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Cornejo C, Scheidegger C. Multi-gene phylogeny of the genus Lobaria: Evidence of species-pair and allopatric cryptic speciation in East Asia. AMERICAN JOURNAL OF BOTANY 2015; 102:2058-2073. [PMID: 26672013 DOI: 10.3732/ajb.1500207] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 10/13/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Accurate species delimitation has critical implications for ecological and conservation studies. The lichen genus Lobaria is widely distributed in old-growth forests. Particularly in East Asia, this genus includes many rare and poorly known taxa that are circumscribed as morpho- or chemospecies, as well as species-pairs. METHODS To critically examine the relationships between species identified via morphological and chemical criteria, phylogenetic species recognition (PSR) was applied to the genus Lobaria. Morphological and chemical patterns of 87 individuals were examined and three independent nuclear loci were sequenced. The East Asian L. meridionalis-group was additionally studied using split decomposition and haplotype network analysis. KEY RESULTS The genus Lobaria and most of its species were strongly supported statistically. Split decomposition and haplotype networks suggest complex evolutionary histories of species within the East Asian L. meridionalis-group. CONCLUSIONS Phylogenetic analyses confirmed the monophyly of the genus Lobaria, including L. anomala. Within Lobaria, three major clades were found. These clades associate with different photobionts and comprise 18 known species and 5 undescribed species. Several chemical compounds were found to be neither stable nor invariant characters. Some taxa of the L. meridionalis-group appear to be monophyletic but remain as allopatric cryptic species. In three clades, this study found evidence for diversification processes between isidiate and nonisidiate specimens (species-pair). These findings are discussed in the context of evolutionary hypotheses for speciation processes.
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Affiliation(s)
- Carolina Cornejo
- Swiss Federal Research Institute WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Christoph Scheidegger
- Swiss Federal Research Institute WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland
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Sánchez-Ramírez S, Tulloss RE, Guzmán-Dávalos L, Cifuentes-Blanco J, Valenzuela R, Estrada-Torres A, Ruán-Soto F, Díaz-Moreno R, Hernández-Rico N, Torres-Gómez M, León H, Moncalvo JM. In and out of refugia: historical patterns of diversity and demography in the North American Caesar's mushroom species complex. Mol Ecol 2015; 24:5938-56. [PMID: 26465233 DOI: 10.1111/mec.13413] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 10/05/2015] [Accepted: 10/06/2015] [Indexed: 11/30/2022]
Abstract
Some of the effects of past climate dynamics on plant and animal diversity make-up have been relatively well studied, but to less extent in fungi. Pleistocene refugia are thought to harbour high biological diversity (i.e. phylogenetic lineages and genetic diversity), mainly as a product of increased reproductive isolation and allele conservation. In addition, high extinction rates and genetic erosion are expected in previously glaciated regions. Some of the consequences of past climate dynamics might involve changes in range and population size that can result in divergence and incipient or cryptic speciation. Many of these dynamic processes and patterns can be inferred through phylogenetic and coalescent methods. In this study, we first delimit species within a group of closely related edible ectomycorrhizal Amanita from North America (the American Caesar's mushrooms species complex) using multilocus coalescent-based approaches; and then address questions related to effects of Pleistocene climate change on the diversity and genetics of the group. Our study includes extensive geographical sampling throughout the distribution range, and DNA sequences from three nuclear protein-coding genes. Results reveal cryptic diversity and high speciation rates in refugia. Population sizes and expansions seem to be larger at midrange latitudes (Mexican highlands and SE USA). Range shifts are proportional to population size expansions, which were overall more common during the Pleistocene. This study documents responses to past climate change in fungi and also highlights the applicability of the multispecies coalescent in comparative phylogeographical analyses and diversity assessments that include ancestral species.
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Affiliation(s)
- Santiago Sánchez-Ramírez
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks, Toronto, ON, M5S 3B2, Canada
| | | | - Laura Guzmán-Dávalos
- Departamento de Botánica y Zoología, Universidad de Guadalajara, Zapopan, 45101, México
| | - Joaquín Cifuentes-Blanco
- Facultad de Ciencias, Departamento de Biología Comparada, UNAM, Ciudad Universitaria, México City, 04510, México
| | - Ricardo Valenzuela
- Escuela Nacional de Ciencias Biólogicas, Instituto Politécnico Nacional, México City, 11340, México
| | - Arturo Estrada-Torres
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, 90122, México
| | - Felipe Ruán-Soto
- Facultad de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez, 29039, Mexico
| | - Raúl Díaz-Moreno
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, 34120, México
| | - Nallely Hernández-Rico
- Laboratorio de Etnobiología, Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Hidalgo, Pachuca, México
| | - Mariano Torres-Gómez
- Centro de Investigaciones en Ecosistemas CIEco, Antigua carretera a Pátzcuaro # 8701, Col. Ex-Hacienda de San José de La Huerta, Morelia, 58190, México
| | - Hugo León
- Coleccion Etnomicológica "Dr. Teófilo Herrera Suárez", Instituto Tecnológico del Valle de Oaxaca, Xoxocotlán, 71230, México
| | - Jean-Marc Moncalvo
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks, Toronto, ON, M5S 3B2, Canada
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53
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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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54
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Kraichak E, Lücking R, Aptroot A, Beck A, Dornes P, John V, Lendemer JC, Nelsen MP, Neuwirth G, Nutakki A, Parnmen S, Sohrabi M, Tønsberg T, Lumbsch HT. Hidden diversity in the morphologically variable script lichen (Graphis scripta) complex (Ascomycota, Ostropales, Graphidaceae). ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0219-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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55
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Núñez-Zapata J, Cubas P, Hawksworth DL, Crespo A. Biogeography and Genetic Structure in Populations of a Widespread Lichen (Parmelina tiliacea, Parmeliaceae, Ascomycota). PLoS One 2015; 10:e0126981. [PMID: 25961726 PMCID: PMC4427293 DOI: 10.1371/journal.pone.0126981] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/09/2015] [Indexed: 11/18/2022] Open
Abstract
The genetic diversity and population structure of the foliose lichenized fungus Parmelina tiliacea has been analyzed through its geographical range, including samples from Macaronesia (Canary Islands), the Mediterranean, and Eurosiberia. DNA sequences from the nuclear ribosomal internal transcribed spacer, the mitochondrial large subunit ribosomal RNA gene, and the translation elongation factor 1-α were used as molecular markers. The haplotypes of the three markers and the molecular variance analyses of multilocus haplotypes showed the highest diversity in the Canary Islands, while restricted haplotypes occurred at high frequencies in Mediterranean coastal samples. The multilocus haplotypes formed three unevenly distributed clusters (clusters 1-3). In the Canary Islands all the haplotypes were present in a similar proportion, while the coastal Mediterranean sites had almost exclusively haplotypes of cluster 3; cluster 2 predominated in inland Mediterranean sites; and cluster 1 was more abundant in central and northern Europe (Eurosiberian area). The distribution of clusters is partially explained by climatic factors, and its interaction with local spatial structure, but much of the variation remains unexplained. The high frequency of individuals in the Canary Islands with haplotypes shared with other areas suggests that could be a refugium of genetic diversity, and the high frequency of individuals of the Mediterranean coastal sites with restricted haplotypes indicates that gene flow to contiguous areas may be restricted. This is significant for the selection of areas for conservation purposes, as those with most genetic variation may reflect historical factors and biological properties of the species.
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Affiliation(s)
- Jano Núñez-Zapata
- 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
- * E-mail:
| | - David L. Hawksworth
- 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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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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Zúñiga C, Leiva D, Ramírez-Fernández L, Carú M, Yahr R, Orlando J. Phylogenetic Diversity of Peltigera Cyanolichens and Their Photobionts in Southern Chile and Antarctica. Microbes Environ 2015; 30:172-9. [PMID: 25925273 PMCID: PMC4462928 DOI: 10.1264/jsme2.me14156] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/06/2015] [Indexed: 11/24/2022] Open
Abstract
The lichen genus Peltigera has been mainly revised in the Northern Hemisphere, with most species being recorded in Europe and North America. This study assessed the phylogenetic diversity of the mycobionts and cyanobionts of Peltigera cyanolichens collected in Southern Chile and Antarctica, areas in which lichens are extremely diverse but poorly studied. The operational taxonomic units (OTUs) of each symbiont were defined by analyzing the genetic diversity of the LSU and SSU rDNA of the mycobionts and cyanobionts, respectively, and a phylogenetic approach was used to relate these OTUs with sequences previously reported for Peltigera and Nostoc. Among the 186 samples collected, 8 Peltigera and 15 Nostoc OTUs were recognized, corresponding to sections Peltigera, Horizontales, and Polydactylon, in the case of the mycobionts, and to the Nostoc clade II, in the case of the cyanobionts. Since some of the OTUs recognized in this study had not previously been described in these areas, our results suggest that the diversity of Peltigera reported to date in the regions studied using traditional morphological surveys has underestimated the true diversity present; therefore, further explorations of these areas are recommended.
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Affiliation(s)
- Catalina Zúñiga
- Department of Ecological Sciences, Faculty of Sciences, Universidad de ChileCasilla 653. SantiagoChile
| | - Diego Leiva
- Department of Ecological Sciences, Faculty of Sciences, Universidad de ChileCasilla 653. SantiagoChile
| | - Lía Ramírez-Fernández
- Department of Ecological Sciences, Faculty of Sciences, Universidad de ChileCasilla 653. SantiagoChile
| | - Margarita Carú
- Department of Ecological Sciences, Faculty of Sciences, Universidad de ChileCasilla 653. SantiagoChile
| | - Rebecca Yahr
- Royal Botanic Garden Edinburgh20A Inverleith Row, EdinburghUK EH3 5LR
| | - Julieta Orlando
- Department of Ecological Sciences, Faculty of Sciences, Universidad de ChileCasilla 653. SantiagoChile
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58
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Hagen F, Khayhan K, Theelen B, Kolecka A, Polacheck I, Sionov E, Falk R, Parnmen S, Lumbsch HT, Boekhout T. Recognition of seven species in the Cryptococcus gattii/Cryptococcus neoformans species complex. Fungal Genet Biol 2015; 78:16-48. [PMID: 25721988 DOI: 10.1016/j.fgb.2015.02.009] [Citation(s) in RCA: 472] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 02/12/2015] [Accepted: 02/15/2015] [Indexed: 02/08/2023]
Abstract
Phylogenetic analysis of 11 genetic loci and results from many genotyping studies revealed significant genetic diversity with the pathogenic Cryptococcus gattii/Cryptococcus neoformans species complex. Genealogical concordance, coalescence-based, and species tree approaches supported the presence of distinct and concordant lineages within the complex. Consequently, we propose to recognize the current C. neoformans var. grubii and C. neoformans var. neoformans as separate species, and five species within C. gattii. The type strain of C. neoformans CBS132 represents a serotype AD hybrid and is replaced. The newly delimited species differ in aspects of pathogenicity, prevalence for patient groups, as well as biochemical and physiological aspects, such as susceptibility to antifungals. MALDI-TOF mass spectrometry readily distinguishes the newly recognized species.
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Affiliation(s)
- Ferry Hagen
- CBS-KNAW Fungal Biodiversity Centre, Basidiomycete and Yeast Research, Utrecht, The Netherlands; Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Kantarawee Khayhan
- CBS-KNAW Fungal Biodiversity Centre, Basidiomycete and Yeast Research, Utrecht, The Netherlands; Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, Thailand
| | - Bart Theelen
- CBS-KNAW Fungal Biodiversity Centre, Basidiomycete and Yeast Research, Utrecht, The Netherlands
| | - Anna Kolecka
- CBS-KNAW Fungal Biodiversity Centre, Basidiomycete and Yeast Research, Utrecht, The Netherlands
| | - Itzhack Polacheck
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Edward Sionov
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel; Department of Food Quality & Safety, Institute for Postharvest and Food Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Rama Falk
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel; Department of Fisheries and Aquaculture, Ministry of Agriculture and Rural Development, Nir-David, Israel
| | - Sittiporn Parnmen
- Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | | | - Teun Boekhout
- CBS-KNAW Fungal Biodiversity Centre, Basidiomycete and Yeast Research, Utrecht, The Netherlands; Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China; Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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59
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Epitypification and neotypification: guidelines with appropriate and inappropriate examples. FUNGAL DIVERS 2014. [DOI: 10.1007/s13225-014-0315-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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60
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Abstract
The number of Fungi is estimated at between 1.5 and 3 million. Lichenized species are thought to make up a comparatively small portion of this figure, with unrecognized species richness hidden among little-studied, tropical microlichens. Recent findings, however, suggest that some macrolichens contain a large number of unrecognized taxa, increasing known species richness by an order of magnitude or more. Here we report the existence of at least 126 species in what until recently was believed to be a single taxon: the basidiolichen fungus Dictyonema glabratum, also known as Cora pavonia. Notably, these species are not cryptic but morphologically distinct. A predictive model suggests an even larger number, with more than 400 species. These results call into question species concepts in presumably well-known macrolichens and demonstrate the need for accurately documenting such species richness, given the importance of these lichens in endangered ecosystems such as paramos and the alarming potential for species losses throughout the tropics.
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62
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Altermann S, Leavitt SD, Goward T, Nelsen MP, Lumbsch HT. How do you solve a problem like Letharia? A new look at cryptic species in lichen-forming fungi using Bayesian clustering and SNPs from multilocus sequence data. PLoS One 2014; 9:e97556. [PMID: 24831224 PMCID: PMC4022584 DOI: 10.1371/journal.pone.0097556] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 04/21/2014] [Indexed: 11/19/2022] Open
Abstract
The inclusion of molecular data is increasingly an integral part of studies assessing species boundaries. Analyses based on predefined groups may obscure patterns of differentiation, and population assignment tests provide an alternative for identifying population structure and barriers to gene flow. In this study, we apply population assignment tests implemented in the programs STRUCTURE and BAPS to single nucleotide polymorphisms from DNA sequence data generated for three previous studies of the lichenized fungal genus Letharia. Previous molecular work employing a gene genealogical approach circumscribed six species-level lineages within the genus, four putative lineages within the nominal taxon L. columbiana (Nutt.) J.W. Thomson and two sorediate lineages. We show that Bayesian clustering implemented in the program STRUCTURE was generally able to recover the same six putative Letharia lineages. Population assignments were largely consistent across a range of scenarios, including: extensive amounts of missing data, the exclusion of SNPs from variable markers, and inferences based on SNPs from as few as three gene regions. While our study provided additional evidence corroborating the six candidate Letharia species, the equivalence of these genetic clusters with species-level lineages is uncertain due, in part, to limited phylogenetic signal. Furthermore, both the BAPS analysis and the ad hoc ΔK statistic from results of the STRUCTURE analysis suggest that population structure can possibly be captured with fewer genetic groups. Our findings also suggest that uneven sampling across taxa may be responsible for the contrasting inferences of population substructure. Our results consistently supported two distinct sorediate groups, ‘L. lupina’ and L. vulpina, and subtle morphological differences support this distinction. Similarly, the putative apotheciate species ‘L. lucida’ was also consistently supported as a distinct genetic cluster. However, additional studies will be required to elucidate the relationships of other L. columbiana s.l. populations with the two sorediate genetic clusters.
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Affiliation(s)
- Susanne Altermann
- Biology Department, Whitman College, Walla Walla, Washington, United States of America
| | - Steven D. Leavitt
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America
- Science and Education, The Field Museum, Chicago, Illinois, United States of America
- * E-mail:
| | - Trevor Goward
- Beaty Biodiversity Museum, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew P. Nelsen
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America
- Science and Education, The Field Museum, Chicago, Illinois, United States of America
| | - H. Thorsten Lumbsch
- Science and Education, The Field Museum, Chicago, Illinois, United States of America
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63
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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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Millanes AM, Truong C, Westberg M, Diederich P, Wedin M. Host switching promotes diversity in host-specialized mycoparasitic fungi: uncoupled evolution in the Biatoropsis-usnea system. Evolution 2014; 68:1576-93. [PMID: 24495034 DOI: 10.1111/evo.12374] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 01/24/2014] [Indexed: 12/15/2022]
Abstract
Fungal mycoparasitism-fungi parasitizing other fungi-is a common lifestyle in some basal lineages of the basidiomycetes, particularly within the Tremellales. Relatively nonaggressive mycoparasitic fungi of this group are in general highly host specific, suggesting cospeciation as a plausible speciation mode in these associations. Species delimitation in the Tremellales is often challenging because morphological characters are scant. Host specificity is therefore a great aid to discriminate between species but appropriate species delimitation methods that account for actual diversity are needed to identify both specialist and generalist taxa and avoid inflating or underestimating diversity. We use the Biatoropsis-Usnea system to study factors inducing parasite diversification. We employ morphological, ecological, and molecular data-methods including genealogical concordance phylogenetic species recognition (GCPSR) and the general mixed Yule-coalescent (GMYC) model-to assess the diversity of fungi currently assigned to Biatoropsis usnearum. The degree of cospeciation in this association is assessed with two cophylogeny analysis tools (ParaFit and Jane 4.0). Biatoropsis constitutes a species complex formed by at least seven different independent lineages and host switching is a prominent force driving speciation, particularly in host specialists. Combining ITS and nLSU is recommended as barcode system in tremellalean fungi.
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Affiliation(s)
- Ana M Millanes
- Departamento de Biología y Geología, Universidad Rey Juan Carlos, E-28933 Móstoles, Spain.
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65
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Meiser A, Bálint M, Schmitt I. Meta-analysis of deep-sequenced fungal communities indicates limited taxon sharing between studies and the presence of biogeographic patterns. THE NEW PHYTOLOGIST 2014; 201:623-635. [PMID: 24111803 DOI: 10.1111/nph.12532] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 08/27/2013] [Indexed: 06/02/2023]
Abstract
High-throughput amplicon sequencing gives new insights into fungal community ecology. Massively generated molecular data lead to the discovery of vast fungal diversity. However, it is unclear to what extent operational taxonomic units (OTUs) overlap among independent studies, because no comparative studies exist. We compared fungal diversity based on the internal transcribed spacer (ITS1) region among 10 published studies. Starting from the raw 454 pyrosequencing data, we used a uniform pipeline to prune the reads. We investigated fungal richness and taxonomic composition among phyllosphere and soil fungal communities, as well as biogeographic signals in the data. We did not find globally distributed OTUs, even when comparing fungal communities from similar habitats (phyllosphere or soil). This suggests that high local fungal diversity scales up to high global diversity. The most OTU-rich classes in the phyllosphere were Dothideomycetes (21%) and Sordariomycetes (14%), and in the soil were Sordariomycetes (13%) and Agaricomycetes (12%). The richness estimates suggest the presence of undiscovered fungal diversity even in deeply sequenced study systems. The small number of OTUs shared among studies indicates that globally distributed taxa and habitat generalists may be rare. Latitudinal diversity decline and distance decay relationships suggest the presence of biogeographic patterns similar to those in plants and animals.
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Affiliation(s)
- Anjuli Meiser
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre BiK-F, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Miklós Bálint
- Biodiversity and Climate Research Centre BiK-F, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Imke Schmitt
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre BiK-F, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
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66
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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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67
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DNA barcoding of brown Parmeliae (Parmeliaceae) species: a molecular approach for accurate specimen identification, emphasizing species in Greenland. ORG DIVERS EVOL 2013. [DOI: 10.1007/s13127-013-0147-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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68
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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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69
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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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70
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Pino-Bodas R, Martín MP, Burgaz AR, Lumbsch HT. Species delimitation in Cladonia (Ascomycota): a challenge to the DNA barcoding philosophy. Mol Ecol Resour 2013; 13:1058-68. [PMID: 23437908 DOI: 10.1111/1755-0998.12086] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 01/30/2013] [Accepted: 01/31/2013] [Indexed: 01/28/2023]
Abstract
The lichen-forming fungal genus Cladonia is species-rich with approximately 500 described species. The accepted barcode for fungi (ITS rDNA) often fails in identifying Cladonia spp. In order to find other markers that, in combination with the ITS rDNA region can be used for species identification in Cladonia, we studied the loci IGS rDNA, ef1α, rpb2 and cox1. A total of 782 sequences from 36 species have been analyzed. PCR amplification success rate, intraspecific and interspecific genetic distance variation, calculated using the K2P model, and the correct identification percentage (PCI) were taken into account to assess possible barcode regions. The marker showing the least intraspecific genetic distance range was cox1, followed by ITS rDNA and ef1α. Of the five studied markers only cox1 showed a barcoding gap. The rpb2 locus showed the highest PCI values, but it was the most difficult to amplify. The highest correct identification rates using blast method were obtained with rpb2.
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Affiliation(s)
- Raquel Pino-Bodas
- Departamento Biología Vegetal 1, Facultad de Biología, Universidad Complutense de Madrid, E-28040, Madrid, Spain
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71
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Fernández-Mendoza F, Printzen C. Pleistocene expansion of the bipolar lichenCetraria aculeatainto the Southern hemisphere. Mol Ecol 2013; 22:1961-83. [DOI: 10.1111/mec.12210] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 12/11/2012] [Accepted: 12/13/2012] [Indexed: 11/30/2022]
Affiliation(s)
- Fernando Fernández-Mendoza
- Abt. Botanik und Molekulare Evolutionsforschung; Senckenberg Forschungsinstitut und Naturmuseum; Senckenberganlage 25 D-60325 Frankfurt am Main Germany
- Biodiversity and Climate Research Centre; Senckenberganlage 25 D-60325 Frankfurt am Main Germany
| | - Christian Printzen
- Abt. Botanik und Molekulare Evolutionsforschung; Senckenberg Forschungsinstitut und Naturmuseum; Senckenberganlage 25 D-60325 Frankfurt am Main Germany
- Biodiversity and Climate Research Centre; Senckenberganlage 25 D-60325 Frankfurt am Main Germany
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72
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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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73
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Parnmen S, Rangsiruji A, Mongkolsuk P, Boonpragob K, Nutakki A, Lumbsch HT. Using phylogenetic and coalescent methods to understand the species diversity in the Cladia aggregata complex (Ascomycota, Lecanorales). PLoS One 2012; 7:e52245. [PMID: 23272229 PMCID: PMC3525555 DOI: 10.1371/journal.pone.0052245] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 11/16/2012] [Indexed: 11/17/2022] Open
Abstract
The Cladia aggregata complex is one of the phenotypically most variable groups in lichenized fungi, making species determination difficult and resulting in different classifications accepting between one to eight species. Multi-locus DNA sequence data provide an avenue to test species delimitation scenarios using genealogical and coalescent methods, employing gene and species trees. Here we tested species delimitation in the complex using molecular data of four loci (nuITS and IGS rDNA, protein-coding GAPDH and Mcm-7), including 474 newly generated sequences. Using a combination of ML and Bayesian gene tree topologies, species tree inferences, coalescent-based species delimitation, and examination of phenotypic variation we assessed the circumscription of lineages. We propose that results from our analyses support a 12 species delimitation scenario, suggesting that there is a high level of species diversity in the complex. Morphological and chemical characters often do not characterize lineages but show some degree of plasticity within at least some of the clades. However, clades can often be characterized by a combination of several phenotypical characters. In contrast to the amount of homoplasy in the morphological characters, the data set exhibits some geographical patterns with putative species having distribution patterns, such as austral, Australasian or being endemic to Australia, New Zealand or Tasmania.
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Affiliation(s)
- Sittiporn Parnmen
- Department of Biology, Srinakharinwirot University, Bangkok, Thailand
- Department of Biology, Ramkhamhaeng University, Bangkok, Thailand
- Botany Department, The Field Museum, Chicago, Illinois, United States of America
| | | | | | | | - Aparna Nutakki
- Department of Biological Sciences, University of Chicago, Chicago, Illinois, United States of America
| | - H. Thorsten Lumbsch
- Botany Department, The Field Museum, Chicago, Illinois, United States of America
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74
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Parnmen S, Lücking R, Lumbsch HT. Phylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: a case study in graphidaceae (ascomycota). PLoS One 2012; 7:e51392. [PMID: 23251515 PMCID: PMC3520900 DOI: 10.1371/journal.pone.0051392] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 10/30/2012] [Indexed: 11/19/2022] Open
Abstract
Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed.
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Affiliation(s)
- Sittiporn Parnmen
- Botany Department, The Field Museum, Chicago, Illinois, United States of America
| | - Robert Lücking
- Botany Department, The Field Museum, Chicago, Illinois, United States of America
| | - H. Thorsten Lumbsch
- Botany Department, The Field Museum, Chicago, Illinois, United States of America
- * E-mail:
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75
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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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76
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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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77
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Nagy LG, Desjardin DE, Vágvölgyi C, Kemp R, Papp T. Phylogenetic analyses of Coprinopsis sections Lanatuli and Atramentarii identify multiple species within morphologically defined taxa. Mycologia 2012; 105:112-24. [PMID: 23074175 DOI: 10.3852/12-136] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Sections Lanatuli and Atramentarii of the genus Coprinopsis contain some of the best known and most important agaric species, including C. cinerea and C. lagopus, yet a critical, phylogeny-based assessment of the species limits has not been carried out. Taxa have been characterized chiefly on the basis of morphological characters, which however show little discriminatory power and/or considerable overlap between several species pairs. We used ITS and LSU sequence data of 29 described taxa in Coprinopsis sections Lanatuli and Atramentarii to infer species limits and the correspondence between morphological characters and species lineages, as well as to examine the phylogenetic affinities of sections Lanatuli and Atramentarii. Our analyses recovered three large clades, implying a paraphyly for section Lanatuli. Based on morphology and clade structure, we estimate ca. 38 species in the two sections, including several potentially new taxa, three of which are described herein. Coprinopsis pachyderma, C. lagopus var. vacillans, C. acuminata, C. spelaiophila, Coprinus citrinovelatus and Cop. brunneistrangulatus were found to be synonymous with other, earlier described species. Congruent with previous mating studies, our analyses recovered multiple, morphologically indistinguishable lineages within C. lagopus, which included C. lagopus var. vacillans, an ephemeral, developmental variant. Morphological traits supporting the inferred clade structure are discussed. Three new taxa (C. fusispora, C. babosiae, C. villosa), and one new combination (C. mitraespora) are proposed.
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Affiliation(s)
- László G Nagy
- Department of Microbiology, University of Szeged, Szeged, Hungary.
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78
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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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79
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Fedrowitz K, Kaasalainen U, Rikkinen J. Geographic mosaic of symbiont selectivity in a genus of epiphytic cyanolichens. Ecol Evol 2012; 2:2291-303. [PMID: 23139887 PMCID: PMC3488679 DOI: 10.1002/ece3.343] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 07/03/2012] [Accepted: 07/04/2012] [Indexed: 11/26/2022] Open
Abstract
In symbiotic systems, patterns of symbiont diversity and selectivity are crucial for the understanding of fundamental ecological processes such as dispersal and establishment. The lichen genus Nephroma (Peltigerales, Ascomycota) has a nearly cosmopolitan distribution and is thus an attractive model for the study of symbiotic interactions over a wide range of spatial scales. In this study, we analyze the genetic diversity of Nephroma mycobionts and their associated Nostoc photobionts within a global framework. The study is based on Internal Transcribed Spacer (ITS) sequences of fungal symbionts and tRNA(L) (eu) (UAA) intron sequences of cyanobacterial symbionts. The full data set includes 271 Nephroma and 358 Nostoc sequences, with over 150 sequence pairs known to originate from the same lichen thalli. Our results show that all bipartite Nephroma species associate with one group of Nostoc different from Nostoc typically found in tripartite Nephroma species. This conserved association appears to have been inherited from the common ancestor of all extant species. While specific associations between some symbiont genotypes can be observed over vast distances, both symbionts tend to show genetic differentiation over wide geographic scales. Most bipartite Nephroma species share their Nostoc symbionts with one or more other fungal taxa, and no fungal species associates solely with a single Nostoc genotype, supporting the concept of functional lichen guilds. Symbiont selectivity patterns within these lichens are best described as a geographic mosaic, with higher selectivity locally than globally. This may reflect specific habitat preferences of particular symbiont combinations, but also the influence of founder effects.
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Affiliation(s)
- Katja Fedrowitz
- Department of Ecology, Swedish University of Agricultural Sciences (SLU) P.O. 7044, SE-750 07, Uppsala, Sweden
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80
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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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Abstract
This chapter describes methods currently used for DNA barcoding of fungi, including some comments on the barcoding of aged herbarium material. The collecting procedures are focussed on macro-fungi. The laboratory methods are for medium-throughput DNA barcoding, targeted at the 96-well format, but without the assistance of robotics. In the absence of an approved and standardized DNA barcoding locus for fungi, the chapter outlines the amplification and sequencing of nuclear ribosomal genes, ITS, and LSU D1/D2 which are most widely used for the identification of fungi from diverse environments.
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Affiliation(s)
- Ursula Eberhardt
- CBS-KNAW Fungal Biodiversity Centre, Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands.
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82
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Wirtz N, Printzen C, Lumbsch HT. Using haplotype networks, estimation of gene flow and phenotypic characters to understand species delimitation in fungi of a predominantly Antarctic Usnea group (Ascomycota, Parmeliaceae). ORG DIVERS EVOL 2011. [DOI: 10.1007/s13127-011-0066-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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83
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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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84
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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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85
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Research News. IMA Fungus 2011. [DOI: 10.1007/bf03449490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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