Environmental DNA in Biodiversity Studies

Rsearch: An R interface to VSEARCH supporting visualization and parameter tuning

Rsearch runs VSEARCH from R with quality plots, trimming optimizers and phyloseq conversion; on a 16S mock community it matched DADA2's abundance accuracy with fewer, more prevalent OTUs.

Classical baselines outperform released deep-learning ITS classifiers, which collapse on ITS2 where predictions follow the flanking regions

MycoAI ITS classifiers trail alignment, SINTAX and HiTaC on full-length ITS and drop to 28.3% and 18.5% seen-genus family accuracy on ITS2, as predictions track flanking regions.

Characterizing mitochondrial copy number variation and PCR amplification bias as sources of quantitative constraints in DNA metabarcoding

COI metabarcoding of 81 arthropod mock communities shows PCR amplification bias is taxon-specific but non-exponential, so cycle calibration fails while a constant-bias model recovers mtDNA copies.

A breath of fresh air: comparative evaluation of passive versus active airborne eDNA sampling strategies

Passive 3D-printed Nutshell air eDNA samplers hung up to 96 hours at Rotterdam Zoo detected 76 vertebrate species, versus 50 and 25 for two active samplers.

DNA Specimen Preservation using DESS and DNA Extraction in Museum Collections: A Case Study Report

DESS (DMSO/EDTA/saturated NaCl) kept DNA at room temperature in animals, seagrasses and a brown alga, even after evaporating from bird muscle, but dissolves gastropod shells and holothurian ossicles.

High-throughput biodiversity surveying sheds new light on the brightest of insect taxa

One year of COI metabarcoding of 197 Malaise traps across Sweden detected 1,535 of 2,990 known Lepidoptera species, plus specimen-validated new country records, range extensions and putative undescribed species.

eDNA metabarcoding as a biomonitoring tool for marine protected areas

eDNA metabarcoding at a California marine reserve recovered 76% of diver-recorded fish species, distinguished communities 50 m apart, yet reversed the visual inside-versus-outside richness pattern.