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Mamut R, Anwar G, Wang L, Fang J. The mitogenomes characterization of two Peltigera species (Peltigera elisabethae and Peltigera polydactylon) and comparative mitogenomic analyses of six Peltigera. J Appl Genet 2023; 64:819-829. [PMID: 37821790 DOI: 10.1007/s13353-023-00791-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/15/2023] [Accepted: 09/23/2023] [Indexed: 10/13/2023]
Abstract
In the present study, the mitochondrial genomes of Peltigera elisabethae and P. polydactylon were sequenced and assembled. The two mitogenomes were composed of circular DNA molecules, with sizes of 64,034 bp and 59,208 bp, respectively. Comparative analysis showed that the genome size, GC content, GC skew, and AT skew varied between the two mitochondrial genomes. In codon analysis, phenylalanine (Phe), isoleucine (Ile), and leucine (Leu) were most frequently used in six Peltigera genomes. Evolutionary analysis showed that all 14 protein-coding genes (PCGs) were subject to purifying selection in the six Peltigera species. Regarding gene rearrangement, the PCGs of Peltigera had the same gene sequence and gene content, and a few intron sequences and spacer sequences were rearranged in Peltigera. In the phylogenetic analysis, we used Bayesian and ML methods to construct a phylogenetic tree. Two phylogenetic trees with consistent topology with high support indicate that mitochondrial genes were reliable molecular markers for analyzing the phylogenetic relationships. The present study enriches the mitochondrial genome data of Peltigera and promotes further understanding of the genetics and evolution of the Peltigera genus.
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Affiliation(s)
- Reyim Mamut
- College of Life Sciences and Technology, Xinjiang University, No.777 Huarui Street, Urumchi, 830017, Xinjiang, China.
| | - Gulmira Anwar
- College of Life Sciences and Technology, Xinjiang University, No.777 Huarui Street, Urumchi, 830017, Xinjiang, China
| | - Lidan Wang
- College of Life Sciences and Technology, Xinjiang University, No.777 Huarui Street, Urumchi, 830017, Xinjiang, China
| | - Jinjin Fang
- College of Life Sciences and Technology, Xinjiang University, No.777 Huarui Street, Urumchi, 830017, Xinjiang, China
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Ye C, Liu D, Huang K, Li D, Ma X, Jin Y, Xiong H. Isolation of starch and protein degrading strain Bacillus subtilis FYZ1-3 from tobacco waste and genomic analysis of its tolerance to nicotine and inhibition of fungal growth. Front Microbiol 2023; 14:1260149. [PMID: 38033584 PMCID: PMC10687635 DOI: 10.3389/fmicb.2023.1260149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
Aerobic fermentation is an effective technique for the large-scale processing of tobacco waste. However, the specificity of the structure and composition of tobacco-derived organic matter and the toxic alkaloids in the material make it currently difficult to directly use microbial agents. In this study, a functional strain FYZ1-3 was isolated and screened from thermophilic phase samples of tobacco waste composting. This strain could withstand temperatures as high as 80°C and grow normally at 0.6% nicotine content. Furthermore, it had a strong decomposition capacity of tobacco-derived starch and protein, with amylase activity of 122.3 U/mL and protease activity and 52.3 U/mL, respectively. To further understand the mechanism of the metabolic transformation of the target, whole genome sequencing was used and the secondary metabolite gene cluster was predicted. The inhibitory effect of the strain on common tobacco fungi was verified using the plate confrontation and agar column methods. The results showed that the strain FYZ1-3 was Bacillus subtilis, with a genome size of 4.17 Mb and GC content of 43.68%; 4,338 coding genes were predicted. The genome was annotated and analyzed using multiple databases to determine its ability to efficiently degrade starch proteins at the molecular level. Moreover, 14 functional genes related to nicotine metabolism were identified, primarily located on the distinct genomic island of FYZ1-3, giving a speculation for its nicotine tolerance capability on the molecular mechanism. By mining the secondary metabolite gene cluster prediction, we found potential synthetic bacteriocin, antimicrobial peptide, and other gene clusters on its chromosome, which may have certain antibacterial properties. Further experiments confirmed that the FYZ1-3 strain was a potent growth inhibitor of Penicillium chrysogenum, Aspergillus sydowii, A. fumigatus, and Talaromyces funiculosus. The creation and industrial use of the functional strains obtained in this study provide a theoretical basis for its industrial use, where it would be of great significance to improve the utilization rate of tobacco waste.
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Affiliation(s)
- Changwen Ye
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
- China Tobacco Standardization Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Dandan Liu
- China Tobacco Standardization Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Kuo Huang
- China Tobacco Standardization Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Dong Li
- China Tobacco Standardization Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Xinxin Ma
- School of Environment, Tsinghua University, Beijing, China
| | - Yiying Jin
- School of Environment, Tsinghua University, Beijing, China
| | - Hanguo Xiong
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
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Magain N, Miadlikowska J, Goffinet B, Goward T, Pardo-De la Hoz C, Jüriado I, Simon A, Mercado-Díaz J, Barlow T, Moncada B, Lücking R, Spielmann A, Canez L, Wang L, Nelson P, Wheeler T, Lutzoni F, Sérusiaux E. High species richness in the lichen genus Peltigera ( Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science. PERSOONIA 2023; 51:1-88. [PMID: 38665978 PMCID: PMC11041898 DOI: 10.3767/persoonia.2023.51.01] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 10/10/2022] [Indexed: 04/28/2024]
Abstract
Applying molecular methods to fungi establishing lichenized associations with green algae or cyanobacteria has repeatedly revealed the existence of numerous phylogenetic taxa overlooked by classical taxonomic approaches. Here, we report taxonomical conclusions based on multiple species delimitation and validation analyses performed on an eight-locus dataset that includes world-wide representatives of the dolichorhizoid and scabrosoid clades in section Polydactylon of the genus Peltigera. Following the recommendations resulting from a consensus species delimitation approach and additional species validation analysis (BPP) performed in this study, we present a total of 25 species in the dolichorhizoid clade and nine in the scabrosoid clade, including respectively 18 and six species that are new to science and formally described. Additionally, one combination and three varieties (including two new to science) are proposed in the dolichorhizoid clade. The following 24 new species are described: P. appalachiensis, P. asiatica, P. borealis, P. borinquensis, P. chabanenkoae, P. clathrata, P. elixii, P. esslingeri, P. flabellae, P. gallowayi, P. hawaiiensis, P. holtanhartwigii, P. itatiaiae, P. hokkaidoensis, P. kukwae, P. massonii, P. mikado, P. nigriventris, P. orientalis, P. rangiferina, P. sipmanii, P. stanleyensis, P. vitikainenii and P. willdenowii; the following new varieties are introduced: P. kukwae var. phyllidiata and P. truculenta var. austroscabrosa; and the following new combination is introduced: P. hymenina var. dissecta. Each species from the dolichorhizoid and scabrosoid clades is morphologically and chemically described, illustrated, and characterised with ITS sequences. Identification keys are provided for the main biogeographic regions where species from the two clades occur. Morphological and chemical characters that are commonly used for species identification in the genus Peltigera cannot be applied to unambiguously recognise most molecularly circumscribed species, due to high variation of thalli formed by individuals within a fungal species, including the presence of distinct morphs in some cases, or low interspecific variation in others. The four commonly recognised morphospecies: P. dolichorhiza, P. neopolydactyla, P. pulverulenta and P. scabrosa in the dolichorhizoid and scabrosoid clades represent species complexes spread across multiple and often phylogenetically distantly related lineages. Geographic origin of specimens is often helpful for species recognition; however, ITS sequences are frequently required for a reliable identification. Citation: Magain N, Miadlikowska J, Goffinet B, et al. 2023. High species richness in the lichen genus Peltigera (Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science. Persoonia 51: 1-88. doi: 10.3767/persoonia.2023.51.01.
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Affiliation(s)
- N. Magain
- Evolution and Conservation Biology, InBioS Research Center, University of Liège, Sart Tilman B22, Quartier vallée 1, Chemin de la vallée 4, B-4000 Liège, Belgium
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - J. Miadlikowska
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - B. Goffinet
- Ecology and Evolutionary Biology, Unit 3043, University of Connecticut, 75 North Eagleville road, Storrs CT, 06269-3043 USA
| | - T. Goward
- Beaty Biodiversity Museum, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - C.J. Pardo-De la Hoz
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - I. Jüriado
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu 50409, Estonia; Institute of Agricultural & Environmental Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 5, Tartu 51006, Estonia
| | - A. Simon
- Evolution and Conservation Biology, InBioS Research Center, University of Liège, Sart Tilman B22, Quartier vallée 1, Chemin de la vallée 4, B-4000 Liège, Belgium
- Ecology and Evolutionary Biology, Unit 3043, University of Connecticut, 75 North Eagleville road, Storrs CT, 06269-3043 USA
| | - J.A. Mercado-Díaz
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois, 60605 USA
| | - T. Barlow
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - B. Moncada
- Licenciatura en Biología, Universidad Distrital Francisco José de Caldas, Cra. 4 No. 26B-54, Torre de Laboratorios, Herbario, Bogotá, Colombia; current address: Botanischer Garten, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
| | - R. Lücking
- Botanischer Garten, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
| | - A. Spielmann
- Laboratòrio de Botanica / Liquenologia, Instituto de Biociencias, Universidade Federal de Mato Grosso do Sul, Campo Grande – MS, Brazil
| | - L. Canez
- Laboratòrio de Botanica / Liquenologia, Instituto de Biociencias, Universidade Federal de Mato Grosso do Sul, Campo Grande – MS, Brazil
| | - L.S. Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, CAS, Kunming 650201, China
| | - P. Nelson
- Natural and Behavioral Sciences Division, University of Maine – Fort Kent, Fort Kent, ME, USA
| | - T. Wheeler
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - F. Lutzoni
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - E. Sérusiaux
- Evolution and Conservation Biology, InBioS Research Center, University of Liège, Sart Tilman B22, Quartier vallée 1, Chemin de la vallée 4, B-4000 Liège, Belgium
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Pardo‐De la Hoz CJ, Medeiros ID, Gibert JP, Chagnon P, Magain N, Miadlikowska J, Lutzoni F. Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks. Ecol Evol 2022; 12:e8649. [PMID: 35261742 PMCID: PMC8888259 DOI: 10.1002/ece3.8649] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/25/2021] [Accepted: 01/28/2022] [Indexed: 01/02/2023] Open
Abstract
Biotic specialization holds information about the assembly, evolution, and stability of biological communities. Partner availabilities can play an important role in enabling species interactions, where uneven partner availabilities can bias estimates of biotic specialization when using phylogenetic diversity indices. It is therefore important to account for partner availability when characterizing biotic specialization using phylogenies. We developed an index, phylogenetic structure of specialization (PSS), that avoids bias from uneven partner availabilities by uncoupling the null models for interaction frequency and phylogenetic distance. We incorporate the deviation between observed and random interaction frequencies as weights into the calculation of partner phylogenetic α‐diversity. To calculate the PSS index, we then compare observed partner phylogenetic α‐diversity to a null distribution generated by randomizing phylogenetic distances among the same number of partners. PSS quantifies the phylogenetic structure (i.e., clustered, overdispersed, or random) of the partners of a focal species. We show with simulations that the PSS index is not correlated with network properties, which allows comparisons across multiple systems. We also implemented PSS on empirical networks of host–parasite, avian seed‐dispersal, lichenized fungi–cyanobacteria, and hummingbird pollination interactions. Across these systems, a large proportion of taxa interact with phylogenetically random partners according to PSS, sometimes to a larger extent than detected with an existing method that does not account for partner availability. We also found that many taxa interact with phylogenetically clustered partners, while taxa with overdispersed partners were rare. We argue that species with phylogenetically overdispersed partners have often been misinterpreted as generalists when they should be considered specialists. Our results highlight the important role of randomness in shaping interaction networks, even in highly intimate symbioses, and provide a much‐needed quantitative framework to assess the role that evolutionary history and symbiotic specialization play in shaping patterns of biodiversity. PSS is available as an R package at https://github.com/cjpardodelahoz/pss.
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Affiliation(s)
| | | | - Jean P. Gibert
- Department of BiologyDuke UniversityDurhamNorth CarolinaUSA
| | - Pierre‐Luc Chagnon
- Département des Sciences BiologiquesUniversité de MontréalMontréalQuébecCanada
| | - Nicolas Magain
- Biologie de l’évolution et de la ConservationUniversité de LiègeLiègeBelgium
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Lücking R, Leavitt SD, Hawksworth DL. Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00477-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
AbstractLichens are symbiotic associations resulting from interactions among fungi (primary and secondary mycobionts), algae and/or cyanobacteria (primary and secondary photobionts), and specific elements of the bacterial microbiome associated with the lichen thallus. The question of what is a species, both concerning the lichen as a whole and its main fungal component, the primary mycobiont, has faced many challenges throughout history and has reached new dimensions with the advent of molecular phylogenetics and phylogenomics. In this paper, we briefly revise the definition of lichens and the scientific and vernacular naming conventions, concluding that the scientific, Latinized name usually associated with lichens invariably refers to the primary mycobiont, whereas the vernacular name encompasses the entire lichen. Although the same lichen mycobiont may produce different phenotypes when associating with different photobionts or growing in axenic culture, this discrete variation does not warrant the application of different scientific names, but must follow the principle "one fungus = one name". Instead, broadly agreed informal designations should be used for such discrete morphologies, such as chloromorph and cyanomorph for lichens formed by the same mycobiont but with either green algae or cyanobacteria. The taxonomic recognition of species in lichen-forming fungi is not different from other fungi and conceptual and nomenclatural approaches follow the same principles. We identify a number of current challenges and provide recommendations to address these. Species delimitation in lichen-forming fungi should not be tailored to particular species concepts but instead be derived from empirical evidence, applying one or several of the following principles in what we call the LPR approach: lineage (L) coherence vs. divergence (phylogenetic component), phenotype (P) coherence vs. divergence (morphological component), and/or reproductive (R) compatibility vs. isolation (biological component). Species hypotheses can be established based on either L or P, then using either P or L (plus R) to corroborate them. The reliability of species hypotheses depends not only on the nature and number of characters but also on the context: the closer the relationship and/or similarity between species, the higher the number of characters and/or specimens that should be analyzed to provide reliable delimitations. Alpha taxonomy should follow scientific evidence and an evolutionary framework but should also offer alternative practical solutions, as long as these are scientifically defendable. Taxa that are delimited phylogenetically but not readily identifiable in the field, or are genuinely cryptic, should not be rejected due to the inaccessibility of proper tools. Instead, they can be provisionally treated as undifferentiated complexes for purposes that do not require precise determinations. The application of infraspecific (gamma) taxonomy should be restricted to cases where there is a biological rationale, i.e., lineages of a species complex that show limited phylogenetic divergence but no evidence of reproductive isolation. Gamma taxonomy should not be used to denote discrete phenotypical variation or ecotypes not warranting the distinction at species level. We revise the species pair concept in lichen-forming fungi, which recognizes sexually and asexually reproducing morphs with the same underlying phenotype as different species. We conclude that in most cases this concept does not hold, but the actual situation is complex and not necessarily correlated with reproductive strategy. In cases where no molecular data are available or where single or multi-marker approaches do not provide resolution, we recommend maintaining species pairs until molecular or phylogenomic data are available. This recommendation is based on the example of the species pair Usnea aurantiacoatra vs. U. antarctica, which can only be resolved with phylogenomic approaches, such as microsatellites or RADseq. Overall, we consider that species delimitation in lichen-forming fungi has advanced dramatically over the past three decades, resulting in a solid framework, but that empirical evidence is still missing for many taxa. Therefore, while phylogenomic approaches focusing on particular examples will be increasingly employed to resolve difficult species complexes, broad screening using single barcoding markers will aid in placing as many taxa as possible into a molecular matrix. We provide a practical protocol how to assess and formally treat taxonomic novelties. While this paper focuses on lichen fungi, many of the aspects discussed herein apply generally to fungal taxonomy. The new combination Arthonia minor (Lücking) Lücking comb. et stat. nov. (Bas.: Arthonia cyanea f. minor Lücking) is proposed.
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Cornet L, Magain N, Baurain D, Lutzoni F. Exploring syntenic conservation across genomes for phylogenetic studies of organisms subjected to horizontal gene transfers: A case study with Cyanobacteria and cyanolichens. Mol Phylogenet Evol 2021; 162:107100. [PMID: 33592234 DOI: 10.1016/j.ympev.2021.107100] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/22/2021] [Accepted: 02/01/2021] [Indexed: 11/16/2022]
Abstract
Understanding the evolutionary history of symbiotic Cyanobacteria at a fine scale is essential to unveil patterns of associations with their hosts and factors driving their spatiotemporal interactions. As for bacteria in general, Horizontal Gene Transfers (HGT) are expected to be rampant throughout their evolution, which justified the use of single-locus phylogenies in macroevolutionary studies of these photoautotrophic bacteria. Genomic approaches have greatly increased the amount of molecular data available, but the selection of orthologous, congruent genes that are more likely to reflect bacterial macroevolutionary histories remains problematic. In this study, we developed a synteny-based approach and searched for Collinear Orthologous Regions (COR), under the assumption that genes that are present in the same order and orientation across a wide monophyletic clade are less likely to have undergone HGT. We searched sixteen reference Nostocales genomes and identified 99 genes, part of 28 COR comprising three to eight genes each. We then developed a bioinformatic pipeline, designed to minimize inter-genome contamination and processed twelve Nostoc-associated lichen metagenomes. This reduced our original dataset to 90 genes representing 25 COR, which were used to infer phylogenetic relationships within Nostocales and among lichenized Cyanobacteria. This dataset was narrowed down further to 71 genes representing 22 COR by selecting only genes part of one (largest) operon per COR. We found a relatively high level of congruence among trees derived from the 90-gene dataset, but congruence was only slightly higher among genes within a COR compared to genes across COR. However, topological congruence was significantly higher among the 71 genes part of one operon per COR. Nostocales phylogenies resulting from concatenation and species tree approaches based on the 90- and 71-gene datasets were highly congruent, but the most highly supported result was obtained when using synteny, collinearity, and operon information (i.e., 71-gene dataset) as gene selection criteria, which outperformed larger datasets with more genes.
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Affiliation(s)
- Luc Cornet
- InBioS - PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Nicolas Magain
- Department of Biology, Duke University, Durham, NC, USA; Evolution and Conservation Biology, InBioS, University of Liège, Liège, Belgium
| | - Denis Baurain
- InBioS - PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium.
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Towards Genomic Criteria for Delineating Fungal Species. J Fungi (Basel) 2020; 6:jof6040246. [PMID: 33114441 PMCID: PMC7711752 DOI: 10.3390/jof6040246] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/15/2020] [Accepted: 10/23/2020] [Indexed: 02/06/2023] Open
Abstract
The discussion of fungal species delineation has yet to reach a consensus, despite the advancements in technology, which helped modernise traditional approaches. In particular, the phylogenetic species concept was one of the tools that has been used with considerable success across the fungal kingdom. The fast rise of fungal genomics provides an unprecedented opportunity to expand measuring the relatedness of fungal strains to the level of whole genomes. However, the use of genomic information in taxonomy has only just begun, and few methodological guidelines have been suggested so far. Here, a simple approach of computationally measuring genomic distances and their use as a standard for species delineation is investigated. A fixed threshold genomic distance calculated by the quick and easy-to-use tools Mash and Dashing proved to be an unexpectedly widely applicable and robust criterion for determining whether two genomes belong to the same or to different species. The accuracy of species delineation in an uncurated dataset of GenBank fungal genomes was close to 90%—and exceeded 90% with minimal curation. As expected, the discriminative power of this approach was lower at higher taxonomic ranks, but still significantly larger than zero. Simple instructions for calculation of a genomic distance between two genomes and species similarity thresholds at different k-mer sizes are suggested. The calculation of genomic distance is identified as a powerful approach for delineating fungal species and is proposed—not as the only criterion—but as an additional tool in the versatile toolbox of fungal taxonomy.
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Spjut R, Simon A, Guissard M, Magain N, Sérusiaux E. The fruticose genera in the Ramalinaceae (Ascomycota, Lecanoromycetes): their diversity and evolutionary history. MycoKeys 2020; 73:1-68. [PMID: 32994702 PMCID: PMC7501315 DOI: 10.3897/mycokeys.73.47287] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 07/19/2020] [Indexed: 02/08/2023] Open
Abstract
We present phylogenetic analyses of the fruticose Ramalinaceae based on extensive collections from many parts of the world, with a special focus on the Vizcaíno deserts in north-western Mexico and the coastal desert in Namibia. We generate a four-locus DNA sequence dataset for accessions of Ramalina and two additional loci for Niebla and Vermilacinia. Four genera are strongly supported: the subcosmopolitan Ramalina, the new genus Namibialina endemic to SW Africa, and a duo formed by Niebla and Vermilacinia, endemic to the New World except the sorediate V. zebrina that disjunctly occurs in Namibia. The latter three genera are restricted to coastal desert and chaparral where vegetation depends on moisture from ocean fog. Ramalina is subcosmopolitan and much more diverse in its ecology. We show that Ramalina and its sister genus Namibialina diverged from each other at c. 48 Myrs, whereas Vermilacinia and Niebla split at c. 30 Myrs. The phylogeny of the fruticose genera remains unresolved to their ancestral crustose genera. Species delimitation within Namibialina and Ramalina is rather straightforward. The phylogeny and taxonomy of Vermilacinia are fully resolved, except for the two youngest clades of corticolous taxa, and support current taxonomy, including four new taxa described here. Secondary metabolite variation in Niebla generally coincides with major clades which are comprised of species complexes with still unresolved phylogenetic relationships. A micro-endemism pattern of allopatric species is strongly suspected for both genera, except for the corticolous taxa within Vermilacinia. Both Niebla and saxicolous Vermilacinia have chemotypes unique to species clades that are largely endemic to the Vizcaíno deserts. The following new taxa are described: Namibialina gen. nov. with N. melanothrix (comb. nov.) as type species, a single new species of Ramalina (R. krogiae) and four new species of Vermilacinia (V. breviloba, V. lacunosa, V. pustulata and V. reticulata). The new combination V. granulans is introduced. Two epithets are re-introduced for European Ramalina species: R. crispans (= R. peruviana auct. eur.) and R. rosacea (= R. bourgeana auct. p.p). A lectotype is designated for Vermilacinia procera. A key to saxicolous species of Vermilacinia is presented.
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Affiliation(s)
- Richard Spjut
- World Botanical Associates, PO Box 81145, Bakersfield, California 93380, USA World Botanical Associates Bakersfield, CA United States of America
| | - Antoine Simon
- Evolution and Conservation Biology Unit, Sart Tilman B22, Quartier Vallée 1, chemin de la vallée 4, B-4000 Liège, Belgium Evolution and Conservation Biology Unit Liège Belgium
| | - Martin Guissard
- Evolution and Conservation Biology Unit, Sart Tilman B22, Quartier Vallée 1, chemin de la vallée 4, B-4000 Liège, Belgium Evolution and Conservation Biology Unit Liège Belgium
| | - Nicolas Magain
- Evolution and Conservation Biology Unit, Sart Tilman B22, Quartier Vallée 1, chemin de la vallée 4, B-4000 Liège, Belgium Evolution and Conservation Biology Unit Liège Belgium
| | - Emmanuël Sérusiaux
- Evolution and Conservation Biology Unit, Sart Tilman B22, Quartier Vallée 1, chemin de la vallée 4, B-4000 Liège, Belgium Evolution and Conservation Biology Unit Liège Belgium
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Lücking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, Kirk PM, Malosso E, May TW, Meyer W, Öpik M, Robert V, Stadler M, Thines M, Vu D, Yurkov AM, Zhang N, Schoch CL. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 2020; 11:14. [PMID: 32714773 PMCID: PMC7353689 DOI: 10.1186/s43008-020-00033-z] [Citation(s) in RCA: 178] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
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Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
| | - M. Catherine Aime
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
| | - Andrew N. Miller
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820-6970 USA
| | - Hiran A. Ariyawansa
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipe City, Taiwan
| | - Takayuki Aoki
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Agriculture and Food Research Organization, Genetic Resources Center, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Gianluigi Cardinali
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
| | - Pedro W. Crous
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Irina S. Druzhinina
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - David M. Geiser
- Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802 USA
| | - David L. Hawksworth
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS UK
- Geography and Environment, University of Southampton, Southampton, SO17 1BJ UK
- Jilin Agricultural University, Changchun, 130118 Jilin Province China
| | - Kevin D. Hyde
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- World Agroforestry Centre, East and Central Asia, Kunming, 650201 Yunnan China
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Rai, 50150 Thailand
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Rajesh Jeewon
- Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius
| | - Peter R. Johnston
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Manaaki Whenua – Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | | | - Elaine Malosso
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Universidade Federal de Pernambuco, Centro de Biociências, Departamento de Micologia, Laboratório de Hifomicetos de Folhedo, Avenida da Engenharia, s/n Cidade Universitária, Recife, PE 50.740-600 Brazil
| | - Tom W. May
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004 Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Maarja Öpik
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- University of Tartu, 40 Lai Street, 51 005 Tartu, Estonia
| | - Vincent Robert
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marc Stadler
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Marco Thines
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60439 Frankfurt (Main); Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Andrey M. Yurkov
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ning Zhang
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901 USA
| | - Conrad L. Schoch
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
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Optimal markers for the identification of Colletotrichum species. Mol Phylogenet Evol 2019; 143:106694. [PMID: 31786239 DOI: 10.1016/j.ympev.2019.106694] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/15/2019] [Accepted: 11/25/2019] [Indexed: 01/19/2023]
Abstract
Colletotrichum is among the most important genera of fungal plant pathogens. Molecular phylogenetic studies over the last decade have resulted in a much better understanding of the evolutionary relationships and species boundaries within the genus. There are now approximately 200 species accepted, most of which are distributed among 13 species complexes. Given their prominence on agricultural crops around the world, rapid identification of a large collection of Colletotrichum isolates is routinely needed by plant pathologists, regulatory officials, and fungal biologists. However, there is no agreement on the best molecular markers to discriminate species in each species complex. Here we calculate the barcode gap distance and intra/inter-specific distance overlap to evaluate each of the most commonly applied molecular markers for their utility as a barcode for species identification. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone-3 (HIS3), DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locus MAT1-2-1 (APN2/MAT-IGS), and intergenic spacer between GAPDH and a hypothetical protein (GAP2-IGS) have the properties of good barcodes, whereas sequences of actin (ACT), chitin synthase (CHS-1) and nuclear rDNA internal transcribed spacers (nrITS) are not able to distinguish most species. Finally, we assessed the utility of these markers for phylogenetic studies using phylogenetic informativeness profiling, the genealogical sorting index (GSI), and Bayesian concordance analyses (BCA). Although GAPDH, HIS3 and β-tubulin (TUB2) were frequently among the best markers, there was not a single set of markers that were best for all species complexes. Eliminating markers with low phylogenetic signal tends to decrease uncertainty in the topology, regardless of species complex, and leads to a larger proportion of markers that support each lineage in the Bayesian concordance analyses. Finally, we reconstruct the phylogeny of each species complex using a minimal set of phylogenetic markers with the strongest phylogenetic signal and find the majority of species are strongly supported as monophyletic.
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Jüriado I, Kaasalainen U, Jylhä M, Rikkinen J. Relationships between mycobiont identity, photobiont specificity and ecological preferences in the lichen genus Peltigera (Ascomycota) in Estonia (northeastern Europe). FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2018.11.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Species in section Peltidea (aphthosa group) of the genus Peltigera remain cryptic after molecular phylogenetic revision. ACTA ACUST UNITED AC 2018. [DOI: 10.2478/pfs-2018-0007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AbstractClosely related lichen-forming fungal species circumscribed using phenotypic traits (morphospecies) do not always align well with phylogenetic inferences based on molecular data. Using multilocus data obtained from a worldwide sampling, we inferred phylogenetic relationships among five currently accepted morphospecies of Peltigera section Peltidea (P. aphthosa group). Monophyletic circumscription of all currently recognized morphospecies (P. britannica, P. chionophila, P. frippii and P. malacea) except P. aphthosa, which contained P. britannica, was confirmed with high bootstrap support. Following their re-delimitation using bGMYC and Structurama, BPP validated 14 putative species including nine previously unrecognized potential species (five within P. malacea, five within P. aphthosa, and two within P. britannica). Because none of the undescribed potential species are corroborated morphologically, chemically, geographically or ecologically, we concluded that these monophyletic entities represent intraspecific phylogenetic structure, and, therefore, should not be recognized as new species. Cyanobionts associated with Peltidea mycobionts (51 individuals) represented 22 unique rbcLX haplotypes from five phylogroups in Clade II subclades 2 and 3. With rare exceptions, Nostoc taxa involved in trimembered and bimembered associations are phylogenetically closely related (subclade 2) or identical, suggesting a mostly shared cyanobiont pool with infrequent switches. Based on a broad geographical sampling, we confirm a high specificity of Nostoc subclade 2 with their mycobionts, including a mutualistically exclusive association between phylogroup III and specific lineages of P. malacea.
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14
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Pardo-De la Hoz CJ, Magain N, Lutzoni F, Goward T, Restrepo S, Miadlikowska J. Contrasting Symbiotic Patterns in Two Closely Related Lineages of Trimembered Lichens of the Genus Peltigera. Front Microbiol 2018; 9:2770. [PMID: 30505297 PMCID: PMC6250826 DOI: 10.3389/fmicb.2018.02770] [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: 05/18/2018] [Accepted: 10/29/2018] [Indexed: 11/13/2022] Open
Abstract
Species circumscription is key to the characterization of patterns of specificity in symbiotic systems at a macroevolutionary scale. Here, a worldwide phylogenetic framework was used to assess the biodiversity and symbiotic patterns of association among partners in trimembered lichens from the genus Peltigera, section Chloropeltigera. We sequenced six loci of the main fungal partner and performed species discovery and validation analyses to establish putative species boundaries. Single locus phylogenies were used to establish the identity of both photobionts, Nostoc (cyanobacterium) and Coccomyxa (green alga). Distribution and specificity patterns were compared to the closely related clade, section Peltidea, which includes mainly Peltigera species with trimembered thalli. For section Chloropeltigera, eight fungal species (including five newly delimited putative species) were found in association with nine Nostoc phylogroups and two Coccomyxa species. In contrast, eight fungal species (including three newly delimited putative species) in section Peltidea were found in association with only four Nostoc phylogroups and the same two Coccomyxa species as for section Chloropeltigera. This difference in cyanobiont biodiversity between these two sections can potentially be explained by a significantly higher frequency of sexual reproductive structures in species from section Chloropeltigera compared to section Peltidea. Therefore, horizontal transmission of the cyanobiont might be more prevalent in Chloropeltigera species, while vertical transmission might be more common in Peltidea species. All Peltigera species in section Chloropeltigera are generalists in their association with Nostoc compared to more specialized Peltigera species in section Peltidea. Constrained distributions of Peltigera species that associate strictly with one species of green algae (Coccomyxa subellipsoidea) indicate that the availability of the green alga and the specificity of the interaction might be important factors limiting geographic ranges of trimembered Peltigera, in addition to constraints imposed by their interaction with Nostoc partners and by climatic factors.
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Affiliation(s)
- Carlos José Pardo-De la Hoz
- Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
- Department of Biology, Duke University, Durham, NC, United States
| | - Nicolas Magain
- Department of Biology, Duke University, Durham, NC, United States
| | - François Lutzoni
- Department of Biology, Duke University, Durham, NC, United States
| | - Trevor Goward
- UBC Herbarium, Beaty Biodiversity Museum, University of British Columbia, Vancouver, BC, Canada
| | - Silvia Restrepo
- Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
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15
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Lu J, Magain N, Miadlikowska J, Coyle JR, Truong C, Lutzoni F. Bioclimatic factors at an intrabiome scale are more limiting than cyanobiont availability for the lichen-forming genus Peltigera. AMERICAN JOURNAL OF BOTANY 2018; 105:1198-1211. [PMID: 30001470 DOI: 10.1002/ajb2.1119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Factors shaping spatiotemporal patterns of associations in mutualistic systems are poorly understood. We used the lichen-forming fungi Peltigera and their cyanobacterial partners Nostoc to investigate the spatial structure of this symbiosis at an intrabiome scale and to identify potential factors shaping these associations. METHODS Ninety-three thalli were sampled in Québec, Canada, along a south-north and an east-west transect of ~1300 km each. We identified the two main partners (Peltigera species and Nostoc phylogroups) using molecular markers and modeled the effects of environmental variables and partner occurrence on Peltigera-Nostoc distributions. KEY RESULTS Peltigera species showed a high degree of specialization toward cyanobionts, whereas two Nostoc phylogroups dominated both transects by associating with several Peltigera species. Peltigera species had narrower ranges than these two main cyanobionts. Distributions of three Peltigera species were highly associated with precipitation and temperature variables, which was not detected for Nostoc phylogroups at this spatial scale. CONCLUSIONS For these cyanolichens, factors driving patterns of symbiotic associations are scale dependent. Contrary to global-scale findings, generalist Peltigera species were not more widespread within the boreal biome than specialists. Nostoc availability was not the only driver of Peltigera species' geographic ranges; environmental factors also contributed to their intrabiome distributions. Climatic conditions (especially precipitation) limited the range of some Peltigera species more than the range of their cyanobacterial partners at an intrabiome (boreal) scale.
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Affiliation(s)
- Jade Lu
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Nicolas Magain
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | | | - Jessica R Coyle
- Department of Biology, Stanford University, Stanford, California, 94305, USA
| | - Camille Truong
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
- Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), C.P. 04510, Mexico City, Mexico
| | - François Lutzoni
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
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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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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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