A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses

A Hakimzadeh, A Abdala Asbun… - Molecular Ecology …, 2024 - Wiley Online Library
Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for
monitoring biodiversity in ecology. However, taxa identifications produced through …

Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods

P Arribas, C Andújar, K Bohmann, JR DeWaard… - …, 2022 - academic.oup.com
Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity,
with diverse projects currently generating massive quantities of community-level data. The …

To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography

A Antich, C Palacin, OS Wangensteen, X Turon - BMC bioinformatics, 2021 - Springer
Background The recent blooming of metabarcoding applications to biodiversity studies
comes with some relevant methodological debates. One such issue concerns the treatment …

Dynamics of species-rich predator–prey networks and seasonal alternations of core species

SS Suzuki, YG Baba, H Toju - Nature Ecology & Evolution, 2023 - nature.com
In nature, entangled webs of predator–prey interactions constitute the backbones of
ecosystems. Uncovering the network architecture of such trophic interactions has been …

The limited spatial scale of dispersal in soil arthropods revealed with whole‐community haplotype‐level metabarcoding

P Arribas, C Andújar, A Salces‐Castellano… - Molecular …, 2021 - Wiley Online Library
Soil arthropod communities are highly diverse and critical for ecosystem functioning.
However, our knowledge of spatial structure and the underlying processes of community …

Groundwater environmental DNA metabarcoding reveals hidden diversity and reflects land‐use and geology

M Couton, S Hürlemann, A Studer, R Alther… - Molecular …, 2023 - Wiley Online Library
Despite being the most important source of liquid freshwater on the planet, groundwater is
severely threatened by climate change, agriculture, or industrial mining. It is thus extensively …

Metabarcoding reveals high‐resolution biogeographical and metaphylogeographical patterns through marine barriers

A Antich, C Palacín, J Zarcero… - Journal of …, 2023 - Wiley Online Library
Aim It has been predicted that there should be concordance between biogeographical and
phylogeographical processes structuring multi‐species regional assemblages. We …

Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation

TJ Creedy, C Andújar… - Molecular Ecology …, 2022 - Wiley Online Library
Metabarcoding of DNA extracted from community samples of whole organisms (whole
organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and …

Spineless and overlooked: DNA metabarcoding of autonomous reef monitoring structures reveals intra‐and interspecific genetic diversity in Mediterranean …

A Thomasdotter, P Shum, F Mugnai… - Molecular Ecology …, 2023 - Wiley Online Library
The ability to gather genetic information using DNA metabarcoding of bulk samples obtained
directly from the environment is crucial to determine biodiversity baselines and understand …

Interrogating 1000 insect genomes for NUMTs: A risk assessment for estimates of species richness

PDN Hebert, DG Bock, SWJ Prosser - PLoS One, 2023 - journals.plos.org
The nuclear genomes of most animal species include NUMTs, segments of the mitogenome
incorporated into their chromosomes. Although NUMT counts are known to vary greatly …