Sujeevan Ratnasingham
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View article: Common to rare transfer learning (CORAL) enables inference and prediction for a quarter million rare Malagasy arthropods
Common to rare transfer learning (CORAL) enables inference and prediction for a quarter million rare Malagasy arthropods Open
DNA-based biodiversity surveys result in massive-scale data, including up to millions of species—of which, most are rare. Making the most of such data for inference and prediction requires modeling approaches that can relate species occurr…
View article: Caterpillar diet breadth in Área de Conservación Guanacaste, a large and diverse Neotropical wildland in northwestern Costa Rica: toxins, silica, aluminum, and sclerophylly
Caterpillar diet breadth in Área de Conservación Guanacaste, a large and diverse Neotropical wildland in northwestern Costa Rica: toxins, silica, aluminum, and sclerophylly Open
Caterpillar–food plant records collected over approximately 38 years in the Area de Conservación Guanacaste (ACG) in northwestern Costa Rica are described and summarized. The data comprise 431,212 individual rearing records, 197,366 of whi…
View article: Farmland Biodiversity Monitoring Using DNA Metabarcoding
Farmland Biodiversity Monitoring Using DNA Metabarcoding Open
Although 5–20% of global crop production is lost to arthropod damage, current biomonitoring programs are extremely limited. This study evaluates the feasibility of using metabarcoding to assess overall insect diversity and detect pest spec…
View article: Enhancing Digital Infrastructures and Data Handling Practices for Single Specimen Barcoding - the 2024 BGE Barcoding Hackathon
Enhancing Digital Infrastructures and Data Handling Practices for Single Specimen Barcoding - the 2024 BGE Barcoding Hackathon Open
The 2024 BGE Barcoding Hackathon, hosted by the Biodiversity Genomics Europe (BGE) project in Leiden, Netherlands, focused on advancing digital infrastructures and data handling practices for single specimen barcoding. This event brought t…
View article: Farmland Biodiversity Monitoring Using DNA Metabarcoding
Farmland Biodiversity Monitoring Using DNA Metabarcoding Open
Although 5-20% of global crop production is lost to arthropod damage, current biomonitoring programs are extremely limited. This study evaluates the feasibility of using metabarcoding to assess overall insect diversity and detect pest spec…
View article: Metabarcoding arthropods in agroecosystems in Southern Ontario, Canada
Metabarcoding arthropods in agroecosystems in Southern Ontario, Canada Open
Metabarcoding can generate large numbers of georeferenced occurrence data from bulk samples at low cost. Its integration into the practice of agricultural invertebrate biomonitoring currently lacks both standard methods and example dataset…
View article: Metabarcoding arthropods in agroecosystems in Southern Ontario, Canada
Metabarcoding arthropods in agroecosystems in Southern Ontario, Canada Open
Metabarcoding can generate large numbers of georeferenced occurrence data from bulk samples at low cost. Its integration into the practice of agricultural invertebrate biomonitoring currently lacks both standard methods and example dataset…
View article: Taxonomic Reasoning for Rare Arthropods: Combining Dense Image Captioning and RAG for Interpretable Classification
Taxonomic Reasoning for Rare Arthropods: Combining Dense Image Captioning and RAG for Interpretable Classification Open
In the context of pressing climate change challenges and the significant biodiversity loss among arthropods, automated taxonomic classification from organismal images is a subject of intense research. However, traditional AI pipelines base…
View article: Towards a Taxonomy Machine: A Training Set of 5.6 Million Arthropod Images
Towards a Taxonomy Machine: A Training Set of 5.6 Million Arthropod Images Open
The taxonomic identification of organisms from images is an active research area within the machine learning community. Current algorithms are very effective for object recognition and discrimination, but they require extensive training da…
View article: Common to rare transfer learning (CORAL) enables inference and prediction for a quarter million rare Malagasy arthropods
Common to rare transfer learning (CORAL) enables inference and prediction for a quarter million rare Malagasy arthropods Open
Modern DNA-based biodiversity surveys result in massive-scale data, including up to millions of species – of which most are rare. Making the most of such data for inference and prediction requires modelling approaches that can relate speci…
View article: Towards a Taxonomy Machine – A Training Set of 5.6 Million Arthropod Images
Towards a Taxonomy Machine – A Training Set of 5.6 Million Arthropod Images Open
The taxonomic identification of organisms from images is an active research area within the machine learning community. Current algorithms are very effective for object recognition and discrimination, but they require extensive training da…
View article: Global arthropod beta-diversity is spatially and temporally structured by latitude
Global arthropod beta-diversity is spatially and temporally structured by latitude Open
Global biodiversity gradients are generally expected to reflect greater species replacement closer to the equator. However, empirical validation of global biodiversity gradients largely relies on vertebrates, plants, and other less diverse…
View article: PROTAX-GPU: a scalable probabilistic taxonomic classification system for DNA barcodes
PROTAX-GPU: a scalable probabilistic taxonomic classification system for DNA barcodes Open
DNA-based identification is vital for classifying biological specimens, yet methods to quantify the uncertainty of sequence-based taxonomic assignments are scarce. Challenges arise from noisy reference databases, including mislabelled entr…
View article: BOLD v4: A Centralized Bioinformatics Platform for DNA-based Biodiversity Data
BOLD v4: A Centralized Bioinformatics Platform for DNA-based Biodiversity Data Open
BOLD, the Barcode of Life Data System, supports the acquisition, storage, validation, analysis, and publication of DNA barcodes, activities requiring the integration of molecular, morphological, and distributional data. Its pivotal role in…
View article: Spatio-temporal determinants of arthropod biodiversity across an agro-ecosystem landscape
Spatio-temporal determinants of arthropod biodiversity across an agro-ecosystem landscape Open
Arthropod communities globally are declining while undergoing taxonomic and functional homogenization, with agricultural activity being a strong contributory factor. Here we use DNA metabarcoding to quantify how variation in climate, agric…
View article: Spatial and seasonal determinants of arthropod community composition across an agro-ecosystem landscape
Spatial and seasonal determinants of arthropod community composition across an agro-ecosystem landscape Open
We used Malaise traps to sample arthropod community composition at biweekly intervals across an agroecosystem landscape in southern Ontario, Canada, to evaluate the relative impact of site spacing, seasonal timing, weather conditions, loca…
View article: Global Arthropod beta-diversity is spatially and temporally structured by latitude
Global Arthropod beta-diversity is spatially and temporally structured by latitude Open
Aim: Global gradients in species biodiversity may or may not be associated with greater species replacement closer to the equator. Yet, empirical validation of these patterns has so far focused on less diverse taxa, with comparable assessm…
View article: Minimalist revision of Mesochorus Gravenhorst, 1829 (Hymenoptera: Ichneumonidae: Mesochorinae) from Área de Conservación Guanacaste, Costa Rica, with 158 new species and host records for 129 species
Minimalist revision of Mesochorus Gravenhorst, 1829 (Hymenoptera: Ichneumonidae: Mesochorinae) from Área de Conservación Guanacaste, Costa Rica, with 158 new species and host records for 129 species Open
Introduction: Species of Mesochorus are found worldwide and members of this genus are primarily hyperparasitoids of Ichneumonoidea and Tachinidae. Objectives: To describe species of Costa Rican Mesochorus reared from caterpillars and to a …
View article: A Step Towards Worldwide Biodiversity Assessment: The BIOSCAN-1M Insect Dataset
A Step Towards Worldwide Biodiversity Assessment: The BIOSCAN-1M Insect Dataset Open
In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information inclu…
View article: BIOSCAN-1M Insect Dataset
BIOSCAN-1M Insect Dataset Open
Overview In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-1M Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic infor…
View article: BIOSCAN-1M Insect Dataset
BIOSCAN-1M Insect Dataset Open
Overview In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-1M Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic infor…
View article: BIOSCAN-1M Insect Dataset
BIOSCAN-1M Insect Dataset Open
In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-1M Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information in…
View article: BIOSCAN-1M Insect Dataset
BIOSCAN-1M Insect Dataset Open
In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-1M Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information in…
View article: Arthropod beta-diversity is spatially and temporally structured by latitude
Arthropod beta-diversity is spatially and temporally structured by latitude Open
Global gradients in species biodiversity are expected to reflect tighter packing of species closer to the equator. Yet, empirical validation of these patterns has so far focused on less diverse taxa, with comparable assessments of mega-div…
View article: More discussion of minimalist species descriptions and clarifying some misconceptions contained in Meier et al. 2021
More discussion of minimalist species descriptions and clarifying some misconceptions contained in Meier et al. 2021 Open
This is a response to a preprint version of “A re-analysis of the data in Sharkey et al.’s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science”, https://www.biorxi…
View article: DNA barcodes reveal striking arthropod diversity and unveil seasonal patterns of variation in the southern Atlantic Forest
DNA barcodes reveal striking arthropod diversity and unveil seasonal patterns of variation in the southern Atlantic Forest Open
The Atlantic Forest harbors 7% of global biodiversity and possesses high levels of endemism, but many of its component taxa remain unstudied. Due to the importance of tropical forests and the urgency to protect them, there is a compelling …
View article: Message in a Bottle—Metabarcoding enables biodiversity comparisons across ecoregions
Message in a Bottle—Metabarcoding enables biodiversity comparisons across ecoregions Open
Background Traditional biomonitoring approaches have delivered a basic understanding of biodiversity, but they cannot support the large-scale assessments required to manage and protect entire ecosystems. This study used DNA metabarcoding t…