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 …
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
Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity,
with diverse projects currently generating massive quantities of community-level data. The …
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
Background The recent blooming of metabarcoding applications to biodiversity studies
comes with some relevant methodological debates. One such issue concerns the treatment …
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
In nature, entangled webs of predator–prey interactions constitute the backbones of
ecosystems. Uncovering the network architecture of such trophic interactions has been …
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
Soil arthropod communities are highly diverse and critical for ecosystem functioning.
However, our knowledge of spatial structure and the underlying processes of community …
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
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 …
severely threatened by climate change, agriculture, or industrial mining. It is thus extensively …
Metabarcoding reveals high‐resolution biogeographical and metaphylogeographical patterns through marine barriers
Aim It has been predicted that there should be concordance between biogeographical and
phylogeographical processes structuring multi‐species regional assemblages. We …
phylogeographical processes structuring multi‐species regional assemblages. We …
Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation
Metabarcoding of DNA extracted from community samples of whole organisms (whole
organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and …
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 …
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
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 …
incorporated into their chromosomes. Although NUMT counts are known to vary greatly …