What are fungal species and how to delineate them?

KWT Chethana, IS Manawasinghe, VG Hurdeal… - Fungal Diversity, 2021 - Springer
This is the opening paper in the special issue of Fungal Diversity, which collates the data on
defining species. Defining and recognizing species has long been a controversial issue …

Integrative approaches for species delimitation in Ascomycota

SSN Maharachchikumbura, Y Chen, HA Ariyawansa… - Fungal Diversity, 2021 - Springer
Biodiversity loss from disturbances caused by human activities means that species are
disappearing at an ever increasing rate. The high number of species that have yet to be …

ASAP: assemble species by automatic partitioning

N Puillandre, S Brouillet, G Achaz - Molecular Ecology …, 2021 - Wiley Online Library
Abstract Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new
method to build species partitions from single locus sequence alignments (ie, barcode data …

Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo

P Kapli, S Lutteropp, J Zhang, K Kobert… - …, 2017 - academic.oup.com
Motivation In recent years, molecular species delimitation has become a routine approach
for quantifying and classifying biodiversity. Barcoding methods are of particular importance …

Comparison of methods for molecular species delimitation across a range of speciation scenarios

A Luo, C Ling, SYW Ho, CD Zhu - Systematic Biology, 2018 - academic.oup.com
Species are fundamental units in biological research and can be defined on the basis of
various operational criteria. There has been growing use of molecular approaches for …

[PDF][PDF] Classifying the evolutionary and ecological features of neoplasms

CC Maley, A Aktipis, TA Graham, A Sottoriva… - Nature Reviews …, 2017 - nature.com
Neoplasms change over time through a process of cell-level evolution, driven by genetic
and epigenetic alterations. However, the ecology of the microenvironment of a neoplastic …

Investigating species boundaries in Colletotrichum

CS Bhunjun, C Phukhamsakda, RS Jayawardena… - Fungal Diversity, 2021 - Springer
Colletotrichum is one of the most important plant pathogenic genera that is responsible for
numerous diseases which can have a profound impact on the agricultural sector. Species …

A general species delimitation method with applications to phylogenetic placements

J Zhang, P Kapli, P Pavlidis, A Stamatakis - Bioinformatics, 2013 - academic.oup.com
Motivation: Sequence-based methods to delimit species are central to DNA taxonomy,
microbial community surveys and DNA metabarcoding studies. Current approaches either …

[HTML][HTML] Recognition of seven species in the Cryptococcus gattii/Cryptococcus neoformans species complex

F Hagen, K Khayhan, B Theelen, A Kolecka… - Fungal genetics and …, 2015 - Elsevier
Phylogenetic analysis of 11 genetic loci and results from many genoty** studies revealed
significant genetic diversity with the pathogenic Cryptococcus gattii/Cryptococcus …

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

R Lücking, SD Leavitt, DL Hawksworth - Fungal Diversity, 2021 - Springer
Lichens are symbiotic associations resulting from interactions among fungi (primary and
secondary mycobionts), algae and/or cyanobacteria (primary and secondary photobionts) …