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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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Szczepańska K, Urbaniak J, Śliwa L. Taxonomic recognition of some species-level lineages circumscribed in nominal Rhizoplaca subdiscrepans s. lat. (Lecanoraceae, Ascomycota). PeerJ 2020; 8:e9555. [PMID: 32832264 PMCID: PMC7409781 DOI: 10.7717/peerj.9555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/25/2020] [Indexed: 11/29/2022] Open
Abstract
Background Rhizoplaca subdiscrepans (Nyl.) R. Sant., a saxicolous, placodioid lichen, is considered to have a worldwide distribution in warm-temperate to boreal-arctic areas in Asia, Europe and North America. However, recent studies have revealed that this species includes five unrecognized species-level lineages—‘subd A, B, C, D and E’. During research focused on the diversity of saxicolous lichens in mountainous areas of southern Poland, some interesting representatives of the genus Rhizoplaca were found. The main aim of our study was to determine the taxonomic status of the collected specimens by means of molecular tools and a comparative analysis of similar herbarium materials. Methods Detailed morphological, anatomical and chemical examinations of reference material from Asia, Europe and North and South America focused primarily on a selected group of lecanoroid taxa with a placodioid thallus. In addition, 21 new generated sequences representing Lecanora pseudomellea, Protoparmeliopsis muralis, Rhizoplaca opiniconensis, R. subdiscrepans s. lat. and R. phaedrophthalma were selected for molecular study using the internal transcribed spacer region (ITS rDNA), together with 95 available GenBank sequences mainly from the genus Rhizoplaca. Results Polish specimens that clustered with members of a potential species-level lineage ‘subd E’ of Rhizoplaca subdiscrepans complex were recovered. Comprehensive analyses of the lichen group led us to the conclusion that lineage ‘subd E’ represents R. subdiscrepans s. str. and that the taxon appears to have a limited geographical distribution and specific habitat preferences. Furthermore, some of the recently defined species candidates within R. subdiscrepans s. lat.—‘subd D’ and ‘subd A’—should be assigned to two previously known species of Rhizoplaca, namely R. opiniconensis (Brodo) Leavitt, Zhao Xin & Lumbsch and R. phaedrophthalma (Poelt) Leavitt, Zhao Xin & Lumbsch, respectively. These two species are characterized by phenotypic features observed as well in analyzed specimens representing lineages ’subd D’ and ’subd A’. Moreover, the representatives of these lineages demonstrate some differences in occupied habitat and geographical range that also correspond with the indicated species. Additionally, it was found that Lecanora pseudomellea B.D. Ryan is a strongly supported monophyletic lineage within Rhizoplaca, and therefore an appropriate new combination for the species is proposed.
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Affiliation(s)
- Katarzyna Szczepańska
- Department of Botany and Plant Ecology, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Jacek Urbaniak
- Department of Botany and Plant Ecology, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Lucyna Śliwa
- Department of Lichenology, W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
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Autumn K, Barcenas-Peña A, Kish-Levine S, Huang JP, Lumbsch HT. Repeated Colonization Between Arid and Seasonal Wet Habitats, Frequent Transition Among Substrate Preferences, and Chemical Diversity in Western Australian Xanthoparmelia Lichens. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Dai C, Dong F, Yang X. Morphotypes or distinct species? A multilocus assessment of two East Asian scimitar babblers (Aves, Timaliidae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chuanyin Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University) Ministry of Education Guilin China
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology Guangxi Normal University Guilin China
- School of Biological Sciences Guizhou Normal College Guiyang China
| | - Feng Dong
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Xiaojun Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
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Frisch A, Moen VS, Grube M, Bendiksby M. Integrative taxonomy confirms three species of Coniocarpon (Arthoniaceae) in Norway. MycoKeys 2020; 62:27-51. [PMID: 32025188 PMCID: PMC6992689 DOI: 10.3897/mycokeys.62.48480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/23/2019] [Indexed: 11/12/2022] Open
Abstract
We have studied the highly oceanic genus Coniocarpon in Norway. Our aim has been to delimit species of Coniocarpon in Norway based on an integrative taxonomic approach. The material studied comprises 120 specimens of Coniocarpon, obtained through recent collecting efforts (2017 and 2018) or received from major fungaria in Denmark, Finland, Norway and Sweden, as well as from private collectors. We have assessed (1) species delimitations and relationships based on Bayesian and maximum likelihood phylogenetic analyses of three genetic markers (mtSSU, nucITS and RPB2), (2) morphology and anatomy using standard light microscopy, and (3) secondary lichen chemistry using high-performance thin-layer chromatography. The results show three genetically distinct lineages of Coniocarpon, representing C.cinnabarinum, C.fallax and C.cuspidans comb. nov. The latter was originally described as Arthoniacinnabarinaf.cuspidans and is herein raised to species level. All three species are supported by morphological, anatomical and chemical data.
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Affiliation(s)
- Andreas Frisch
- NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Victoria Stornes Moen
- NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Martin Grube
- Institute of Plant Sciences, Karl-Franzens-University Graz, Holteigasse 6, 8010 Graz, Austria
| | - Mika Bendiksby
- NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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Ellingham O, David J, Culham A. Enhancing identification accuracy for powdery mildews using previously underexploited DNA loci. Mycologia 2019; 111:798-812. [DOI: 10.1080/00275514.2019.1643644] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Oliver Ellingham
- School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6AS, UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - John David
- Royal Horticultural Society Garden Wisley, Woking, Surrey, GU23 6QB, UK
| | - Alastair Culham
- School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6AS, UK
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Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi ( Bryoria sect. Implexae, Parmeliaceae). PERSOONIA 2019; 42:75-100. [PMID: 31551615 PMCID: PMC6712543 DOI: 10.3767/persoonia.2019.42.04] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 06/18/2018] [Indexed: 01/07/2023]
Abstract
In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach - including morphological, chemical, molecular, and distributional characters - to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, GAPDH, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are Bryoria fuscescens, B. glabra, B. kockiana, and B. pseudofuscescens. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the B. fuscescens complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of Bryoria are outlined.
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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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Seminara A, Fritz J, Brenner MP, Pringle A. A universal growth limit for circular lichens. J R Soc Interface 2018; 15:20180063. [PMID: 29875282 PMCID: PMC6030627 DOI: 10.1098/rsif.2018.0063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/15/2018] [Indexed: 11/15/2022] Open
Abstract
Lichens fix carbon dioxide from the air to build biomass. Crustose and foliose lichens grow as nearly flat, circular disks. Smaller individuals grow slowly, but with small, steady increases in radial growth rate over time. Larger individuals grow more quickly and with a roughly constant radial velocity maintained over the lifetime of the lichen. We translate the coffee drop effect to model lichen growth and demonstrate that growth patterns follow directly from the diffusion of carbon dioxide in the air around a lichen. When a lichen is small, carbon dioxide is fixed across its surface, and the entire thallus contributes to radial growth, but when a lichen is larger carbon dioxide is disproportionately fixed at the edges of an individual, which are the primary drivers of growth. Tests of the model against data suggest it provides an accurate, robust, and universal framework for understanding the growth dynamics of both large and small lichens in nature.
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Affiliation(s)
- Agnese Seminara
- CNRS, Université Côte d'Azur, Institut de Physique de Nice, UMR7010, Parc Valrose 06108, Nice, France
| | - Joerg Fritz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Michael P Brenner
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Anne Pringle
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
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Matteucci E, Occhipinti A, Piervittori R, Maffei ME, Favero-Longo SE. Morphological, Secondary Metabolite and ITS (rDNA) Variability within Usnic Acid-Containing Lichen Thalli ofXanthoparmeliaExplored at the Local Scale of Rock Outcrop in W-Alps. Chem Biodivers 2017; 14. [DOI: 10.1002/cbdv.201600483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/08/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Enrica Matteucci
- Unità di Lichenologia; Dipartimento di Scienze della Vita e Biologia dei Sistemi; Università degli Studi di Torino; Viale Mattioli 25 10125 Torino Italia
| | - Andrea Occhipinti
- Unità di Fisiologia Vegetale; Dipartimento di Scienze della Vita e Biologia dei Sistemi; Università degli Studi di Torino; Via Quarello 15/A 10135 Torino Italia
| | - Rosanna Piervittori
- Unità di Lichenologia; Dipartimento di Scienze della Vita e Biologia dei Sistemi; Università degli Studi di Torino; Viale Mattioli 25 10125 Torino Italia
| | - Massimo E. Maffei
- Unità di Fisiologia Vegetale; Dipartimento di Scienze della Vita e Biologia dei Sistemi; Università degli Studi di Torino; Via Quarello 15/A 10135 Torino Italia
| | - Sergio E. Favero-Longo
- Unità di Lichenologia; Dipartimento di Scienze della Vita e Biologia dei Sistemi; Università degli Studi di Torino; Viale Mattioli 25 10125 Torino Italia
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Otálora MAG, Martínez I, Aragón G, Wedin M. Species delimitation and phylogeography of the Pectenia species-complex: A misunderstood case of species-pairs in lichenized fungi, where reproduction mode does not delimit lineages. Fungal Biol 2017; 121:222-233. [PMID: 28215350 DOI: 10.1016/j.funbio.2016.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 11/02/2016] [Accepted: 12/01/2016] [Indexed: 10/20/2022]
Abstract
The main goal of this work was to study species boundaries in the genus Pectenia and elucidate the biogeographic history of the four currently accepted species. To accomplish this, we included 92 specimens across the range of Pectenia in Europe and northern Africa. We used three nuclear loci and assessed species circumscription using two Bayesian coalescent-based methods and the Bayes Factor approach. We reviewed the value of reproductive mode and other morphological features as predictors of monophyletic groups. Our results suggest that the production of asexual propagules and sexual structures are not characterizing monophyletic groups. The genus includes two morphologically well-characterized main lineages, where one lineage is composed by two sub-lineages that are with a case of cryptic speciation explained by a biogeographic pattern. We suggest treating the two lineages as two species, which are characterized by lobe structure: Pectenia plumbea and P. atlantica. Both of these species include samples with asexual propagules and apothecia, and thus do not correspond to any of the earlier morphologically defined species. The results of the biogeographic analysis indicate that the Mediterranean basin is the most likely ancestral distribution area of P. plumbea, whereas P. atlantica probably originated in Macaronesia.
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Affiliation(s)
- Mónica A G Otálora
- Department of Botany, The Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden; Department of Biology, Geology, Physic and Inorganic Chemical, Rey Juan Carlos University, Móstoles, 28932, Spain.
| | - Isabel Martínez
- Department of Biology, Geology, Physic and Inorganic Chemical, Rey Juan Carlos University, Móstoles, 28932, Spain
| | - Gregorio Aragón
- Department of Biology, Geology, Physic and Inorganic Chemical, Rey Juan Carlos University, Móstoles, 28932, Spain
| | - Mats Wedin
- Department of Botany, The Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
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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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Overview of Phylogenetic Approaches to Mycorrhizal Biogeography, Diversity and Evolution. BIOGEOGRAPHY OF MYCORRHIZAL SYMBIOSIS 2017. [DOI: 10.1007/978-3-319-56363-3_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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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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Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota). PLoS One 2016; 11:e0163664. [PMID: 27828951 PMCID: PMC5102465 DOI: 10.1371/journal.pone.0163664] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/12/2016] [Indexed: 11/29/2022] Open
Abstract
Delimiting species boundaries among closely related lineages often requires a range of independent data sets and analytical approaches. Similar to other organismal groups, robust species circumscriptions in fungi are increasingly investigated within an empirical framework. Here we attempt to delimit species boundaries in a closely related clade of lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group (Parmeliaceae). In the current classification, the Hypogymnia hypotrypa group includes two species: H. hypotrypa and H. flavida, which are separated based on distinctive reproductive modes, the former producing soredia but absent in the latter. We reexamined the relationship between these two species using phenotypic characters and molecular sequence data (ITS, GPD, and MCM7 sequences) to address species boundaries in this group. In addition to morphological investigations, we used Bayesian clustering to identify potential genetic groups in the H. hypotrypa/H. flavida clade. We also used a variety of empirical, sequence-based species delimitation approaches, including: the “Automatic Barcode Gap Discovery” (ABGD), the Poisson tree process model (PTP), the General Mixed Yule Coalescent (GMYC), and the multispecies coalescent approach BPP. Different species delimitation scenarios were compared using Bayes factors delimitation analysis, in addition to comparisons of pairwise genetic distances, pairwise fixation indices (FST). The majority of the species delimitation analyses implemented in this study failed to support H. hypotrypa and H. flavida as distinct lineages, as did the Bayesian clustering analysis. However, strong support for the evolutionary independence of H. hypotrypa and H. flavida was inferred using BPP and further supported by Bayes factor delimitation. In spite of rigorous morphological comparisons and a wide range of sequence-based approaches to delimit species, species boundaries in the H. hypotrypa group remain uncertain. This study reveals the potential limitations of relying on distinct reproductive strategies as diagnostic taxonomic characters for Hypogymnia and also the challenges of using popular sequence-based species delimitation methods in groups with recent diversification histories.
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Resl P, Mayrhofer H, Clayden SR, Spribille T, Thor G, Tønsberg T, Sheard JW. Morphological, chemical and species delimitation analyses provide new taxonomic insights into two groups of Rinodina. LICHENOLOGIST (LONDON, ENGLAND) 2016; 48:469-488. [PMID: 29398724 PMCID: PMC5793993 DOI: 10.1017/s0024282916000359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The genus Rinodina (Physciaceae), with approximately 300 species, has been subject to few phylogenetic studies. Consequently taxonomic hypotheses in Rinodina are largely reliant on phenotypic data, while hypotheses incorporating DNA dependent methods remain to be tested. Here we investigate Rinodina degeliana/R. subparieta and the Rinodina mniaraea group, which previously have not been subjected to comprehensive molecular and phenotypic studies. We conducted detailed morphological, anatomical, chemical, molecular phylogenetic and species delimitation studies including 24 newly sequenced specimens. We propose that Rinodina degeliana and R. subparieta are conspecific and that chemical morphs within the R. mniaraea group should be recognized as distinct species. We also propose the placement of the recently described genus Oxnerella in Physciaceae.
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Affiliation(s)
- Philipp Resl
- Institute of Plant Sciences, NAWI Graz, University of Graz, Holteigasse 6, 8010 Graz, Austria
| | - Helmut Mayrhofer
- Institute of Plant Sciences, NAWI Graz, University of Graz, Holteigasse 6, 8010 Graz, Austria
| | - Stephen R Clayden
- New Brunswick Museum, 277 Douglas Avenue, Saint John, New Brunswick E2K 1E5, Canada
| | - Toby Spribille
- Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010 Graz, Austria
| | - Göran Thor
- Department of Ecology, Swedish University of Agricultural Sciences, P.O. Box 7044, 750 07 Uppsala, Sweden
| | - Tor Tønsberg
- Department of Natural History, University Museum, University of Bergen, Allégaten 41, P.O. Box 7800, 5020 Bergen, Norway
| | - John W Sheard
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
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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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Zhao X, Zhang LL, Zhao ZT, Wang WC, Leavitt SD, Lumbsch HT. A Molecular Phylogeny of the Lichen Genus Lecidella Focusing on Species from Mainland China. PLoS One 2015; 10:e0139405. [PMID: 26414323 PMCID: PMC4586381 DOI: 10.1371/journal.pone.0139405] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/11/2015] [Indexed: 11/19/2022] Open
Abstract
The phylogeny of Lecidella species is studied, based on a 7-locus data set using ML and Bayesian analyses. Phylogenetic relationships among 43 individuals representing 11 Lecidella species, mainly from mainland China, were included in the analyses and phenotypical characters studied and mapped onto the phylogeny. The Lecidella species fall into three major clades, which are proposed here as three informal groups-Lecidella stigmatea group, L. elaeochroma group and L. enteroleucella group, each of them strongly supported. Our phylogenetic analyses support traditional species delimitation based on morphological and chemical traits in most but not all cases. Individuals considered as belonging to the same species based on phenotypic characters were found to be paraphyletic, indicating that cryptic species might be hidden under these names (e.g. L. carpathica and L. effugiens). Potentially undescribed species were found within the phenotypically circumscribed species L. elaeochroma and L. stigmatea. Additional sampling across a broader taxonomic and geographic scale will be crucial to fully resolving the taxonomy in this cosmopolitan genus.
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Affiliation(s)
- Xin Zhao
- College of Life Sciences, Shandong Normal University, Jinan, 250014, P. R. China
| | - Lu Lu Zhang
- College of Life Sciences, Shandong Normal University, Jinan, 250014, P. R. China
| | - Zun Tian Zhao
- College of Life Sciences, Shandong Normal University, Jinan, 250014, P. R. China
| | - Wei Cheng Wang
- College of Life Sciences, Shandong Normal University, Jinan, 250014, P. R. China
| | - Steven D. Leavitt
- Science & Education, The Field Museum, Chicago, Illinois, United States of America
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Helge Thorsten Lumbsch
- Science & Education, The Field Museum, Chicago, Illinois, United States of America
- * E-mail:
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Leavitt SD, Divakar PK, Ohmura Y, Wang LS, Esslinger TL, Lumbsch HT. Who’s getting around? Assessing species diversity and phylogeography in the widely distributed lichen-forming fungal genus Montanelia (Parmeliaceae, Ascomycota). Mol Phylogenet Evol 2015; 90:85-96. [DOI: 10.1016/j.ympev.2015.04.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 02/13/2015] [Accepted: 04/30/2015] [Indexed: 10/23/2022]
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Leavitt SD, Kraichak E, Nelsen MP, Altermann S, Divakar PK, Alors D, Esslinger TL, Crespo A, Lumbsch T. Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen‐forming family Parmeliaceae (Ascomycota). Mol Ecol 2015; 24:3779-97. [DOI: 10.1111/mec.13271] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 06/04/2015] [Accepted: 06/10/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Steven D. Leavitt
- Committee on Evolutionary Biology University of Chicago Chicago IL USA
- Science & Education The Field Museum Chicago IL USA
| | - Ekaphan Kraichak
- Science & Education The Field Museum Chicago IL USA
- Department of Botany Faculty of Science Kasetsart University Bangkok Thailand
| | - Matthew P. Nelsen
- Geological and Environmental Sciences Stanford University Stanford CA USA
| | | | - Pradeep K. Divakar
- Departamento de Biología Vegetal II Facultad de Farmacia Universidad Complutense de Madrid Madrid Spain
| | - David Alors
- Departamento de Biología Vegetal II Facultad de Farmacia Universidad Complutense de Madrid Madrid Spain
| | | | - Ana Crespo
- Departamento de Biología Vegetal II Facultad de Farmacia Universidad Complutense de Madrid Madrid Spain
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Warner PA, van Oppen MJH, Willis BL. Unexpected cryptic species diversity in the widespread coralSeriatopora hystrixmasks spatial-genetic patterns of connectivity. Mol Ecol 2015; 24:2993-3008. [DOI: 10.1111/mec.13225] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/25/2015] [Accepted: 04/29/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Patricia A. Warner
- AIMS@JCU; Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
- College of Marine and Environmental Sciences; James Cook University; Townsville Qld 4811 Australia
| | - Madeleine J. H. van Oppen
- AIMS@JCU; Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
- Australian Institute of Marine Science; PMB3, Townsville MC; Townsville Qld 4810 Australia
| | - Bette L. Willis
- AIMS@JCU; Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
- College of Marine and Environmental Sciences; James Cook University; Townsville Qld 4811 Australia
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Singh G, Dal Grande F, Divakar PK, Otte J, Leavitt SD, Szczepanska K, Crespo A, Rico VJ, Aptroot A, Cáceres MEDS, Lumbsch HT, Schmitt I. Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota). PLoS One 2015; 10:e0124625. [PMID: 25932996 PMCID: PMC4416777 DOI: 10.1371/journal.pone.0124625] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/17/2015] [Indexed: 11/18/2022] Open
Abstract
Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal -arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods – BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence.
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Affiliation(s)
- Garima Singh
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Grüneburgplatz 1, 60323, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- * E-mail: (GS); (IS)
| | - Francesco Dal Grande
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Pradeep K. Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Plaza de Ramon y Cajal s/n, E-28040, Madrid, Spain
| | - Jürgen Otte
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Steven D. Leavitt
- Science & Education, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL, 60605, United States of America
| | - Katarzyna Szczepanska
- Department of Botany and Plant Ecology, Wroclaw University of Environmental and Life Sciences, pl. Grunwaldzki 24a, 50-363, Wroclaw, Poland
| | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Plaza de Ramon y Cajal s/n, E-28040, Madrid, Spain
| | - Víctor J. Rico
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Plaza de Ramon y Cajal s/n, E-28040, Madrid, Spain
| | - André Aptroot
- Advice Bureau for Bryology and Lichenology Herbarium, Soest, The Netherlands
| | | | - H. Thorsten Lumbsch
- Science & Education, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL, 60605, United States of America
| | - Imke Schmitt
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Grüneburgplatz 1, 60323, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- * E-mail: (GS); (IS)
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26
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Molecules support morphology: species status of South Indian populations of the widely distributed Hanuman langur. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0638-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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27
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Sadowska-Deś AD, Dal Grande F, Lumbsch HT, Beck A, Otte J, Hur JS, Kim JA, Schmitt I. Integrating coalescent and phylogenetic approaches to delimit species in the lichen photobiont Trebouxia. Mol Phylogenet Evol 2014; 76:202-10. [PMID: 24685499 DOI: 10.1016/j.ympev.2014.03.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 03/04/2014] [Accepted: 03/17/2014] [Indexed: 02/05/2023]
Abstract
The accurate assessment of species boundaries in symbiotic systems is a prerequisite for the study of speciation, co-evolution and selectivity. Many studies have shown the high genetic diversity of green algae from the genus Trebouxia, the most common photobiont of lichen-forming fungi. However, the phylogenetic relationships, and the amount of cryptic diversity of these algae are still poorly understood, and an adequate species concept for trebouxiophycean algae is still missing. In this study we used a multifaceted approach based on coalescence (GMYC, STEM) and phylogenetic relationships to assess species boundaries in the trebouxioid photobionts of the lichen-forming fungus Lasallia pustulata. We further investigated whether putative species of Trebouxia found in L. pustulata are shared with other lichen-forming fungi. We found that L. pustulata is associated with at least five species of Trebouxia and most of them are shared with other lichen-forming fungi, showing different patterns of species-to-species and species-to-community interactions. We also show that one of the putative Trebouxia species is found exclusively in association with L. pustulata and is restricted to thalli from localities with Mediterranean microclimate. We suggest that the species delimitation method presented in this study is a promising tool to address species boundaries within the heterogeneous genus Trebouxia.
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Affiliation(s)
- Anna D Sadowska-Deś
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany; Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt, Germany.
| | - Francesco Dal Grande
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt, Germany
| | - H Thorsten Lumbsch
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Andreas Beck
- Department of Lichenology and Bryology, Botanische Staatssammlung München, Menzinger Straße 67, D-80638 München, Germany; GeoBio-Center, Ludwig-Maximilians Universität München, Richard-Wagner-Str. 10, D-80333 München, Germany
| | - Jürgen Otte
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt, Germany
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon 540-742, South Korea
| | - Jung A Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon 540-742, South Korea
| | - Imke Schmitt
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany; Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt, Germany.
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Pastore AI, Prather CM, Gornish ES, Ryan WH, Ellis RD, Miller TE. Testing the competition–colonization trade-off with a 32-year study of a saxicolous lichen community. Ecology 2014; 95:306-15. [DOI: 10.1890/13-0253.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Leavitt SD, Lumbsch HT, Stenroos S, Clair LLS. Pleistocene speciation in North American lichenized fungi and the impact of alternative species circumscriptions and rates of molecular evolution on divergence estimates. PLoS One 2013; 8:e85240. [PMID: 24386465 PMCID: PMC3873437 DOI: 10.1371/journal.pone.0085240] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 11/24/2013] [Indexed: 12/04/2022] Open
Abstract
Pleistocene climatic fluctuations influenced patterns of genetic variation and promoted speciation across a wide range of species groups. Lichens are commonly found in habitats that were directly impacted by glacial cycles; however, the role of Pleistocene climate in driving speciation in most lichen symbionts remains unclear. This uncertainty is due in part to limitations in our ability to accurately recognize independently evolving lichen-forming fungal lineages and a lack of relevant fossil calibrations. Using a coalescent-based species tree approach, we estimated divergence times for two sister clades in the genus Xanthoparmelia (Parmeliaceae) restricted to western North America. We assessed the influence of two different species circumscription scenarios and various locus-specific rates of molecular evolution on divergence estimates. Species circumscriptions were validated using the program BP&P. although speciation was generally supported in both scenarios, divergence times differed between traditional species circumscriptions and those based on genetic data, with more recent estimates resulting from the former. Similarly, rates of evolution for different loci resulted in variable divergence time estimates. However, our results unambiguously indicate that diversification in the sampled Xanthoparmelia clades occurred during the Pleistocene. Our study highlights the potential impact of ambiguous species circumscriptions and uncertain rates of molecular evolution on estimating divergence times within a multilocus species tree framework.
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Affiliation(s)
- Steven D. Leavitt
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America
- Science & Education, The Field Museum, Chicago, Illinois, United States of America
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, Utah, United States of America
- * E-mail:
| | - H. Thorsten Lumbsch
- Science & Education, The Field Museum, Chicago, Illinois, United States of America
| | - Soili Stenroos
- Botanical Museum, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Larry L. St. Clair
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, Utah, United States of America
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Truong C, Divakar PK, Yahr R, Crespo A, Clerc P. Testing the use of ITS rDNA and protein-coding genes in the generic and species delimitation of the lichen genus Usnea (Parmeliaceae, Ascomycota). Mol Phylogenet Evol 2013; 68:357-72. [DOI: 10.1016/j.ympev.2013.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 02/01/2013] [Accepted: 04/02/2013] [Indexed: 12/31/2022]
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31
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Leavitt S, Fernández-Mendoza F, Pérez-Ortega S, Sohrabi M, Divakar P, Lumbsch T, St. Clair L. DNA barcode identification of lichen-forming fungal species in the Rhizoplaca melanophthalma species-complex (Lecanorales, Lecanoraceae), including five new species. MycoKeys 2013. [DOI: 10.3897/mycokeys.7.4508] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Sadowska-Deś AD, Bálint M, Otte J, Schmitt I. Assessing intraspecific diversity in a lichen-forming fungus and its green algal symbiont: Evaluation of eight molecular markers. FUNGAL ECOL 2013. [DOI: 10.1016/j.funeco.2012.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Leavitt SD, Esslinger TL, Spribille T, Divakar PK, Thorsten Lumbsch H. Multilocus phylogeny of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota): Insights on diversity, distributions, and a comparison of species tree and concatenated topologies. Mol Phylogenet Evol 2013; 66:138-52. [DOI: 10.1016/j.ympev.2012.09.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 08/31/2012] [Accepted: 09/16/2012] [Indexed: 10/27/2022]
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Leavitt SD, Esslinger TL, Divakar PK, Lumbsch HT. Miocene divergence, phenotypically cryptic lineages, and contrasting distribution patterns in common lichen-forming fungi (Ascomycota: Parmeliaceae). Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01978.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Steven D. Leavitt
- Department of Botany; The Field Museum; 1400 S. Lake Shore Drive; Chicago; IL; 60605; USA
| | - Theodore L. Esslinger
- Department of Biological Sciences; North Dakota State University; #2715, PO Box 6050, Stevens Hall; Fargo; ND; 58108-6050; USA
| | - Pradeep K. Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia; Universidad Complutense de Madrid; Madrid; 28040; Spain
| | - H. Thorsten Lumbsch
- Department of Botany; The Field Museum; 1400 S. Lake Shore Drive; Chicago; IL; 60605; USA
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Leavitt SD, Esslinger TL, Lumbsch HT. Neogene-dominated diversification in neotropical montane lichens: dating divergence events in the lichen-forming fungal genus Oropogon (Parmeliaceae). AMERICAN JOURNAL OF BOTANY 2012; 99:1764-1777. [PMID: 23092994 DOI: 10.3732/ajb.1200146] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY Diversification in neotropical regions has been attributed to both Tertiary geological events and Pleistocene climatic fluctuations. However, the timing and processes driving speciation in these regions remain unexplored in many important groups. Here, we address the timing of diversification in the neotropical lichenized fungal genus Oropogon (Ascomycota) and assess traditional species boundaries. METHODS We analyzed sequence data from three loci to assess phenotypically circumscribed Oropogon species from the Oaxacan Highlands, Mexico. We provide a comparison of dated divergence estimates between concatenated gene trees and a calibrated multilocus species-tree using substitution rates for two DNA regions. We also compare estimates from a data set excluding ambiguously aligned regions and a data set including the hyper-variable regions in two ribosomal markers. KEY RESULTS Phylogenetic reconstructions were characterized by well-supported monophyletic clades corresponding to traditionally circumscribed species, with the exception of a single taxon. Divergence estimates indicate that most diversification of the sampled Oropogon species occurred throughout the Oligocene and Miocene, although diversification of a single closely related clade appears to have occurred during the late Pliocene and into the Pleistocene. Divergence estimates calculated from a data set with ambiguously aligned regions removed were much more recent than those from the full data set. CONCLUSIONS Overall, our analyses place the majority of divergence events of Oropogon species from the Oaxacan Highlands within the Neogene and provide strong evidence that climatic changes during the Pleistocene were not a major factor driving speciation in the lichenized genus Oropogon in neotropical highlands.
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Affiliation(s)
- Steven D Leavitt
- The Field Museum, Department of Botany, 1400 S. Lake Shore Drive, Chicago, Illinois 60605, USA. sleavitt@fi eldmuseum.org
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Leavitt SD, Esslinger TL, Divakar PK, Lumbsch HT. Miocene and Pliocene dominated diversification of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota) and Pleistocene population expansions. BMC Evol Biol 2012; 12:176. [PMID: 22963132 PMCID: PMC3499221 DOI: 10.1186/1471-2148-12-176] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 08/30/2012] [Indexed: 01/22/2023] Open
Abstract
Background Factors promoting diversification in lichen symbioses remain largely unexplored. While Pleistocene events have been important for driving diversification and affecting distributions in many groups, recent estimates suggest that major radiations within some genera in the largest clade of macrolichens (Parmeliaceae, Ascomycota) vastly predate the Pleistocene. To better understand the temporal placement and sequence of diversification events in lichens, we estimated divergence times in a common lichen-forming fungal genus, Melanohalea, in the Northern Hemisphere. Divergence times were estimated using both concatenated gene tree and coalescent-based multilocus species tree approaches to assess the temporal context of major radiation events within Melanohalea. In order to complement our understanding of processes impacting genetic differentiation, we also evaluated the effects of Pleistocene glacial cycles on population demographics of distinct Melanohalea lineages, differing in reproductive strategies. Results We found that divergence estimates, from both concatenated gene tree and coalescent-based multilocus species tree approaches, suggest that diversification within Melanohalea occurred predominantly during the Miocene and Pliocene, although estimated of divergence times differed by up to 8.3 million years between the two methods. These results indicate that, in some cases, taxonomically diagnostic characters may be maintained among divergent lineages for millions of years. In other cases, similar phenotypic characters among non-sister taxa, including reproductive strategies, suggest the potential for convergent evolution due to similar selective pressures among distinct lineages. Our analyses provide evidence of population expansions predating the last glacial maximum in the sampled lineages. These results suggest that Pleistocene glaciations were not inherently unfavorable or restrictive for some Melanohalea species, albeit with apparently different demographic histories between sexually and vegetatively reproducing lineages. Conclusions Our results contribute to the understanding of how major changes during the Miocene and Pliocene have been important in promoting diversification within common lichen-forming fungi in the northern Hemisphere. Additionally, we provide evidence that glacial oscillations have influenced current population structure of broadly distributed lichenized fungal species throughout the Holarctic.
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Pérez-Ortega S, Ortiz-Álvarez R, Allan Green T, de los Ríos A. Lichen myco- and photobiont diversity and their relationships at the edge of life (McMurdo Dry Valleys, Antarctica). FEMS Microbiol Ecol 2012; 82:429-48. [DOI: 10.1111/j.1574-6941.2012.01422.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 05/24/2012] [Accepted: 05/25/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
| | | | - T.G. Allan Green
- Departamento de Biología Vegetal II; Facultad de Farmacia; Universidad Complutense de Madrid; Madrid; Spain
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38
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de Paz GA, Cubas P, Crespo A, Elix JA, Lumbsch HT. Transoceanic dispersal and subsequent diversification on separate continents shaped diversity of the Xanthoparmelia pulla group (Ascomycota). PLoS One 2012; 7:e39683. [PMID: 22745810 PMCID: PMC3379998 DOI: 10.1371/journal.pone.0039683] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 05/25/2012] [Indexed: 11/18/2022] Open
Abstract
In traditional morphology-based concepts many species of lichenized fungi have world-wide distributions. Molecular data have revolutionized the species delimitation in lichens and have demonstrated that we underestimated the diversity of these organisms. The aim of this study is to explore the phylogeography and the evolutionary patterns of the Xanthoparmelia pulla group, a widespread group of one of largest genera of macrolichens. We used a dated phylogeny based on nuITS and nuLSU rDNA sequences and performed an ancestral range reconstruction to understand the processes and explain their current distribution, dating the divergence of the major lineages in the group. An inferred age of radiation of parmelioid lichens and the age of a Parmelia fossil were used as the calibration points for the phylogeny. The results show that many species of the X. pulla group as currently delimited are polyphyletic and five major lineages correlate with their geographical distribution and the biosynthetic pathways of secondary metabolites. South Africa is the area where the X. pulla group radiated during the Miocene times, and currently is the region with the highest genetic, morphological and chemical diversity. From this center of radiation the different lineages migrated by long-distance dispersal to others areas, where secondary radiations developed. The ancestral range reconstruction also detected that a secondary lineage migrated from Australia to South America via long-distance dispersal and subsequent continental radiation.
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Affiliation(s)
- Guillermo Amo de Paz
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Paloma Cubas
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - John A. Elix
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - H. Thorsten Lumbsch
- Department of Botany, The Field Museum, Chicago, Illinois, United States of America
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Pérez-Ortega S, Fernández-Mendoza F, Raggio J, Vivas M, Ascaso C, Sancho LG, Printzen C, de Los Ríos A. Extreme phenotypic variation in Cetraria aculeata (lichenized Ascomycota): adaptation or incidental modification? ANNALS OF BOTANY 2012; 109:1133-1148. [PMID: 22451601 PMCID: PMC3336953 DOI: 10.1093/aob/mcs042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 02/02/2012] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS Phenotypic variability is a successful strategy in lichens for colonizing different habitats. Vagrancy has been reported as a specific adaptation for lichens living in steppe habitats around the world. Among the facultatively vagrant species, the cosmopolitan Cetraria aculeata apparently forms extremely modified vagrant thalli in steppe habitats of Central Spain. The aim of this study was to investigate whether these changes are phenotypic plasticity (a single genotype producing different phenotypes), by characterizing the anatomical and ultrastructural changes observed in vagrant morphs, and measuring differences in ecophysiological performance. METHODS Specimens of vagrant and attached populations of C. aculeata were collected on the steppes of Central Spain. The fungal internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase (GPD) and the large sub-unit of the mitochondrial ribosomal DNA (mtLSUm), and the algal ITS and actin were studied within a population genetics framework. Semi-thin and ultrathin sections were analysed by means of optical, scanning electron and transmission electron microscopy. Gas exchange and chlorophyll fluorescence were used to compare the physiological performance of both morphs. KEY RESULTS AND CONCLUSIONS Vagrant and attached morphs share multilocus haplotypes which may indicate that they belong to the same species in spite of their completely different anatomy. However, differentiation tests suggested that vagrant specimens do not represent a random sub-set of the surrounding population. The morphological differences were related to anatomical and ultrastructural differences. Large intercalary growth rates of thalli after the loss of the basal-apical thallus polarity may be the cause of the increased growth shown by vagrant specimens. The anatomical and morphological changes lead to greater duration of ecophysiological activity in vagrant specimens. Although the anatomical and physiological changes could be chance effects, the genetic differentiation between vagrant and attached sub-populations and the higher biomass of the former show fitness effects and adaptation to dry environmental conditions in steppe habitats.
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Affiliation(s)
- Sergio Pérez-Ortega
- Museo Nacional de Ciencias Naturales, MNCN-CSIC, c/ Serrano 115 dpdo, E-28006 Madrid, Spain.
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Amo de Paz G, Cubas P, Divakar PK, Lumbsch HT, Crespo A. Origin and diversification of major clades in parmelioid lichens (Parmeliaceae, Ascomycota) during the Paleogene inferred by Bayesian analysis. PLoS One 2011; 6:e28161. [PMID: 22174775 PMCID: PMC3234259 DOI: 10.1371/journal.pone.0028161] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 11/02/2011] [Indexed: 11/19/2022] Open
Abstract
There is a long-standing debate on the extent of vicariance and long-distance dispersal events to explain the current distribution of organisms, especially in those with small diaspores potentially prone to long-distance dispersal. Age estimates of clades play a crucial role in evaluating the impact of these processes. The aim of this study is to understand the evolutionary history of the largest clade of macrolichens, the parmelioid lichens (Parmeliaceae, Lecanoromycetes, Ascomycota) by dating the origin of the group and its major lineages. They have a worldwide distribution with centers of distribution in the Neo- and Paleotropics, and semi-arid subtropical regions of the Southern Hemisphere. Phylogenetic analyses were performed using DNA sequences of nuLSU and mtSSU rDNA, and the protein-coding RPB1 gene. The three DNA regions had different evolutionary rates: RPB1 gave a rate two to four times higher than nuLSU and mtSSU. Divergence times of the major clades were estimated with partitioned BEAST analyses allowing different rates for each DNA region and using a relaxed clock model. Three calibrations points were used to date the tree: an inferred age at the stem of Lecanoromycetes, and two dated fossils: Parmelia in the parmelioid group, and Alectoria. Palaeoclimatic conditions and the palaeogeological area cladogram were compared to the dated phylogeny of parmelioid. The parmelioid group diversified around the K/T boundary, and the major clades diverged during the Eocene and Oligocene. The radiation of the genera occurred through globally changing climatic condition of the early Oligocene, Miocene and early Pliocene. The estimated divergence times are consistent with long-distance dispersal events being the major factor to explain the biogeographical distribution patterns of Southern Hemisphere parmelioids, especially for Africa-Australia disjunctions, because the sequential break-up of Gondwana started much earlier than the origin of these clades. However, our data cannot reject vicariance to explain South America-Australia disjunctions.
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Affiliation(s)
- Guillermo Amo de Paz
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - Paloma Cubas
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - Pradeep K. Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - H. Thorsten Lumbsch
- Department of Botany, The Field Museum, Chicago, Illinois, United States of America
| | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
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Leavitt SD, Johnson LA, Goward T, St. Clair LL. Species delimitation in taxonomically difficult lichen-forming fungi: An example from morphologically and chemically diverse Xanthoparmelia (Parmeliaceae) in North America. Mol Phylogenet Evol 2011; 60:317-32. [DOI: 10.1016/j.ympev.2011.05.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 05/13/2011] [Accepted: 05/16/2011] [Indexed: 01/03/2023]
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Lumbsch HT, Leavitt SD. Goodbye morphology? A paradigm shift in the delimitation of species in lichenized fungi. FUNGAL DIVERS 2011. [DOI: 10.1007/s13225-011-0123-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Complex patterns of speciation in cosmopolitan “rock posy” lichens – Discovering and delimiting cryptic fungal species in the lichen-forming Rhizoplaca melanophthalma species-complex (Lecanoraceae, Ascomycota). Mol Phylogenet Evol 2011; 59:587-602. [DOI: 10.1016/j.ympev.2011.03.020] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 12/16/2010] [Accepted: 03/17/2011] [Indexed: 11/19/2022]
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Spribille T, Klug B, Mayrhofer H. A phylogenetic analysis of the boreal lichen Mycoblastus sanguinarius (Mycoblastaceae, lichenized Ascomycota) reveals cryptic clades correlated with fatty acid profiles. Mol Phylogenet Evol 2011; 59:603-14. [PMID: 21443957 PMCID: PMC3093615 DOI: 10.1016/j.ympev.2011.03.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 12/24/2010] [Accepted: 03/17/2011] [Indexed: 11/02/2022]
Abstract
Lichens are a prominent feature of northern conifer forests and a large number of species are thought to be circumboreal. Whether or not circumboreal lichen species really constitute monophyletic groups has seldom been tested. We investigated molecular phylogenetic patterns in the mycobiont of Mycoblastus sanguinarius, a well known epiphytic lichen species of the boreal forest, based on material collected from across the high latitude northern hemisphere. A three-locus dataset of internal transcribed spacer rDNA, translation elongation factor 1-α and replication licensing factor Mcm7 DNA sequences revealed that material treated until now as belonging to M. sanguinarius does indeed form a monophyletic group within the genus and is distinct from a strongly supported Mycoblastus affinis. The M. sanguinarius complex appears closely related to the rare Mycoblastus glabrescens, which is currently known only from the Pacific Northwest and was rediscovered during the present study. However, within M. sanguinarius s.lat. in the northern hemisphere, two deeply divergent and morphologically coherent species can be recovered, one of which matches the southern hemisphere species Mycoblastus sanguinarioides and turns out to be widespread in North America and Asia, and one of which corresponds to M. sanguinarius s.str. Both M. sanguinarius and M. sanguinarioides exhibit additional low-level genetic differentiation into geographically structured clades, the most prominent of which are distributed in East Asia/eastern North America and western North America/Europe, respectively. Individuals from these lowest-level clades are morphologically indistinguishable but chemical analyses by thin layer chromatography revealed that each clade possesses its own fatty acid profile, suggesting that chemical differentiation precedes morphological differentiation and may be a precursor to speciation.
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Affiliation(s)
- Toby Spribille
- Institute of Plant Sciences, University of Graz, Holteigasse 6, A-8010 Graz, Austria.
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