Cryptic species as a window into the paradigm shift of the species concept

C Fišer, CT Robinson, F Malard - Molecular Ecology, 2018 - Wiley Online Library
The species concept is the cornerstone of biodiversity science, and any paradigm shift in the
delimitation of species affects many research fields. Many biologists now are embracing a …

Review and interpretation of trends in DNA barcoding

R DeSalle, P Goldstein - Frontiers in Ecology and Evolution, 2019 - frontiersin.org
Interpretations and analytical practices surrounding DNA barcoding are examined using a
compilation of 3,756 papers (as of December 31, 2018) with “DNA Barcode” in the abstract …

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 …

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 …

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 …

Notes for genera: Ascomycota

NN Wijayawardene, KD Hyde, KC Rajeshkumar… - Fungal diversity, 2017 - Springer
Abstract Knowledge of the relationships and thus the classification of fungi, has developed
rapidly with increasingly widespread use of molecular techniques, over the past 10–15 …

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 genotyping studies revealed
significant genetic diversity with the pathogenic Cryptococcus gattii/Cryptococcus …

A DNA-based registry for all animal species: the Barcode Index Number (BIN) system

S Ratnasingham, PDN Hebert - PloS one, 2013 - journals.plos.org
Because many animal species are undescribed, and because the identification of known
species is often difficult, interim taxonomic nomenclature has often been used in biodiversity …