Publications by authors named "Pradeep K Divakar"

42 Publications

Fungal Taxa Responsible for Mucormycosis/"Black Fungus" among COVID-19 Patients in India.

J Fungi (Basel) 2021 Aug 7;7(8). Epub 2021 Aug 7.

Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Complutense University of Madrid, 28040 Madrid, Spain.

Mucormycosis is caused by fungi belonging to the order Mucorales. The term "Black Fungus" has been widely applied to human pathogenic Mucorales in India. They mainly infect the sinuses and brain, lungs, stomach and intestines, and skin. While this has been considered a rare disease, thousands of cases have been reported during the second wave of COVID-19 in India, between the months of April and June 2021. Hitherto, more than 45,374 cases and over 4300 deaths have been reported among COVID-19 patients across India from April 2021 to July 21, 2021. Though the mortality rate is estimated to be 50%, it could be above 90% if left untreated. In India, has been related to be the most common species to cause human mucormycosis, followed by , , and . Accurate sample identification of human pathogenic Mucorales species is challenging especially due to the frequent lack of diagnostic morphological features. Traditionally, the culture-based approach has been extensively used to isolate and characterize human pathogenic Mucorales. However, this may not be an appropriate approach to objectively isolate and characterize all species, as the germination and growth of fungal spores are highly dependent on culture media and environmental conditions. Therefore, a robust approach to the accurate and rapid identification of human pathogenic Mucorales species is a prerequisite. The metagenomic approach comprehensively sequences and analyzes all genetic material in a complex biological sample and, consequently, this could be an appropriate approach to objectively characterize human pathogenic Mucorales taxa without the need for in vitro culture. The precise identification of the species will not only be useful for the correct diagnosis of this disease, but also for the development of antifungal drugs specific for each species. Accurate and rapid species identification is desperately needed to save lives in the mucormycosis outbreak among COVID-19 patients in India and neighboring countries.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/jof7080641DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8402169PMC
August 2021

Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota).

IMA Fungus 2020 Dec 14;11(1):27. Epub 2020 Dec 14.

Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA.

Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s43008-020-00051-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7734834PMC
December 2020

Genome-Wide Analysis of Biosynthetic Gene Cluster Reveals Correlated Gene Loss with Absence of Usnic Acid in Lichen-Forming Fungi.

Genome Biol Evol 2020 10;12(10):1858-1868

Department of Science & Education, The Field Museum, Chicago, Illinois.

Lichen-forming fungi are known to produce a large number of secondary metabolites. Some metabolites are deposited in the cortical layer of the lichen thallus where they exert important ecological functions, such as UV filtering. The fact that closely related lineages of lichen-forming fungi can differ in cortical chemistry suggests that natural product biosynthesis in lichens can evolve independent from phylogenetic constraints. Usnic acid is one of the major cortical pigments in lichens. Here we used a comparative genomic approach on 46 lichen-forming fungal species of the Lecanoromycetes to elucidate the biosynthetic gene content and evolution of the gene cluster putatively responsible for the biosynthesis of usnic acid. Whole-genome sequences were gathered from taxa belonging to different orders and families of Lecanoromycetes, where Parmeliaceae is the most well-represented taxon, and analyzed with a variety of genomic tools. The highest number of biosynthetic gene clusters was found in Evernia prunastri, Pannoparmelia angustata, and Parmotrema austrosinense, respectively, and lowest in Canoparmelia nairobiensis, Bulbothrix sensibilis, and Hypotrachyna scytodes. We found that all studied species producing usnic acid contain the putative usnic acid biosynthetic gene cluster, whereas the cluster was absent in all genomes of species lacking usnic acid. The absence of the gene cluster was supported by an additional unsuccessful search for ß-ketoacylsynthase, the most conserved domain of the gene cluster, in the genomes of species lacking usnic acid. The domain architecture of this PKS cluster-homologous to the already known usnic acid PKS cluster (MPAS) and CYT450 (MPAO)-varies within the studied species, whereas the gene arrangement is highly similar in closely related taxa. We hypothesize that the ancestor of these lichen-forming fungi contained the putative usnic acid producing PKS cluster and that the gene cluster was lost repeatedly during the evolution of these groups. Our study provides insight into the genomic adaptations to the evolutionary success of these lichen-forming fungal species and sets a baseline for further exploration of biosynthetic gene content and its evolutionary significance.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/gbe/evaa189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7643366PMC
October 2020

IMA Genome - F13: Draft genome sequences of , and .

IMA Fungus 2020 24;11:19. Epub 2020 Sep 24.

Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028 South Africa.

Draft genomes of the fungal species , and are presented. is an important lichen forming fungus and is an ambrosia beetle symbiont. and are agriculturally relevant plant pathogens that cause leaf-spots in brassicaceous vegetables and cucurbits respectively. causes severe leaf blight and defoliation of trees. These genomes provide a valuable resource for understanding the molecular processes in these economically important fungi.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s43008-020-00039-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7513301PMC
September 2020

Draft genome sequences of five species from plantations in China, , and .

IMA Fungus 2019 27;10:22. Epub 2019 Dec 27.

Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa.

Draft genome sequences of five species [including , , , and ], , and are presented. Species of are the causal agents of Eucalyptus leaf blight disease, threatening the growth and sustainability of plantations in China. is the causal agent of stem canker in native and exotic in South Africa. was first discovered in the infructescences of and in South Africa. is fruticose lichen belongs to the alectorioid clade of the family Parmeliaceae. The availability of these genome sequences will facilitate future studies on the systematics, population genetics, and genomics of these fungi.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s43008-019-0023-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325655PMC
December 2019

Discovering cryptic species in the Aspiciliella intermutans complex (Megasporaceae, Ascomycota) - First results using gene concatenation and coalescent-based species tree approaches.

PLoS One 2019 28;14(5):e0216675. Epub 2019 May 28.

Departamento de Farmacología, Farmacognosia y Botánica (U.D. Botánica), Facultad de Farmacia, Universidad Complutense, Madrid, Spain.

Taxonomic identifications in some groups of lichen-forming fungi have been challenge largely due to the scarcity of taxonomically relevant features and limitations of morphological and chemical characters traditionally used to distinguish closely related taxa. Delineating species boundaries in closely related species or species complexes often requires a range of multisource data sets and comprehensive analytical methods. Here we aim to examine species boundaries in a group of saxicolous lichen forming fungi, the Aspiciliella intermutans complex (Megasporaceae), widespread mainly in the Mediterranean. We gathered DNA sequences of the nuclear ribosomal internal transcribed spacer (nuITS), the nuclear large subunit (nuLSU), the mitochondrial small subunit (mtSSU) ribosomal DNA, and the DNA replication licensing factor MCM7 from 80 samples mostly from Iran, Caucasia, Greece and eastern Europe. We used a combination of phylogenetic strategies and a variety of empirical, sequence-based species delimitation approaches to infer species boundaries in this group. The latter included: the automatic barcode gap discovery (ABGD), the multispecies coalescent approach *BEAST and Bayesian Phylogenetics and Phylogeography (BPP) program. Different species delimitation scenarios were compared using Bayes factors species delimitation analysis. Furthermore, morphological, chemical, ecological and geographical features of the sampled specimens were examined. Our study uncovered cryptic species diversity in A. intermutans and showed that morphology-based taxonomy may be unreliable, underestimating species diversity in this group of lichens. We identified a total of six species-level lineages in the A. intermutans complex using inferences from multiple empirical operational criteria. We found little corroboration between morphological and ecological features with our proposed candidate species, while secondary metabolite data do not corroborate tree topology. The present study on the A. intermutans species-complex indicates that the genus Aspiciliella, as currently circumscribed, is more diverse in Eurasia than previously expected.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0216675PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6538240PMC
January 2020

Lichens of Parmelioid Clade as Promising Multitarget Neuroprotective Agents.

Chem Res Toxicol 2019 06 7;32(6):1165-1177. Epub 2019 Jun 7.

Department of Pharmacology, Pharmacognosy and Botanical, Faculty of Pharmacy , Universidad Complutense de Madrid, Plaza Ramon y Cajal s/n, Ciudad Universitaria , 28040 , Madrid , Spain.

Neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease are multifactorial disorders which are increasing in incidence and prevalence over the world without existing effective therapies. The search for new multitarget compounds is the latter therapeutic strategy to address these pathological conditions. Lichens have an important and unknown therapeutic value attributed to their unique secondary metabolites. The aim of this study is to evaluate for the first time the in vitro neuroprotective activities and molecular mechanisms underlying methanol extracts of lichens of the parmelioid clade and to characterize major bioactive secondary metabolites responsible for their pharmacological actions. Of the 15 parmelioid lichen species, our results showed that Parmotrema perlatum and Hypotrachyna formosana methanol extracts exhibited high antioxidant activity as evidenced in ORAC, DPPH, and FRAP assays. Then, SH-SY5Y cells were pretreated with methanol extracts (24 h) followed by Fenton reagent exposure (2 h). Pretreatments with these two more antioxidant methanol lichen extracts increased cell viability, reduced intracellular ROS, prevented oxidative stress biomarkers accumulation, and upregulated antioxidant enzyme (CAT, SOD, GR, and GPx) activity compared to Fenton reagent cells. The neuroprotective activity was much higher for H. formosana than for P. perlatum, even equal to or higher than Trolox (reference compound). Moreover, H. formosana extracts inhibited both AChE and BuChE activities in a concentration dependent manner, and P. perlatum only showed concentration dependent activity against AChE. Finally, chemical composition analysis using TLC and HPLC methods revealed that physodic acid, lividic acid, and lichexanthone are major secondary metabolites in H. formosana and stictic acid and constictic acid are in P. perlatum. These results demonstrated that P. perlatum and, specially, H. formosana are promising multitargeted neuroprotective agents due to their antioxidant and AChE and BuChE inhibition activities.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.chemrestox.9b00010DOI Listing
June 2019

gen. nov. and (Lecanorales, Protoparmelioideae): species description and generic delimitation using DNA barcodes and phenotypical characters.

MycoKeys 2018 14(44):19-50. Epub 2018 Dec 14.

Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.

Multilocus phylogenetic studies revealed a high level of cryptic diversity within the lichen-forming fungal genus (Protoparmelioideae, Parmeliaceae). Coalescent-based species delimitation suggested that most of the cryptic molecular lineages warranted recognition as separate species. Here we study the morphology and chemistry of these taxa and formally describe eight new species based on phenotypical and molecular characters. Further, we evaluate the use of ITS rDNA as a DNA barcode for identifying species in this genus. For the first time, we obtained an ITS sequence of , the type species of the genus and showed that it is phylogenetically not closely related to species currently placed in or . We assembled a dataset of 66 ITS sequences to assess the interspecies genetic distances amongst the twelve species using ITS as DNA barcode. We found that and form a supported monophyletic group whereas is sister to both. We therefore propose a new genus to accommodate the tropical-subtropical species within Protoparmelioideae, with as the type, , , , , , , and as new species and , , , and as new proposed combinations. We provide a key to and confirm the use of ITS for accurately identifying species in this group.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3897/mycokeys.44.29904DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303283PMC
December 2018

Environment and host identity structure communities of green algal symbionts in lichens.

New Phytol 2018 Jan 11;217(1):277-289. Epub 2017 Sep 11.

Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany.

An understanding of how biotic interactions shape species' distributions is central to predicting host-symbiont responses under climate change. Switches to locally adapted algae have been proposed to be an adaptive strategy of lichen-forming fungi to cope with environmental change. However, it is unclear how lichen photobionts respond to environmental gradients, and whether they play a role in determining the fungal host's upper and lower elevational limits. Deep-coverage Illumina DNA metabarcoding was used to track changes in the community composition of Trebouxia algae associated with two phylogenetically closely related, but ecologically divergent fungal hosts along a steep altitudinal gradient in the Mediterranean region. We detected the presence of multiple Trebouxia species in the majority of thalli. Both altitude and host genetic identity were strong predictors of photobiont community assembly in these two species. The predominantly clonally dispersing fungus showed stronger altitudinal structuring of photobiont communities than the sexually reproducing host. Elevation ranges of the host were not limited by the lack of compatible photobionts. Our study sheds light on the processes guiding the formation and distribution of specific fungal-algal combinations in the lichen symbiosis. The effect of environmental filtering acting on both symbiotic partners appears to shape the distribution of lichens.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/nph.14770DOI Listing
January 2018

Circumscription of the genus Lepra, a recently resurrected genus to accommodate the "Variolaria"-group of Pertusaria sensu lato (Pertusariales, Ascomycota).

PLoS One 2017 11;12(7):e0180284. Epub 2017 Jul 11.

Science & Education, The Field Museum, Chicago, Illinois, United States of America.

Pertusarialean lichens include more than 300 species belonging to several independent phylogenetic lineages. Only some of these phylogenetic clades have been comprehensively sampled for molecular data, and formally described as genera. Here we present a taxonomic treatment of a group of pertusarialean lichens formerly known as "Pertusaria amara-group", "Monomurata-group", or "Variolaria-group", which includes widespread and well-known taxa such as P. amara, P. albescens, or P. ophthalmiza. We generated a 6-locus data set with 79 OTUs representing 75 species. The distinction of the Variolaria clade is supported and consequently, the resurrection of the genus Lepra is followed. Thirty-five new combinations into Lepra are proposed and the new species Lepra austropacifica is described from mangroves in the South Pacific. Lepra is circumscribed to include species with disciform ascomata, a weakly to non-amyloid hymenial gel, strongly amyloid asci without clear apical amyloid structures, containing 1 or 2, single-layered, thin-walled ascospores. Chlorinated xanthones are not present, but thamnolic and picrolichenic acids occur frequently, as well as orcinol depsides. Seventy-one species are accepted in the genus. Although the distinction of the genus from Pertusaria is strongly supported, the relationships of Lepra remain unresolved and the genus is tentatively placed in Pertusariales incertae sedis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0180284PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5507398PMC
September 2017

A temporal banding approach for consistent taxonomic ranking above the species level.

Sci Rep 2017 05 23;7(1):2297. Epub 2017 May 23.

Science & Education, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL, 60605, USA.

Comparable taxonomic ranks within clades can facilitate more consistent classifications and objective comparisons among taxa. Here we use a temporal approach to identify taxonomic ranks. This is an extension of the temporal banding approach including a Temporal Error Score that finds an objective cut-off for each taxonomic rank using information for the current classification. We illustrate this method using a data set of the lichenized fungal family Parmeliaceae. To assess its performance, we simulated the effect of taxon sampling and compared our method with the other temporal banding method. For our sampled phylogeny, 11 of the 12 included families remained intact and 55 genera were confirmed, whereas 32 genera were lumped and 15 genera were split. Taxon sampling impacted the method at the genus level, whereas yielded only insignificant changes at the family level. The other available temporal approach also gives a similar cutoff point to our method. Our approach to identify taxonomic ranks enables taxonomists to revise and propose classifications on an objective basis, changing ranks of clades only when inconsistent with most taxa in a phylogenetic tree. An R script to find the time point with the minimal temporal error is provided.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-017-02477-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5442095PMC
May 2017

Panmixia and dispersal from the Mediterranean Basin to Macaronesian Islands of a macrolichen species.

Sci Rep 2017 01 19;7:40879. Epub 2017 Jan 19.

Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain.

The Mediterranean region, comprising the Mediterranean Basin and the Macaronesian Islands, represents a center of diversification for many organisms. The genetic structure and connectivity of mainland and island microbial populations has been poorly explored, in particular in the case of symbiotic fungi. Here we investigated genetic diversity and spatial structure of the obligate outcrossing lichen-forming fungus Parmelina carporrhizans in the Mediterranean region. Using eight microsatellite and mating-type markers we showed that fungal populations are highly diverse but lack spatial structure. This is likely due to high connectivity and long distance dispersal of fungal spores. Consistent with low levels of linkage disequilibrium and lack of clonality, we detected both mating-type idiomorphs in all populations. Furthermore we showed that the Macaronesian Islands are the result of colonization from the Mediterranean Basin. The unidirectional gene flow, though, seemed not to be sufficient to counterbalance the effects of drift, resulting in comparatively allelic poor peripheral populations. Our study is the first to shed light on the high connectivity and lack of population structure in natural populations of a strictly sexual lichen fungus. Our data further support the view of the Macaronesian Islands as the end of the colonization road for this symbiotic ascomycete.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep40879DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5244402PMC
January 2017

Fungal-algal association patterns in lichen symbiosis linked to macroclimate.

New Phytol 2017 Apr 5;214(1):317-329. Epub 2016 Dec 5.

Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Frankfurt am Main, Germany.

Both macroclimate and evolutionary events may influence symbiont association and diversity patterns. Here we assess how climatic factors and evolutionary events shape fungal-algal association patterns in the widely distributed lichen-forming fungal genus Protoparmelia. Multilocus phylogenies of fungal and algal partners were generated using 174 specimens. Coalescent-based species delimitation analysis suggested that 23 fungal hosts are associating with 20 algal species. Principal component analysis (PCA) was performed to infer how fungal-algal association patterns varied with climate. Fungi associated with one to three algal partners whereas algae accepted one to five fungal partners. Both fungi and algae were more specific, associating with fewer partners, in the warmer climates. Interaction with more than one partner was more frequent in cooler climates for both the partners. Cophylogenetic analyses suggest congruent fungal-algal phylogenies. Host switch was a more common event in warm climates, whereas failure of the photobiont to diverge with its fungal host was more frequent in cooler climates. We conclude that both environmental factors and evolutionary events drive fungal and algal evolution in Protoparmelia. The processes leading to phylogenetic congruence of fungi and algae are different in different macrohabitats in our study system. Hence, closely related species inhabiting diverse habitats may follow different evolutionary pathways.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/nph.14366DOI Listing
April 2017

Hidden diversity before our eyes: Delimiting and describing cryptic lichen-forming fungal species in camouflage lichens (Parmeliaceae, Ascomycota).

Fungal Biol 2016 11;120(11):1374-1391

Science & Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA.

Molecular data provide unprecedented insight into diversity of lichenized fungi, although morphologically cryptic species-level lineages circumscribed from sequence data often remain undescribed even in well-studies groups. Using diagnostic characters from DNA sequence data and support from the multispecies coalescent model, we formally describe a total of eleven new species and resurrect two others in the hyperdiverse lichen-forming fungal family Parmeliaceae. These include: four in the genus Melanelixia - M. ahtii sp. nov., M. epilosa comb. nov., M. hawksworthii sp. nov., and M. robertsoniorum sp. nov.; six in Melanohalea - M. austroamericana sp. nov., M. beringiana sp. nov., M. clari sp. nov., M. columbiana sp. nov., M. davidii sp. nov., and M. tahltan sp. nov.; and three species in Montanelia - M. occultipanniformis sp. nov., M. saximontana comb. nov., and M. secwepemc sp. nov. Morphological, ecological and geographical features were revised to corroborate species descriptions. These species can consistently be distinguished by differences in nucleotide position characters in the fungal barcoding marker (ITS) and high speciation probabilities. This study helps close the "taxonomic gap" between molecular species delimitation studies and formal taxonomy by incorporating statistical evaluation of lineage independence, diagnostic differences in DNA data, and additional consideration of differences in morphology and species distributions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.funbio.2016.06.001DOI Listing
November 2016

A Festschrift for David L. Hawksworth.

Fungal Biol 2016 11 20;120(11):1269-1271. Epub 2016 Aug 20.

Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA. Electronic address:

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.funbio.2016.08.003DOI Listing
November 2016

An Integrative Approach for Understanding Diversity in the Punctelia rudecta Species Complex (Parmeliaceae, Ascomycota).

PLoS One 2016 10;11(2):e0146537. Epub 2016 Feb 10.

Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, Madrid, Spain.

High levels of cryptic diversity have been documented in lichenized fungi, especially in Parmeliaceae, and integrating various lines of evidence, including coalescent-based species delimitation approaches, help establish more robust species circumscriptions. In this study, we used an integrative taxonomic approach to delimit species in the lichen-forming fungal genus Punctelia (Parmeliaceae), with a particular focus on the cosmopolitan species P. rudecta. Nuclear, mitochondrial ribosomal DNA and protein-coding DNA sequences were analyzed in phylogenetic and coalescence-based frameworks. Additionally, morphological, ecological and geographical features of the sampled specimens were evaluated. Five major strongly supported monophyletic clades were recognized in the genus Punctelia, and each clade could be characterized by distinct patterns in medullary chemistry. Punctelia rudecta as currently circumscribed was shown to be polyphyletic. A variety of empirical species delimitation methods provide evidence for a minimum of four geographically isolated species within the nominal taxon Punctelia rudecta, including a newly described saxicolous species, P. guanchica, and three corticolous species. In order to facilitate reliable sample identification for biodiversity, conservation, and air quality bio-monitoring research, these three species have been epitypified, in addition to the description of a new species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0146537PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4749632PMC
July 2016

Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi.

New Phytol 2015 Dec 24;208(4):1217-26. Epub 2015 Aug 24.

Biodiversity and Climate Research Centre BiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.

We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/nph.13553DOI Listing
December 2015

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 07 14;24(14):3779-97. Epub 2015 Jul 14.

Science & Education, The Field Museum, Chicago, IL, USA.

Microbial symbionts are instrumental to the ecological and long-term evolutionary success of their hosts, and the central role of symbiotic interactions is increasingly recognized across the vast majority of life. Lichens provide an iconic group for investigating patterns in species interactions; however, relationships among lichen symbionts are often masked by uncertain species boundaries or an inability to reliably identify symbionts. The species-rich lichen-forming fungal family Parmeliaceae provides a diverse group for assessing patterns of interactions of algal symbionts, and our study addresses patterns of lichen symbiont interactions at the largest geographic and taxonomic scales attempted to date. We analysed a total of 2356 algal internal transcribed spacer (ITS) region sequences collected from lichens representing ten mycobiont genera in Parmeliaceae, two genera in Lecanoraceae and 26 cultured Trebouxia strains. Algal ITS sequences were grouped into operational taxonomic units (OTUs); we attempted to validate the evolutionary independence of a subset of the inferred OTUs using chloroplast and mitochondrial loci. We explored the patterns of symbiont interactions in these lichens based on ecogeographic distributions and mycobiont taxonomy. We found high levels of undescribed diversity in Trebouxia, broad distributions across distinct ecoregions for many photobiont OTUs and varying levels of mycobiont selectivity and specificity towards the photobiont. Based on these results, we conclude that fungal specificity and selectivity for algal partners play a major role in determining lichen partnerships, potentially superseding ecology, at least at the ecogeographic scale investigated here. To facilitate effective communication and consistency across future studies, we propose a provisional naming system for Trebouxia photobionts and provide representative sequences for each OTU circumscribed in this study.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/mec.13271DOI Listing
July 2015

Who's getting around? Assessing species diversity and phylogeography in the widely distributed lichen-forming fungal genus Montanelia (Parmeliaceae, Ascomycota).

Mol Phylogenet Evol 2015 Sep 16;90:85-96. Epub 2015 May 16.

Science & Education, The Field Museum, Chicago, IL, USA.

Brown parmelioid lichens comprise a number of distinct genera in one of the most species-rich families of lichen-forming fungi, Parmeliaceae (Ascomycota). In spite of their superficial similarity, a number of studies of brown parmelioids have provided important insight into diversification in lichen-forming fungi with cosmopolitan distributions. In this study we assess species diversity, biogeography and diversification of the genus Montanelia, which includes alpine to temperate saxicolous species. We sampled each of the five known species, four of which are known from broad, intercontinental distributions. In order to identify potential biogeographical patterns, each broadly distributed species was represented by individuals collected across their intercontinental distributions. Molecular sequence data were generated for six loci, including three nuclear protein-coding markers (MCM7, RPB1, and RPB2), two nuclear ribosomal markers (ITS and nrLSU), and a fragment of the mitochondrial small subunit. We used three sequence-based species delimitations methods to validate traditional, phenotype-based species and circumscribe previously unrecognized species-level lineages in Montanelia. Relationships among putative lineages and divergence times were estimated within a coalescent-based multi-locus species tree framework. Based on the results of the species delimitation analyses, we propose that the genus Montanelia is likely comprised of six to nine species-level lineages, including previously unrecognized species-level diversity in the nominal taxa M. panniformis and M. tominii. In contrast, molecular sequence data suggest that M. predisjuncta may be conspecific with the widespread taxon M. disjuncta in spite of distinct morphological differences. The rate-based age estimation of the most recent common ancestor of Montanelia (ca. 23.1Ma) was similar to previous estimates based on the fossil record. Furthermore, our data suggest that diversification in Montanelia occurred largely during the Neogene. At least three Montanelia species are broadly distributed throughout Asia, Europe, and North America with no evidence of phylogeographic substructure. In contrast to broadly distributed Montanelia species, our study suggests Pleistocene-dominated diversification and complex biogeographic history in the M. tominii group. Our analyses provide additional insight for understanding diversification and uncovering cryptic diversity in cosmopolitan species of lichen-forming fungi.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ympev.2015.04.029DOI Listing
September 2015

A Tale of Two Hyper-diversities: Diversification dynamics of the two largest families of lichenized fungi.

Sci Rep 2015 May 6;5:10028. Epub 2015 May 6.

Science and Education, The Field Museum, 1400 S Lake Shore Drive, Chicago, IL 60605 USA.

Renewed interests in macroevolutionary dynamics have led to the proliferation of studies on diversification processes in large taxonomic groups, such as angiosperms, mammals, and birds. However, such a study has yet to be conducted in lichenized fungi--an extremely successful and diverse group of fungi. Analysing the most comprehensive time-calibrated phylogenies with a new analytical method, we illustrated drastically different diversification dynamics between two hyper-diverse families of lichenized fungi, Graphidaceae and Parmeliaceae, which represent more than a fourth of the total species diversity of lichenized fungi. Despite adopting a similar nutrition mode and having a similar number of species, Graphidaceae exhibited a lower speciation rate, while Parmeliaceae showed a sharp increase in speciation rate that corresponded with the aridification during the Oligocene-Miocene transition, suggesting their adaptive radiation into a novel arid habitat.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep10028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4421861PMC
May 2015

Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota).

PLoS One 2015 1;10(5):e0124625. Epub 2015 May 1.

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.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0124625PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4416777PMC
January 2016

Characterization of fungus-specific microsatellite markers in the lichen-forming fungus Parmelina carporrhizans (Parmeliaceae).

Appl Plant Sci 2014 Dec 20;2(12). Epub 2014 Nov 20.

Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, Madrid 28040, Spain.

Unlabelled:

Premise Of The Study: Microsatellite loci were developed to study the lichen-forming fungus Parmelina (Parmeliaceae) in different habitats of western Europe and the Mediterranean for baseline studies to understand the effects of climate change on its distribution. •

Methods And Results: We cultured P. carporrhizans from ascospores for genomic sequencing with Illumina HiSeq. We successfully developed 11 polymorphic microsatellite markers and associated primer sets and assessed them with 30 individuals from two of the Canary Islands. The average number of alleles per locus was 8.8. Nei's unbiased gene diversity of these loci ranged from 0.53 to 0.91 in the tested populations. Amplification in two closely related species (P. tiliacea, P. cryptotiliacea) yielded only limited success. •

Conclusions: The new microsatellite markers will allow the study of genetic diversity and population structure in P. carporrhizans. We propose eight markers to combine in two multiplex reactions for further studies on a larger set of populations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3732/apps.1400081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4259457PMC
December 2014

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

Database (Oxford) 2014 30;2014. Epub 2014 Jun 30.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands, Department of Pharmaceutical Sciences - Microbiology, Università degli Studi di Perugia, Perugia, Italy, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The University of Sydney, Westmead Millennium Institute, Westmead, Australia, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden, Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37920, USA, Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK, Natural History Museum, University of Tartu, 46 Vanemuise, 51014 Tartu, Estonia, Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, USA, Institute of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand, Imperial College London, Royal Botanic Gardens, Kew TW9 3DS, England, UK, Muséum National d'Histoire Naturelle, Dépt. Systématique et Evolution CP39, UMR7205, 12 Rue Buffon, F-75005 Paris, France, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, P. R. China, Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain, Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany, Department of Microbiology and Plant Pathology, Forestry Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0001, South Africa, Real Jardín Botánico, RJB-CSIC,

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/database/bau061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4075928PMC
February 2015

Non-developing ascospores in apothecia of asexually reproducing lichen-forming fungi.

Int Microbiol 2013 Sep;16(3):145-55

Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, USA.

The presence of apothecia in mixed species (vegetatively reproducing lichens, occasionally producing ascomata) has been interpreted as a mechanism to increase genetic variability in mostly clonal populations. However, spore viability from these apothecia has not been studied. We asked whether ascospores of the mixed species Physconia grisea are viable and thereby contribute to increasing the genetic diversity within populations of this species. An ontogenetic study of spores in cultures of P. grisea and a related sexual species (P. distorta), showed that although mature apothecia from both species produced and discharged meiospores capable of germination, spores from P. grisea were only rarely (0.43%) able to continue development whereas those from P. distorta germinated and developed successfully. The strongly reduced viability of P. grisea spores suggested that they do not have a strong reproductive function, at least in the two local populations analyzed. Additionally, we show that the segregation of Physconia grisea ssp. lilacina does not have molecular support.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2436/20.1501.01.189DOI Listing
September 2013

Insights into intrathalline genetic diversity of the cosmopolitan lichen symbiotic green alga Trebouxia decolorans Ahmadjian using microsatellite markers.

Mol Phylogenet Evol 2014 Mar 8;72:54-60. Epub 2014 Jan 8.

Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany; Institute of Ecology, Evolution and Diversity, Goethe Universität, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany.

Trebouxia decolorans is a widespread and common symbiotic green alga that is found in association with different species of lichen-forming fungi. By applying T. decolorans-specific microsatellite markers, we investigated the within-thallus diversity of T. decolorans in thalli of Xanthoria parietina and Anaptychia ciliaris. We found several algal strains in most of the thalli of both hosts. High genetic differentiation among thalli suggests that algal diversity is generated de novo via mutation in both fungal hosts. Rarefied allelic richness of the algae was higher in thalli of X. parietina. Our results indicate that in X. parietina intrathalline algal diversity is additionally created by environmental uptake of algae either at the start of the symbiotic association or during the lifetime of the thallus. This study indicates that promiscuous host-symbiont associations in lichen symbioses with Trebouxia spp. may be more common than currently recognized.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ympev.2013.12.010DOI Listing
March 2014

Understanding phenotypical character evolution in parmelioid lichenized fungi (Parmeliaceae, Ascomycota).

PLoS One 2013 29;8(11):e83115. Epub 2013 Nov 29.

Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain.

Parmelioid lichens form a species-rich group of predominantly foliose and fruticose lichenized fungi encompassing a broad range of morphological and chemical diversity. Using a multilocus approach, we reconstructed a phylogeny including 323 OTUs of parmelioid lichens and employed ancestral character reconstruction methods to understand the phenotypical evolution within this speciose group of lichen-forming fungi. Specifically, we were interested in the evolution of growth form, epicortex structure, and cortical chemistry. Since previous studies have shown that results may differ depending on the reconstruction method used, here we employed both maximum-parsimony and maximum-likelihood approaches to reconstruct ancestral character states. We have also implemented binary and multistate coding of characters and performed parallel analyses with both coding types to assess for potential coding-based biases. We reconstructed the ancestral states for nine well-supported major clades in the parmelioid group, two higher-level sister groups and the ancestral character state for all parmelioid lichens. We found that different methods for coding phenotypical characters and different ancestral character state reconstruction methods mostly resulted in identical reconstructions but yield conflicting inferences of ancestral states, in some cases. However, we found support for the ancestor of parmelioid lichens having been a foliose lichen with a non-pored epicortex and pseudocyphellae. Our data suggest that some traits exhibit patterns of evolution consistent with adaptive radiation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0083115PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3843734PMC
August 2014

The sister-group relationships of the largest family of lichenized fungi, Parmeliaceae (Lecanorales, Ascomycota).

Fungal Biol 2013 Oct 13;117(10):715-21. Epub 2013 Aug 13.

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. Electronic address:

Parmeliaceae is the largest family of lichen-forming fungi. In spite of its importance for fungal diversity, its relationships with other families in Lecanorales remain poorly known. To better understand the evolutionary history of the diversification of lineages and species richness in Parmeliaceae it is important to know the phylogenetic relationships of the closest relatives of the family. A recent study based on two molecular loci suggested that either Protoparmelia s. str. or a group consisting of Gypsoplaca and Protoparmelia s. str. were the possible sister-group candidates of Parmeliaceae, but that study could not distinguish between these two alternatives. Here, we used a four-locus phylogeny (nuLSU, ITS, RPB1, MCM7) to reveal relationships of Parmeliaceae with other potential relatives in Lecanorales. Maximum likelihood and Bayesian analyses showed that Protoparmelia is polyphyletic, with Protoparmelia s. str. (including Protoparmelia badia and Protoparmelia picea) being most closely related to Parmeliaceae s. str., while the Protoparmelia atriseda-group formed the sister-group to Miriquidica. Gypsoplaca formed the sister-group to the Parmeliaceae s. str. + Protoparmelia s. str. clade. Monophyly of Protoparmelia as currently circumscribed, and Gypsoplaca as sister-group to Parmeliaceae s. str. were both significantly rejected by alternative hypothesis testing.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.funbio.2013.08.001DOI Listing
October 2013

The lichen genus parmotrema in South Korea.

Mycobiology 2013 Mar 28;41(1):25-36. Epub 2013 Mar 28.

Korean Lichen Research Institute, Sunchon National University, Suncheon 540-742, Korea.

Parmotrema A. Massal. is a common lichen genus scattered throughout the Korean Peninsula; however, no detailed taxonomic or revisionary study of this genus has been conducted for nearly two decades. Therefore, this study revised the taxonomy of this genus based on specimens deposited in the lichen herbarium at the Korean Lichen Research Institute and samples wereidentified using recent literature. In this revisionary study, a total of eighteen species of Parmotrema including eight new records [Parmotrema cetratum (Ach.) Hale, Parmotrema cristiferum (Taylor) Hale, Parmotrema grayanum (Hue) Hale, Parmotrema defectum (Hale) Hale, Parmotrema dilatatum (Vain.) Hale, Parmotrema margaritatum (Hue) Hale, Parmotrema pseudocrinitum (Abbayes) Hale, and Parmotrema subsumptum (Nyl.) Hale] are documented. Detailed descriptions of each species with their morphological, anatomical and chemical characteristics are also given and a key to the known Parmotrema species of the Korean Peninsula is presented.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5941/MYCO.2013.41.1.25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3627967PMC
March 2013

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 Aug 16;68(2):357-72. Epub 2013 Apr 16.

Conservatoire et Jardin botaniques de la Ville de Genève, CP 60, 1292 Chambésy, Switzerland.

In lichen-forming fungi, traditional taxonomical concepts are frequently in conflict with molecular data, and identifying appropriate taxonomic characters to describe phylogenetic clades remains challenging in many groups. The selection of suitable markers for the reconstruction of solid phylogenetic hypotheses is therefore fundamental. The lichen genus Usnea is highly diverse, with more than 350 estimated species, distributed in polar, temperate and tropical regions. The phylogeny and classification of Usnea have been a matter of debate, given the lack of phenotypic characters to describe phylogenetic clades and the low degree of resolution of phylogenetic trees. In this study, we investigated the phylogenetic relationships of 52 Usnea species from across the genus, based on ITS rDNA, nuLSU, and two protein-coding genes RPB1 and MCM7. ITS comprised several highly variable regions, containing substantial genetic signal, but also susceptible to causing bias in the generation of the alignment. We compared several methods of alignment of ITS and found that a simultaneous optimization of alignment and phylogeny (using BAli-phy) improved significantly both the topology and the resolution of the phylogenetic tree. However the resolution was even better when using protein-coding genes, especially RPB1 although it is less variable. The phylogeny based on the concatenated dataset revealed that the genus Usnea is subdivided into four highly-supported clades, corresponding to the traditionally circumscribed subgenera Eumitria, Dolichousnea, Neuropogon and Usnea. However, characters that have been used to describe these clades are often homoplasious within the phylogeny and their parallel evolution is suggested. On the other hand, most of the species were reconstructed as monophyletic, indicating that combinations of phenotypic characters are suitable discriminators for delimitating species, but are inadequate to describe generic subdivisions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ympev.2013.04.005DOI Listing
August 2013

Diversification of the newly recognized lichen-forming fungal lineage Montanelia (Parmeliaceae, Ascomycota) and its relation to key geological and climatic events.

Am J Bot 2012 Dec 30;99(12):2014-26. Epub 2012 Nov 30.

Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain.

Unlabelled:

Premise Of The Study: In spite of the recent advances in generic and species circumscriptions and in recognizing species diversity in lichen-forming fungi, the timing of speciation and the factors that promote diversification in lichens remain largely unexplored. We used brown parmelioids as a model to assess the timing of divergence and explore the impact of geological and climatic events on lineage divergence and diversification in lichenized fungi. Additionally, to clarify the phylogenetic position of the species currently placed in Melanelia disjuncta group, we evaluated the taxonomic status and phylogenetic relationships within Parmeliaceae. •

Methods: Phylogenetic relationships and divergence time estimates were inferred from a four-loci data set. Alternative hypotheses were tested using Shimodaira-Hasegawa and expected likelihood weights tests. •

Key Results: The M. disjuncta group forms a strongly supported, monophyletic lineage independent from Melanelia s.s. The M. disjuncta clade arose ca. 23.1 million years ago (Ma). Our results suggest that most of the lineages within the clade diversified during the Miocene (17.6 to 11.2 Ma). The split of other brown parmelioids, such as Emodomelanelia-Melanelixia occurred ca. 41.70 Ma, and the radiation of Melanelixia began during the Eocene-Oligocene transition (ca. 33.75 Ma). •

Conclusions: Montanelia is described here as a new genus to accommodate species of the Melanelia disjuncta group. Further, the study indicates that the current species delimitation within the newly described genus requires revision. We provide evidence of lineage divergence of Montanelia at the Oligocene-Miocene boundary. Our results indicate that the diversification during Miocene would have happened during major mountain uplifts.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3732/ajb.1200258DOI Listing
December 2012
-->