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DNA Barcoding, Taxonomic

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Review of the genus Shilovia Makarchenko (Diptera: Chironomidae: Diamesinae: Boreoheptagyiini) from the mountains of Central Asia, with morphological description and DNA barcoding of known species.

Zootaxa
Chironomids of the genus Shilovia Makarchenko (Diamesinae, Boreoheptagyiini) from the mountains of Central Asia are revised using both morphological characters and molecular data. Illustrated descriptions of the adult male Shilovia xinhuawangi sp. no...

DiversityScanner: Robotic handling of small invertebrates with machine learning methods.

Molecular ecology resources
Invertebrate biodiversity remains poorly understood although it comprises much of the terrestrial animal biomass, most species and supplies many ecosystem services. The main obstacle is specimen-rich samples obtained with quantitative sampling techni...

Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks.

Proceedings of the National Academy of Sciences of the United States of America
Taxonomic classification, that is, the assignment to biological clades with shared ancestry, is a common task in genetics, mainly based on a genome similarity search of large genome databases. The classification quality depends heavily on the databas...

New deep learning-based methods for visualizing ecosystem properties using environmental DNA metabarcoding data.

Molecular ecology resources
Environmental DNA (eDNA) metabarcoding provides an efficient approach for documenting biodiversity patterns in marine and terrestrial ecosystems. The complexity of these data prevents current methods from extracting and analyzing all the relevant eco...

Classification of DNA Sequence Based on a Non-gradient Algorithm: Pseudoinverse Learners.

Methods in molecular biology (Clifton, N.J.)
This chapter proposes a prototype-based classification approach for analyzing DNA barcodes that uses a spectral representation of DNA sequences and a non-gradient neural network. Biological sequences can be viewed as data components with higher non-f...

Development of a two-layer machine learning model for the forensic application of legal and illegal poppy classification based on sequence data.

Forensic science international. Genetics
Poppies are beneficial plants with a variety of applications, including medicinal, edible, ornamental, and industrial purposes. Some Papaver species are forensically significant plants because they contain opium, a narcotic substance. Internationally...

Image-based recognition of parasitoid wasps using advanced neural networks.

Invertebrate systematics
Hymenoptera has some of the highest diversity and number of individuals among insects. Many of these species potentially play key roles as food sources, pest controllers and pollinators. However, little is known about the diversity and biology and ~8...

Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: insights from metabarcoding and machine learning.

FEMS microbiology ecology
Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composit...

Integrating external stressors in supervised machine learning algorithm achieves high accuracy to predict multi-species biological integrity index of aquaculture wastewater.

Journal of hazardous materials
Monitoring and predicting the environmental impact of wastewater is essential for sustainable aquaculture. The environmental DNA metabarcoding-integrated supervised machine learning (SML) algorithm is an alternative method for ecological quality asse...

Illuminating Entomological Dark Matter with DNA Barcodes in an Era of Insect Decline, Deep Learning, and Genomics.

Annual review of entomology
Most insects encountered in the field are initially entomological dark matter in that they cannot be identified to species while alive. This explains the enduring quest for efficient ways to identify collected specimens. Morphological tools came firs...