Bioinformatic challenges for DNA metabarcoding of plants and animals

E Coissac, T Riaz, N Puillandre - Molecular ecology, 2012 - Wiley Online Library
Almost all empirical studies in ecology have to identify the species involved in the ecological
process under examination. DNA metabarcoding, which couples the principles of DNA …

Multilocus inference of species trees and DNA barcoding

D Mallo, D Posada - … Transactions of the Royal Society B …, 2016 - royalsocietypublishing.org
The unprecedented amount of data resulting from next-generation sequencing has opened
a new era in phylogenetic estimation. Although large datasets should, in theory, increase …

Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets

T Fujisawa, TG Barraclough - Systematic biology, 2013 - academic.oup.com
DNA barcoding-type studies assemble single-locus data from large samples of individuals
and species, and have provided new kinds of data for evolutionary surveys of diversity. An …

[图书][B] Species concepts in biology

FE Zachos - 2016 - Springer
The species problem has triggered the publication of an almost infinite number of theoretical
and practical studies, including quite a number of books. I should, therefore, perhaps briefly …

Guidelines for DNA taxonomy, with a focus on the meiofauna

D Fontaneto, JF Flot, CQ Tang - Marine Biodiversity, 2015 - Springer
Describing biological diversity is a challenging endeavour, especially for the small, cryptic
animals that make up the meiofauna. The field of DNA taxonomy, ie, the use of DNA to …

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

CQ Tang, F Leasi, U Obertegger… - Proceedings of the …, 2012 - National Acad Sciences
Molecular tools have revolutionized the exploration of biodiversity, especially in organisms
for which traditional taxonomy is difficult, such as for microscopic animals (meiofauna) …

Evaluating the Species Boundaries of Green Microalgae (Coccomyxa, Trebouxiophyceae, Chlorophyta) Using Integrative Taxonomy and DNA Barcoding with Further …

T Darienko, L Gustavs, A Eggert, W Wolf, T Proeschold - PloS one, 2015 - journals.plos.org
Integrative taxonomy is an approach for defining species and genera by taking phylogenetic,
morphological, physiological, and ecological data into account. This approach is appropriate …

Taxonomic resolutions based on 18S rRNA genes: a case study of subclass Copepoda

S Wu, J Xiong, Y Yu - PloS one, 2015 - journals.plos.org
Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we
compared the inter-species divergence of variable regions (V1–9) within the copepod 18S …

The Longibrachiatum Clade of Trichoderma: a revision with new species

GJ Samuels, A Ismaiel, TB Mulaw, G Szakacs… - Fungal diversity, 2012 - Springer
Abstract The Longibrachiatum Clade of Trichoderma is revised. Eight new species are
described (T. aethiopicum, T. capillare, T. flagellatum, T. gillesii, T. gracile, T. pinnatum, T …

Lack of statistical rigor in DNA barcoding likely invalidates the presence of a true species' barcode gap

JD Phillips, DJ Gillis, RH Hanner - Frontiers in Ecology and Evolution, 2022 - frontiersin.org
DNA barcoding has been largely successful in satisfactorily exposing levels of standing
genetic diversity for a wide range of taxonomic groups through the employment of only one …