Providing Scale to a Known Taxonomic Unknown—At Least a 70-Fold Increase in Species Diversity in a Cosmopolitan Nominal Taxon of Lichen-Forming Fungi

The guilds in green algal lichens – an insight into the life of terrestrial symbiotic communities

(2022) Ondřej Peksa et al.   FEMS MICROBIOLOGY ECOLOGY

mold , a novel software to compile accurate and reliable DNA diagnoses for taxonomic descriptions

(2022) Alexander Fedosov et al.   Molecular Ecology Resources

Why sequence all eukaryotes?

(2022) Mark Blaxter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput sequencing view on the magnitude of global fungal diversity

(2021) Petr Baldrian et al.   FUNGAL DIVERSITY

Effects of dispersal strategy and migration history on genetic diversity and population structure of Antarctic lichens

(2021) Elisa Lagostina et al.   JOURNAL OF BIOGEOGRAPHY

Incorporating the speciation process into species delimitation

(2021) Jeet Sukumaran et al.   PLoS Computational Biology

What are fungal species and how to delineate them?

(2021) K. W. Thilini Chethana et al.   FUNGAL DIVERSITY

Integrative approaches for species delimitation in Ascomycota

(2021) Sajeewa S. N. Maharachchikumbura et al.   FUNGAL DIVERSITY

Phylogenomic reconstruction addressing the Peltigeralean backbone (Lecanoromycetes, Ascomycota)

(2021) Todd J. Widhelm et al.   FUNGAL DIVERSITY

Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics

(2021) Robert Lücking et al.   FUNGAL DIVERSITY

Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron

(2021) Chao‐Nan Fu et al.   Molecular Ecology Resources

Turnover of Lecanoroid Mycobionts and Their Trebouxia Photobionts Along an Elevation Gradient in Bolivia Highlights the Role of Environment in Structuring the Lichen Symbiosis

(2021) Ian D. Medeiros et al.   Frontiers in Microbiology

Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi

(2020) Michael Bradshaw et al.   BMC EVOLUTIONARY BIOLOGY

Contrasting co‐occurrence patterns of photobiont and cystobasidiomycete yeast associated with common epiphytic lichen species

(2020) Kristiina Mark et al.   NEW PHYTOLOGIST

Genome-scale data reveal the role of hybridization in lichen-forming fungi

(2020) Rachel Keuler et al.   Scientific Reports

Expanding the mutualistic niche: parallel symbiont turnover along climatic gradients

(2020) Gregor Rolshausen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Complete, high-quality genomes from long-read metagenomic sequencing of two wolf lichen thalli reveals enigmatic genome architecture

(2020) Sean K. McKenzie et al.   GENOMICS

ASAP: Assemble Species by Automatic Partitioning

(2020) Nicolas Puillandre et al.   Molecular Ecology Resources

SODA: multi-locus species delimitation using quartet frequencies

(2020) Maryam Rabiee et al.   BIOINFORMATICS

Two Basidiomycete Fungi in the Cortex of Wolf Lichens

(2019) Veera Tuovinen et al.   CURRENT BIOLOGY

More grist for the mill? Species delimitation in the genomic era and its implications for conservation

(2019) David W. G. Stanton et al.   CONSERVATION GENETICS

Parallel Miocene dispersal events explain the cosmopolitan distribution of the Hypogymnioid lichens

(2019) Pradeep K. Divakar et al.   JOURNAL OF BIOGEOGRAPHY

The phylogenetic position of species of Lecanora s. l. containing calycin and usnic acid, with the description of Lecanora solaris Yakovchenko & Davydov sp. nov.

(2019) Lidia S. YAKOVCHENKO et al.   LICHENOLOGIST

DNA sequence-based identification and barcoding of a morphologically highly plastic lichen forming fungal genus (Parmotrema, Parmeliaceae) from the tropics

(2019) Ruth Del-Prado et al.   BRYOLOGIST

Process‐based species delimitation leads to identification of more biologically relevant species

(2019) Megan L. Smith et al.   EVOLUTION

Population genomics revealed cryptic species within host-specific zombie-ant fungi (Ophiocordyceps unilateralis)

(2019) Noppol Kobmoo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The New Tree of Eukaryotes

(2019) Fabien Burki et al.   TRENDS IN ECOLOGY & EVOLUTION

Relative symbiont input and the lichen symbiotic outcome

(2018) Toby Spribille   CURRENT OPINION IN PLANT BIOLOGY

Multiple, Distinct Intercontinental Lineages but Isolation of Australian Populations in a Cosmopolitan Lichen-Forming Fungal Taxon, Psora decipiens (Psoraceae, Ascomycota)

(2018) Steven D. Leavitt et al.   Frontiers in Microbiology

Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae)

(2018) C.G. Boluda et al.   PERSOONIA

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

(2018) Rolf Henrik Nilsson et al.   NUCLEIC ACIDS RESEARCH

Species delimitation at a global scale reveals high species richness with complex biogeography and patterns of symbiont association in Peltigera section Peltigera (lichenized Ascomycota: Lecanoromycetes)

(2018) Nicolas Magain et al.   TAXON

Population genomic analyses of RAD sequences resolves the phylogenetic relationship of the lichen-forming fungal species Usnea antarctica and Usnea aurantiacoatra

(2018) Felix Grewe et al.   MycoKeys

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Turbo-taxonomy to assemble a megadiverse lichen genus: seventy new species of Cora (Basidiomycota: Agaricales: Hygrophoraceae), honouring David Leslie Hawksworth’s seventieth birthday

(2016) Robert Lücking et al.   FUNGAL DIVERSITY

Escape from the cryptic species trap: lichen evolution on both sides of a cyanobacterial acquisition event

(2016) Kevin Schneider et al.   MOLECULAR ECOLOGY

Cryptic diversity and symbiont interactions in rock-posy lichens

(2016) Steven D. Leavitt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Basidiomycete yeasts in the cortex of ascomycete macrolichens

(2016) Toby Spribille et al.   SCIENCE

A new species and new records of Lecanora (Lecanoraceae, lichenized Ascomycota) with usnic acid from the Antarctic region

(2016) IRIS NADIA DE LA ROSA et al.   Phytotaxa

Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches

(2016) Steven D. Leavitt et al.   Scientific Reports

The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences

(2016) Nirav Merchant et al.   PLOS BIOLOGY

HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

(2016) Matthew G. Johnson et al.   Applications in Plant Sciences

A DNA barcoding approach for identification of hidden diversity in Parmeliaceae (Ascomycota):Parmelia sensu strictoas a case study

(2015) Pradeep K. Divakar et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Towards a revised generic classification of lecanoroid lichens (Lecanoraceae, Ascomycota) based on molecular, morphological and chemical evidence

(2015) Xin Zhao et al.   FUNGAL DIVERSITY

Names matter

(2015) Elizabeth S. Barron et al.   PROGRESS IN PHYSICAL GEOGRAPHY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads

(2014) Frederic Bertels et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

A single macrolichen constitutes hundreds of unrecognized species

(2014) R. Lucking et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species Delimitation using Genome-Wide SNP Data

(2014) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

A general species delimitation method with applications to phylogenetic placements

(2013) Jiajie Zhang et al.   BIOINFORMATICS

Does the name really matter? The importance of botanical nomenclature and plant taxonomy in biomedical research

(2013) Bradley C. Bennett et al.   JOURNAL OF ETHNOPHARMACOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

How to fail at species delimitation

(2013) Bryan C. Carstens et al.   MOLECULAR ECOLOGY

Not as Ubiquitous as We Thought: Taxonomic Crypsis, Hidden Diversity and Cryptic Speciation in the Cosmopolitan Fungus Thelonectria discophora (Nectriaceae, Hypocreales, Ascomycota)

(2013) Catalina Salgado-Salazar et al.   PLoS One

DNA barcode identification of lichen-forming fungal species in the Rhizoplaca melanophthalma species-complex (Lecanorales, Lecanoraceae), including five new species

(2013) Steven Leavitt et al.   MycoKeys

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Multi-locus species delimitation in closely related animals and fungi: one marker is not enough

(2012) JULIAN R. DUPUIS et al.   MOLECULAR ECOLOGY

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Symbiotic View of Life: We Have Never Been Individuals

(2012) Scott F. Gilbert et al.   QUARTERLY REVIEW OF BIOLOGY

Coalescent-based species delimitation in an integrative taxonomy

(2012) Matthew K. Fujita et al.   TRENDS IN ECOLOGY & EVOLUTION

Lecanora microloba, a new saxicolous species from Poland

(2011) Lucyna ŚLIWA et al.   LICHENOLOGIST

Species delimitation in taxonomically difficult lichen-forming fungi: An example from morphologically and chemically diverse Xanthoparmelia (Parmeliaceae) in North America

(2011) Steven D. Leavitt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

(2011) Stephen A. Goff et al.   Frontiers in Plant Science

Integrative Taxonomy: A Multisource Approach to Exploring Biodiversity

(2009) Birgit C. Schlick-Steiner et al.   Annual Review of Entomology

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Mineral phases and element composition of the copper hyperaccumulator lichen Lecanora polytropa

(2008) O. W. Purvis et al.   MINERALOGICAL MAGAZINE