
Lichens are classic models of symbiosis, and one of the most frequent nutritional modes among fungi. The ecologically and geographically widespread lichen-forming algal (LFA) genus Trebouxia is one of the best-studied groups of LFA and associates with over 7000 fungal species. Despite its importance, little is known about its diversification. We synthesized twenty years of publicly available data by characterizing the ecological preferences of this group and testing for time-variant shifts in climatic regimes over a distribution of trees. We found evidence for limited shifts among regimes, but that disparate lineages convergently evolved similar ecological tolerances. Early Trebouxia lineages were largely forest specialists or habitat generalists that occupied a regime whose extant members occur in moderate climates. Trebouxia then convergently diversified in non-forested habitats and expanded into regimes whose modern representatives occupy wet-warm and cool-dry climates. We rejected models in which climatic diversification slowed through time, suggesting climatic diversification is inconsistent with that expected under an adaptive radiation. In addition, we found that climatic and vegetative regime shifts broadly coincided with the evolution of biomes and associated or similar taxa. Together, our work illustrates how this keystone symbiont from an iconic symbiosis evolved to occupy diverse habitats across the globe.
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Affiliation(s)
- Matthew P Nelsen
- The Field Museum, Negaunee Integrative Research Center, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Steven D Leavitt
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, 4102 Life Science Building, Provo, UT 84602, USA
| | - Kathleen Heller
- The Field Museum, Negaunee Integrative Research Center, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.,Biological Sciences Division, University of Chicago, 5841 S. Maryland Avenue, Chicago, IL 60637, USA
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, via Giorgieri 10, 34127 Trieste, Italy
| | - H Thorsten Lumbsch
- The Field Museum, Negaunee Integrative Research Center, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
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9
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Grewe F, Ametrano C, Widhelm TJ, Leavitt S, Distefano I, Polyiam W, Pizarro D, Wedin M, Crespo A, Divakar PK, Lumbsch HT. Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota). IMA Fungus 2020; 11:27. [PMID: 33317627 PMCID: PMC7734834 DOI: 10.1186/s43008-020-00051-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/29/2020] [Indexed: 11/10/2022] Open
Abstract
Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow.
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Affiliation(s)
- Felix Grewe
- Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA.
| | - Claudio Ametrano
- Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA
| | - Todd J Widhelm
- Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA
| | - Steven Leavitt
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, UT, USA
| | - Isabel Distefano
- Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA
| | - Wetchasart Polyiam
- Lichen Research Unit, Biology Department, Faculty of Science, Ramkhamhaeng University, Ramkhamhaeng 24 Road, Bangkok, 10240, Thailand
| | - David Pizarro
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Mats Wedin
- Department of Botany, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden
| | - Ana Crespo
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Pradeep K Divakar
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - H Thorsten Lumbsch
- Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA
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10
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Nelsen MP, Lücking R, Boyce CK, Lumbsch HT, Ree RH. The macroevolutionary dynamics of symbiotic and phenotypic diversification in lichens. Proc Natl Acad Sci U S A 2020; 117:21495-21503. [PMID: 32796103 PMCID: PMC7474681 DOI: 10.1073/pnas.2001913117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Symbioses are evolutionarily pervasive and play fundamental roles in structuring ecosystems, yet our understanding of their macroevolutionary origins, persistence, and consequences is incomplete. We traced the macroevolutionary history of symbiotic and phenotypic diversification in an iconic symbiosis, lichens. By inferring the most comprehensive time-scaled phylogeny of lichen-forming fungi (LFF) to date (over 3,300 species), we identified shifts among symbiont classes that broadly coincided with the convergent evolution of phylogenetically or functionally similar associations in diverse lineages (plants, fungi, bacteria). While a relatively recent loss of lichenization in Lecanoromycetes was previously identified, our work instead suggests lichenization was abandoned far earlier, interrupting what had previously been considered a direct switch between trebouxiophycean and trentepohlialean algal symbionts. Consequently, some of the most diverse clades of LFF are instead derived from nonlichenized ancestors and re-evolved lichenization with Trentepohliales algae, a clade that also facilitated lichenization in unrelated lineages of LFF. Furthermore, while symbiont identity and symbiotic phenotype influence the ecology and physiology of lichens, they are not correlated with rates of lineage birth and death, suggesting more complex dynamics underly lichen diversification. Finally, diversification patterns of LFF differed from those of wood-rotting and ectomycorrhizal taxa, likely reflecting contrasts in their fundamental biological properties. Together, our work provides a timeline for the ecological contributions of lichens, and reshapes our understanding of symbiotic persistence in a classic model of symbiosis.
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Affiliation(s)
- Matthew P Nelsen
- Department of Science and Education, Negaunee Integrative Research Center, The Field Museum, Chicago, IL 60605;
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, 14195 Berlin, Germany
| | - C Kevin Boyce
- Department of Geological Sciences, Stanford University, Stanford, CA 94305
| | - H Thorsten Lumbsch
- Department of Science and Education, Negaunee Integrative Research Center, The Field Museum, Chicago, IL 60605
| | - Richard H Ree
- Department of Science and Education, Negaunee Integrative Research Center, The Field Museum, Chicago, IL 60605
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11
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Kosecka M, Jabłońska A, Flakus A, Rodriguez-Flakus P, Kukwa M, Guzow-Krzemińska B. Trentepohlialean Algae (Trentepohliales, Ulvophyceae) Show Preference to Selected Mycobiont Lineages in Lichen Symbioses. JOURNAL OF PHYCOLOGY 2020; 56:979-993. [PMID: 32198895 DOI: 10.1111/jpy.12994] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/02/2020] [Indexed: 05/29/2023]
Abstract
The main aims of this work were to assess phylogenetic relationships of the trentepohlialean photobionts in tropical, mainly sterile, lichens collected in Bolivia, to examine their genetic diversity, host specificity, and the impact of habitat factors on the occurrence of Trentepohliales. Based on rbcL marker analysis, we constructed a phylogenetic tree with eight major clades of Trentepohliales, of which seven free-living species are intermingled with lichenized ones. Our analyses show that the studied photobionts are scattered across the phylogenetic tree and algae from temperate and tropical regions do not form monophyletic groups, except within one clade that seems to be restricted to the tropics. There is no significant occurrence pattern of lichenized Trentepohliaceae on a specific substratum, except Cephaleuros spp. and Phycopeltis spp., which are restricted to leaves, while some clades with lichenized algae may be specialized to tree bark and wood. Moreover, we found two patterns of associations: first, closely related algae can associate with distantly related mycobionts; second, some other trentepohlioid algae associate with selected lineages of fungi (e.g., Arthoniaceae or Graphidaceae). We also found that some lineages of photobionts are even more selective and associate exclusively with one species (e.g., Dichosporidium nigrocinctum, Diorygma antillarum) or closely related lichen-forming fungi (Herpothallon spp.). Concluding, we found that occurrence of some trentepohlialean photobionts may correlate with the particular type of the mycobiont.
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Affiliation(s)
- Magdalena Kosecka
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, PL-80-308, Gdańsk, Poland
| | - Agnieszka Jabłońska
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, PL-80-308, Gdańsk, Poland
| | - Adam Flakus
- Department of Lichenology, W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512, Kraków, Poland
| | - Pamela Rodriguez-Flakus
- Department of Vascular Plants, W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512, Kraków, Poland
| | - Martin Kukwa
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, PL-80-308, Gdańsk, Poland
| | - Beata Guzow-Krzemińska
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, PL-80-308, Gdańsk, Poland
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12
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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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13
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Huang JP, Kraichak E, Leavitt SD, Nelsen MP, Lumbsch HT. Accelerated diversifications in three diverse families of morphologically complex lichen-forming fungi link to major historical events. Sci Rep 2019; 9:8518. [PMID: 31253825 PMCID: PMC6599062 DOI: 10.1038/s41598-019-44881-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/20/2019] [Indexed: 11/09/2022] Open
Abstract
Historical mass extinction events had major impacts on biodiversity patterns. The most recent and intensively studied event is the Cretaceous - Paleogene (K-Pg) boundary (ca. 66 million years ago [MYA]). However, the factors that may have impacted diversification dynamics vary across lineages. We investigated the macroevolutionary dynamics with a specific focus on the impact of major historical events such as the K-Pg mass extinction event on two major subclasses - Lecanoromycetidae and Ostropomycetidae - of lichen-forming fungi and tested whether variation in the rate of diversification can be associated with the evolution of a specific trait state - macrolichen. Our results reveal accelerated diversification events in three families of morphologically complex lichen-forming fungi - Cladoniaceae, Parmeliaceae, and Peltigeraceae - which are from the subclass Lecanoromycetidae and mostly composed of macrolichens, those that form three dimensional structures. Our RTT plot result for the subclass Lecanoromycetidae also reveals accelerated diversification. Changes in diversification rates occurred around the transition between Mesozoic and Cenozoic eras and was likely related to the K-Pg mass extinction event. The phylogenetic positions for rate increases estimated based on marginal shift probability are, however, scattered from 100 to 40 MYA preventing us from making explicit inference. Although we reveal that the phenotypic state of macrolichens is associated with a higher diversification rate than microlichens, we also show that the evolution of macrolichens predated the K-Pg event. Furthermore, the association between macrolichens and increased diversification is not universal and can be explained, in part, by phylogenetic relatedness. By investigating the macroevolutionary dynamics of lichen-forming fungi our study provides a new empirical system suitable to test the effect of major historical event on shaping biodiversity patterns and to investigate why changes in biodiversity patterns are not in concordance across clades. Our results imply that multiple historical events during the transition from Mesozoic to Cenozoic eras, including the K-Pg mass extinction event, impacted the evolutionary dynamics in lichen-forming fungi. However, future studies focusing on individual lichen-forming fungal families are required to ascertain whether diversification rates are associated with growth form and certain geological events.
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Affiliation(s)
- Jen-Pan Huang
- Integrative Research Center, The Field Museum, Chicago, IL, 60605, USA. .,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
| | - Ekaphan Kraichak
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Steven D Leavitt
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, UT, 84602, USA
| | - Matthew P Nelsen
- Integrative Research Center, The Field Museum, Chicago, IL, 60605, USA
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14
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Pogoda CS, Keepers KG, Nadiadi AY, Bailey DW, Lendemer JC, Tripp EA, Kane NC. Genome streamlining via complete loss of introns has occurred multiple times in lichenized fungal mitochondria. Ecol Evol 2019; 9:4245-4263. [PMID: 31016002 PMCID: PMC6467859 DOI: 10.1002/ece3.5056] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/12/2019] [Accepted: 02/22/2019] [Indexed: 12/22/2022] Open
Abstract
Reductions in genome size and complexity are a hallmark of obligate symbioses. The mitochondrial genome displays clear examples of these reductions, with the ancestral alpha-proteobacterial genome size and gene number having been reduced by orders of magnitude in most descendent modern mitochondrial genomes. Here, we examine patterns of mitochondrial evolution specifically looking at intron size, number, and position across 58 species from 21 genera of lichenized Ascomycete fungi, representing a broad range of fungal diversity and niches. Our results show that the cox1gene always contained the highest number of introns out of all the mitochondrial protein-coding genes, that high intron sequence similarity (>90%) can be maintained between different genera, and that lichens have undergone at least two instances of complete, genome-wide intron loss consistent with evidence for genome streamlining via loss of parasitic, noncoding DNA, in Phlyctis boliviensisand Graphis lineola. Notably, however, lichenized fungi have not only undergone intron loss but in some instances have expanded considerably in size due to intron proliferation (e.g., Alectoria fallacina and Parmotrema neotropicum), even between closely related sister species (e.g., Cladonia). These results shed light on the highly dynamic mitochondrial evolution that is occurring in lichens and suggest that these obligate symbiotic organisms are in some cases undergoing recent, broad-scale genome streamlining via loss of protein-coding genes as well as noncoding, parasitic DNA elements.
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Affiliation(s)
- Cloe S. Pogoda
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColorado
| | - Kyle G. Keepers
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColorado
| | - Arif Y. Nadiadi
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColorado
| | - Dustin W. Bailey
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColorado
| | - James C. Lendemer
- Institute of Systematic BotanyThe New York Botanical GardenBronxNew York
| | - Erin A. Tripp
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColorado
- Museum of Natural HistoryUniversity of ColoradoBoulderColorado
| | - Nolan C. Kane
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColorado
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15
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Magallón S, Sánchez-Reyes LL, Gómez-Acevedo SL. Thirty clues to the exceptional diversification of flowering plants. ANNALS OF BOTANY 2019; 123:491-503. [PMID: 30376040 PMCID: PMC6377106 DOI: 10.1093/aob/mcy182] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 10/23/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND AIMS As angiosperms became one of the megadiverse groups of macroscopic eukaryotes, they forged modern ecosystems and promoted the evolution of extant terrestrial biota. Unequal distribution of species among lineages suggests that diversification, the process that ultimately determines species richness, acted differentially through angiosperm evolution. METHODS We investigate how angiosperms became megadiverse by identifying the phylogenetic and temporal placement of exceptional radiations, by combining the most densely fossil-calibrated molecular clock phylogeny with a Bayesian model that identifies diversification shifts among evolutionary lineages and through time. We evaluate the effect of the prior number of expected shifts in the phylogenetic tree. KEY RESULTS Major diversification increases took place over 100 Ma, from the Early Cretaceous to the end of the Paleogene, and are distributed across the angiosperm phylogeny. The long-term diversification trajectory of angiosperms shows moderate rate variation, but is underlain by increasing speciation and extinction, and results from temporally overlapping, independent radiations and depletions in component lineages. CONCLUSIONS The identified deep time diversification shifts are clues to the identification of ultimate drivers of angiosperm megadiversity, which probably involve multivariate interactions among intrinsic traits and extrinsic forces. An enhanced understanding of angiosperm diversification will involve a more precise phylogenetic location of diversification shifts, and integration of fossil information.
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Affiliation(s)
- Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Del. Coyoacán, Ciudad de México, México
| | - Luna L Sánchez-Reyes
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Del. Coyoacán, Ciudad de México, México
| | - Sandra L Gómez-Acevedo
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Del. Coyoacán, Ciudad de México, México
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16
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Gerlach ADCL, Toprak Z, Naciri Y, Caviró EA, da Silveira RMB, Clerc P. New insights into the Usnea cornuta aggregate (Parmeliaceae, lichenized Ascomycota): Molecular analysis reveals high genetic diversity correlated with chemistry. Mol Phylogenet Evol 2019; 131:125-137. [DOI: 10.1016/j.ympev.2018.10.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 09/17/2018] [Accepted: 10/26/2018] [Indexed: 01/01/2023]
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17
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Pizarro D, Divakar PK, Grewe F, Leavitt SD, Huang JP, Dal Grande F, Schmitt I, Wedin M, Crespo A, Lumbsch HT. Phylogenomic analysis of 2556 single-copy protein-coding genes resolves most evolutionary relationships for the major clades in the most diverse group of lichen-forming fungi. FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0407-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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18
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Singh G, Grande FD, Schnitzler J, Pfenninger M, Schmitt I. Different diversification histories in tropical and temperate lineages in the ascomycete subfamily Protoparmelioideae (Parmeliaceae). MycoKeys 2018; 36:1-19. [PMID: 29997448 PMCID: PMC6037653 DOI: 10.3897/mycokeys.36.22548] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 06/19/2018] [Indexed: 11/12/2022] Open
Abstract
Background: Environment and geographic processes affect species' distributions as well as evolutionary processes, such as clade diversification. Estimating the time of origin and diversification of organisms helps us understand how climate fluctuations in the past might have influenced the diversification and present distribution of species. Complementing divergence dating with character evolution could indicate how key innovations have facilitated the diversification of species. Methods: We estimated the divergence times within the newly recognised subfamily Protoparmelioideae (Ascomycota) using a multilocus dataset to assess the temporal context of diversification events. We reconstructed ancestral habitats and substrate using a species tree generated in *Beast. Results: We found that the diversification in Protoparmelioideae occurred during the Miocene and that the diversification events in the tropical clade Maronina predate those of the extratropical Protoparmelia. Character reconstructions suggest that the ancestor of Protoparmelioideae was most probably a rock-dwelling lichen inhabiting temperate environments. Conclusions: Major diversification within the subtropical/tropical genus Maronina occurred between the Paleocene and Miocene whereas the diversifications within the montane, arctic/temperate genus Protoparmelia occurred much more recently, i.e. in the Miocene.
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Affiliation(s)
- Garima Singh
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Jan Schnitzler
- Department of Molecular Evolution and Plant Systematics, Institute of Biology, Leipzig University, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt am Main, Germany
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19
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Leavitt SD, Westberg M, Nelsen MP, Elix JA, Timdal E, Sohrabi M, St. Clair LL, Williams L, Wedin M, Lumbsch HT. Multiple, Distinct Intercontinental Lineages but Isolation of Australian Populations in a Cosmopolitan Lichen-Forming Fungal Taxon, Psora decipiens (Psoraceae, Ascomycota). Front Microbiol 2018; 9:283. [PMID: 29527197 PMCID: PMC5829036 DOI: 10.3389/fmicb.2018.00283] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 02/07/2018] [Indexed: 12/12/2022] Open
Abstract
Multiple drivers shape the spatial distribution of species, including dispersal capacity, niche incumbency, climate variability, orographic barriers, and plate tectonics. However, biogeographic patterns of fungi commonly do not fit conventional expectations based on studies of animals and plants. Fungi, in general, are known to occur across exceedingly broad, intercontinental distributions, including some important components of biological soil crust communities (BSCs). However, molecular data often reveal unexpected biogeographic patterns in lichenized fungal species that are assumed to have cosmopolitan distributions. The lichen-forming fungal species Psora decipiens is found on all continents, except Antarctica and occurs in BSCs across diverse habitats, ranging from hot, arid deserts to alpine habitats. In order to better understand factors that shape population structure in cosmopolitan lichen-forming fungal species, we investigated biogeographic patterns in the cosmopolitan taxon P. decipiens, along with the closely related taxa P. crenata and P. saviczii. We generated a multi-locus sequence dataset based on a worldwide sampling of these taxa in order to reconstruct evolutionary relationships and explore phylogeographic patterns. Both P. crenata and P. decipiens were not recovered as monophyletic; and P. saviczii specimens were recovered as a monophyletic clade closely related to a number of lineages comprised of specimens representing P. decipiens. Striking phylogeographic patterns were observed for P. crenata, with populations from distinct geographic regions belonging to well-separated, monophyletic lineages. South African populations of P. crenata were further divided into well-supported sub-clades. While well-supported phylogenetic substructure was also observed for the nominal taxon P. decipiens, nearly all lineages were comprised of specimens collected from intercontinental populations. However, all Australian specimens representing P. decipiens were recovered within a single well-supported monophyletic clade consisting solely of Australian samples. Our study supports up to 10 candidate species-level lineages in P. decipiens, based on genealogical concordance and coalescent-based species delimitation analyses. Our results support the general pattern of the biogeographic isolation of lichen-forming fungal populations in Australia, even in cases where closely related congeners have documented intercontinental distributions. Our study has important implications for understanding factors influencing diversification and distributions of lichens associated with BSC.
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Affiliation(s)
- Steven D. Leavitt
- Department of Biology and Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT, United States
| | | | | | - John A. Elix
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Einar Timdal
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Mohammad Sohrabi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
| | - Larry L. St. Clair
- Department of Biology and Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT, United States
| | - Laura Williams
- Plant Ecology and Systematics, Biology Institute, University of Kaiserslautern, Kaiserslautern, Germany
| | - Mats Wedin
- Department of Botany, Swedish Museum of Natural History, Stockholm, Sweden
| | - H. T. Lumbsch
- Science and Education, The Field Museum, Chicago, IL, United States
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20
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High diversity, high insular endemism and recent origin in the lichen genus Sticta (lichenized Ascomycota, Peltigerales) in Madagascar and the Mascarenes. Mol Phylogenet Evol 2018; 122:15-28. [PMID: 29360617 DOI: 10.1016/j.ympev.2018.01.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 11/14/2017] [Accepted: 01/13/2018] [Indexed: 11/27/2022]
Abstract
Lichen biodiversity and its generative evolutionary processes are practically unknown in the MIOI (Madagascar and Indian Ocean Islands) biodiversity hotspot. We sought to test the hypothesis that lichenized fungi in this region have undergone a rapid radiation, following a single colonization event, giving rise to narrow endemics, as is characteristic of other lineages of plants. We extensively sampled specimens of the lichen genus Sticta in the Mascarene archipelago (mainly Réunion) and in Madagascar, mainly in the northern range (Amber Mt and Marojejy Mt) and produced the fungal ITS barcode sequence for 148 thalli. We further produced a four-loci data matrix for 68 of them, representing the diversity and geographical distribution of ITS haplotypes. We reconstructed the phylogenetic relationships within this group, established species boundaries with morphological context, and estimated the date of the most recent common ancestor. Our inferences resolve a robust clade comprising 31 endemic species of Sticta that arose from the diversification following a single recent (c. 11 Mya) colonization event. All but three species have a very restricted range, endemic to either the Mascarene archipelago or a single massif in Madagascar. The first genus of lichens to be studied with molecular data in this region underwent a recent radiation, exhibits micro-endemism, and thus exemplifies the biodiversity characteristics found in other taxa in Madagascar and the Mascarenes.
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21
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Bouchenak-Khelladi Y, Linder HP. Frequent and parallel habitat transitions as driver of unbounded radiations in the Cape flora. Evolution 2017; 71:2548-2561. [PMID: 28884804 DOI: 10.1111/evo.13364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 08/25/2017] [Accepted: 08/29/2017] [Indexed: 01/20/2023]
Abstract
The enormous species richness in the Cape Floristic Region (CFR) of Southern Africa is the result of numerous radiations, but the temporal progression and possible mechanisms of these radiations are still poorly understood. Here, we explore the macroevolutionary dynamics of the Restionaceae, which include 340 species that are found in all vegetation types in the Cape flora and are ecologically dominant in fynbos. Using an almost complete (i.e., 98%) species-level time calibrated phylogeny and models of diversification dynamics, we show that species diversification is constant through the Cenozoic, with no evidence of an acceleration with the onset of the modern winter-wet climate, or a recent density-dependent slowdown. Contrary to expectation, species inhabiting the oldest (montane) and most extensive (drylands) habitats did not undergo higher diversification rates than species in the younger (lowlands) and more restricted (wetland) habitats. We show that the rate of habitat transitions is more closely related to the speciation rate than to time, and that more than a quarter of all speciation events are associated with habitat transitions. This suggests that the unbounded Restionaceae diversification resulted from numerous, parallel, habitat shifts, rather than persistence in a habitat stimulating speciation. We speculate that this could be one of the mechanisms resulting in the hyperdiverse Cape flora.
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Affiliation(s)
- Yanis Bouchenak-Khelladi
- Department of Systematic and Evolutionary Botany, University of Zurich, CH 8008 Zurich, Switzerland
| | - H Peter Linder
- Department of Systematic and Evolutionary Botany, University of Zurich, CH 8008 Zurich, Switzerland
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22
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Using a temporal phylogenetic method to harmonize family- and genus-level classification in the largest clade of lichen-forming fungi. FUNGAL DIVERS 2017. [DOI: 10.1007/s13225-017-0379-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Using multi-locus sequence data for addressing species boundaries in commonly accepted lichen-forming fungal species. ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-016-0320-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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24
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Molina MC, Divakar PK, Goward T, Millanes AM, Lumbsch HT, Crespo A. Neogene diversification in the temperate lichen-forming fungal genus Parmelia (Parmeliaceae, Ascomycota). SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1226977] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- 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
| | - Trevor Goward
- UBC Herbarium, Beaty Museum, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Ana M. Millanes
- Departamento de Biología y Geología, Física y Química Inorgánica (Área de Biodiversidad y Conservación), ESCET, Universidad Rey Juan Carlos, Móstoles, 28933 Madrid, Spain
| | | | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
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25
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Sánchez-García M, Matheny PB. Is the switch to an ectomycorrhizal state an evolutionary key innovation in mushroom-forming fungi? A case study in the Tricholomatineae (Agaricales). Evolution 2016; 71:51-65. [PMID: 27767208 DOI: 10.1111/evo.13099] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 10/05/2016] [Accepted: 10/10/2016] [Indexed: 01/31/2023]
Abstract
Although fungi are one of the most diverse groups of organisms, little is known about the processes that shape their high taxonomic diversity. This study focuses on evolution of ectomycorrhizal (ECM) mushroom-forming fungi, symbiotic associates of many trees and shrubs, in the suborder Tricholomatineae of the Agaricales. We used the BiSSE model and BAMM to test the hypothesis that the ECM habit represents an evolutionary key innovation that allowed the colonization of new niches followed by an increase in diversification rate. Ancestral state reconstruction (ASR) supports the ancestor of the Tricholomatineae as non-ECM. We detected two diversification rate increases in the genus Tricholoma and the Rhodopolioid clade of the genus Entoloma. However, no increases in diversification were detected in the four other ECM clades of Tricholomatineae. We suggest that diversification of Tricholoma was not only due to the evolution of the ECM lifestyle, but also to the expansion and dominance of its main hosts and ability to associate with a variety of hosts. Diversification in the Rhodopolioid clade could be due to the unique combination of spore morphology and ECM habit. The spore morphology may represent an exaptation that aided spore dispersal and colonization. This is the first study to investigate rate shifts across a phylogeny that contains both non-ECM and ECM lineages.
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Affiliation(s)
- Marisol Sánchez-García
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, Tennessee, 37996-1610.,Current Address: Biology Department, Clark University, Worcester, Massachusetts, 01610
| | - Patrick Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, Tennessee, 37996-1610
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26
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Mark K, Cornejo C, Keller C, Flück D, Scheidegger C. Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation. Genome 2016; 59:685-704. [DOI: 10.1139/gen-2015-0189] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although lichens (lichen-forming fungi) play an important role in the ecological integrity of many vulnerable landscapes, only a minority of lichen-forming fungi have been barcoded out of the currently accepted ∼18 000 species. Regular Sanger sequencing can be problematic when analyzing lichens since saprophytic, endophytic, and parasitic fungi live intimately admixed, resulting in low-quality sequencing reads. Here, high-throughput, long-read 454 pyrosequencing in a GS FLX+ System was tested to barcode the fungal partner of 100 epiphytic lichen species from Switzerland using fungal-specific primers when amplifying the full internal transcribed spacer region (ITS). The present study shows the potential of DNA barcoding using pyrosequencing, in that the expected lichen fungus was successfully sequenced for all samples except one. Alignment solutions such as BLAST were found to be largely adequate for the generated long reads. In addition, the NCBI nucleotide database—currently the most complete database for lichen-forming fungi—can be used as a reference database when identifying common species, since the majority of analyzed lichens were identified correctly to the species or at least to the genus level. However, several issues were encountered, including a high sequencing error rate, multiple ITS versions in a genome (incomplete concerted evolution), and in some samples the presence of mixed lichen-forming fungi (possible lichen chimeras).
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Affiliation(s)
- Kristiina Mark
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Switzerland
- Institute of Botany and Ecology, University of Tartu, Estonia
| | - Carolina Cornejo
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Switzerland
| | - Christine Keller
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Switzerland
| | - Daniela Flück
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Switzerland
| | - Christoph Scheidegger
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Switzerland
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27
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Del-Prado R, Divakar PK, Lumbsch HT, Crespo AM. Hidden Genetic Diversity in an Asexually Reproducing Lichen Forming Fungal Group. PLoS One 2016; 11:e0161031. [PMID: 27513649 PMCID: PMC4981466 DOI: 10.1371/journal.pone.0161031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/28/2016] [Indexed: 11/19/2022] Open
Abstract
Asexual species with vegetative propagation of both symbiont partners (soredia) in lichens may harbor lower species diversity because they may indeed represent evolutionary dead ends or clones. In this study we aim to critically examine species boundaries in the sorediate lichen forming fungi Parmotrema reticulatum–Parmotrema pseudoreticulatum complex applying coalescent-based approaches and other recently developed DNA-based methods. To this end, we gathered 180 samples from Africa, Asia, Australasia, Europe, North and South America and generated sequences of internal transcribed spacer of nuclear ribosomal DNA (ITS) and DNA replication licensing factor MCM7 (MCM7). The dataset was analysed using different approaches such as traditional phylogeny–maximum likelihood and Bayesian–genetic distances, automatic barcode gap discovery and coalescent-based methods–PTP, GMYC, spedeSTEM and *Beast–in order to test congruence among results. Additionally, the divergence times were also estimated to elucidate diversification events. Delimitations inferred from the different analyses are comparable with only minor differences, and following a conservative approach we propose that the sampled specimens of the P. reticulatum–P. pseudoreticulatum complex belong to at least eight distinct species-level lineages. Seven are currently classified under P. reticulatum and one as P. pseudoreticulatum. In this work we discuss one of only few examples of cryptic species that have so far been found in sorediate reproducing lichen forming fungi. Additionally our estimates suggest a recent origin of the species complex–during the Miocene. Consequently, the wide distribution of several of the cryptic species has to be explained by intercontinental long-distance dispersal events.
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Affiliation(s)
- Ruth Del-Prado
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
- * E-mail:
| | - Pradeep Kumar Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - H. Thorsten Lumbsch
- Science and Education, Field Museum, Chicago, Illinois, United States of America
| | - Ana M. Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
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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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Mark K, Saag L, Leavitt SD, Will-Wolf S, Nelsen MP, Tõrra T, Saag A, Randlane T, Lumbsch HT. Evaluation of traditionally circumscribed species in the lichen-forming genus Usnea, section Usnea (Parmeliaceae, Ascomycota) using a six-locus dataset. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0273-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Alors D, Lumbsch HT, Divakar PK, Leavitt SD, Crespo A. An Integrative Approach for Understanding Diversity in the Punctelia rudecta Species Complex (Parmeliaceae, Ascomycota). PLoS One 2016; 11:e0146537. [PMID: 26863231 PMCID: PMC4749632 DOI: 10.1371/journal.pone.0146537] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 12/18/2015] [Indexed: 11/23/2022] Open
Abstract
High levels of cryptic diversity have been documented in lichenized fungi, especially in Parmeliaceae, and integrating various lines of evidence, including coalescent-based species delimitation approaches, help establish more robust species circumscriptions. In this study, we used an integrative taxonomic approach to delimit species in the lichen-forming fungal genus Punctelia (Parmeliaceae), with a particular focus on the cosmopolitan species P. rudecta. Nuclear, mitochondrial ribosomal DNA and protein-coding DNA sequences were analyzed in phylogenetic and coalescence-based frameworks. Additionally, morphological, ecological and geographical features of the sampled specimens were evaluated. Five major strongly supported monophyletic clades were recognized in the genus Punctelia, and each clade could be characterized by distinct patterns in medullary chemistry. Punctelia rudecta as currently circumscribed was shown to be polyphyletic. A variety of empirical species delimitation methods provide evidence for a minimum of four geographically isolated species within the nominal taxon Punctelia rudecta, including a newly described saxicolous species, P. guanchica, and three corticolous species. In order to facilitate reliable sample identification for biodiversity, conservation, and air quality bio-monitoring research, these three species have been epitypified, in addition to the description of a new species.
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Affiliation(s)
- David Alors
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, Madrid, Spain
| | - H. Thorsten Lumbsch
- Science and Education, Field Museum, Chicago, Illinois, United States of America
| | - Pradeep K. Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, Madrid, Spain
| | - Steven D. Leavitt
- Science and Education, Field Museum, Chicago, Illinois, United States of America
| | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, Madrid, Spain
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