Sujeevan Ratnasingham

University of Guelph | UOGuelph · Centre for Biodiversity Genomics

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 datasets to generate reliable assignments. This study releases 5.6 million images with representatives from 10 ar...

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 species occurrences to environmental and spatial predictors, while incorporating information about taxonomic or phylo...

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 datasets to generate reliable assignments. This study releases 5.6 million images with representatives from 10 ar...

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 taxa. Here we assess the temporal and spatial dynamics of global arthropod biodiversity dynamics using a beta-...

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 entries and missing taxa. PROTAX addresses these issues with a probabilistic approach to taxonomic classification,...

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 curating the reference library of DNA barcodes, coupled with its data management and analysis capabilities, ma...

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, agricultural intensity, and plant community composition shape spatiotemporal variation in a metacommunity of > 10,00...

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 lesser extent Malaise-trapped. Methods: The species are diagnosed by COI mtDNA barcodes, morphological inspec...

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 including raw nucleotide barcode sequences and assigned barcode index numbers, which are genetically-based proxies f...

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-diverse groups historically constrained by the taxonomic impediment. Here we assess the temporal and spatial turno...

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 assessments of mega-diverse groups historically constrained by the taxonomic impediment. Location: Global Time period:...

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 need to address this knowledge gap. To provide more information on its arthropod fauna, a Malaise trap was depl...

• Global insect decline has recently become a cause for major concern, particularly in the tropics where the vast majority of species occurs. Deforestation is suggested as being a major driver of this decline, but how anthropogenic changes in landscape structure affect tropical insect communities has rarely been addressed. • We sampled Saturniidae...

?Abstract Twenty-nine species are treated, most of which have host caterpillar and food plant records, and all but one are new to science. The first host record for the agathidine genus Amputoearinus is given. Gnathopleurajosequesadai Sharkey, sp. nov. is reported as a hyperparasitoid of fly larvae, the first such record for the genus. The followin...

To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this paper, we 1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), 2) publish this library, and 3) deliver a new identifica...

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 employed DNA metabarcoding to assess spatial and temporal variation in species richness and diversity in arthropod communities from 52...

To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this paper, we 1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), 2) publish this library, and 3) deliver a new identifica...

Although the butterflies of North America have received considerable taxonomic attention, overlooked species and instances of hybridization continue to be revealed. The present study assembles a DNA barcode reference library for this fauna to identify groups whose patterns of sequence variation suggest the need for further taxonomic study. Based on...

Background Rickettsia are intracellular bacteria best known as the causative agents of human and animal diseases. Although these medically important Rickettsia are often transmitted via haematophagous arthropods, other Rickettsia, such as those in the Torix group, appear to reside exclusively in invertebrates and protists with no secondary vertebra...

DNA barcoding and metabarcoding are now widely used to advance species discovery and biodiversity assessments. High‐throughput sequencing (HTS) has expanded the volume and scope of these analyses, but elevated error rates introduce noise into sequence records that can inflate estimates of biodiversity. Denoising —the separation of biological signal...

Three new genera are described: Michener (Proteropinae), Bioalfa (Rogadinae), and Hermosomastax (Rogadinae). Keys are given for the New World genera of the following braconid subfamilies: Agathidinae, Braconinae, Cheloninae, Homolobinae, Hormiinae, Ichneutinae, Macrocentrinae, Orgilinae, Proteropinae, Rhysipolinae, and Rogadinae. In these subfamili...

DNA barcoding and metabarcoding are now widely used to advance species discovery and biodiversity assessments. High-throughput sequencing (HTS) has expanded the volume and scope of these analyses, but elevated error rates introduce noise into sequence records that can inflate estimates of biodiversity. Denoising--the separation of biological signal...

We report one year (2013-2014) of biomonitoring an insect community in a tropical old-growth rainforest, during construction of an industrial-level geothermal electricity project. This is the first-year reaction by the species-rich insect biodiversity; six subsequent years are being analyzed now. The site is on the margin of a UNESCO Natural World...

11 Biological conclusions based on DNA barcoding and metabarcoding analyses can be strongly 12 influenced by the methods utilized for data generation and curation, leading to varying levels of success 13 in the separation of biological variation from experimental error. The five-prime region of cytochrome 14 c oxidase subunit I (COI-5P) is the most...

Biological conclusions based on DNA barcoding and metabarcoding analyses can be strongly influenced by the methods utilized for data generation and curation, leading to varying levels of success in the separation of biological variation from experimental error. The 5′ region of cytochrome c oxidase subunit I (COI-5P) is the most common barcode gene...

The severe acute respiratory syndrome virus, SARS-CoV-2 (hereafter COVID-19), rapidly achieved global pandemic status, provoking large-scale screening programs in many nations. Their activation makes it imperative to identify methods that can deliver a diagnostic result at low cost. This paper describes an approach which employs sequence variation...

Applications of biological knowledge, such as forensics, often require the determination of biological materials to a species level. As such, DNA-based approaches to identification, particularly DNA barcoding, are attracting increased interest. The capacity of DNA barcodes to assign newly encountered specimens to a species relies upon access to inf...

The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal speci...

36 Forensic studies often require the determination of biological materials to a species level. As such, DNA-37 based approaches to identification, particularly DNA barcoding, are attracting increased interest. The 38 capacity of DNA barcodes to assign newly encountered specimens to a species relies upon access to 39 informatics platforms, such as...

The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal speci...

Our knowledge of global biodiversity remains incomplete and beset by knowledge shortfalls affecting both the census of species (i.e. the Linnean shortfall) and our understanding of their distributions (i.e. the Wallacean shortfall; Hortal et al. 2015). While alarming rates of species extinction have been reported in most groups of organisms, our ca...

Background: The adoption of DNA barcoding in pest management and regulation has been impeded by 1) gaps in taxonomic coverage, 2) discordances between morphospecies and DNA barcodes, 3) and errors in the identification of reference specimens. Unfortunately, these impediments have been perceived as insurmountable because of the need for diverse taxo...

Although DNA metabarcoding is an attractive approach for monitoring biodiversity, it is often difficult to detect all the species present in a bulk sample. In particular, sequence recovery for a given species depends on its biomass and mitome copy number as well as the primer set employed for PCR. To examine these variables, we constructed a mock c...

DNA metabarcoding is an attractive approach for monitoring biodiversity. However, it is subject to biases that often impede detection of all species in a sample. In particular, the proportion of sequences recovered from each species depends on its biomass, mitome copy number, and primer set employed for PCR. To examine these variables, we construct...

Monitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological approaches. The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly de...

Background: Although high-throughput sequencers (HTS) have largely displaced their Sanger counterparts, the short read lengths and high error rates of most platforms constrain their utility for amplicon sequencing. The present study tests the capacity of single molecule, real-time (SMRT) sequencing implemented on the SEQUEL platform to overcome th...

ABSTRACT: Taxonomic information gap, discordance between species names and BINs, and errors in identification of reference specimens are factors that have impeded the uptake of DNA barcoding use by industry and regulatory organizations. These challenges are more problematic in the context of pest and invasive species detection because the end-users...

Participants in the 7th International Barcode of Life Conference (Kruger National Park, South Africa, 20-24 November 2017) share the latest findings in DNA barcoding research and its increasingly diversified applications. Here, we review prevailing trends synthesized from among 429 invited and contributed abstracts, which are collated in this open-...

Although high-throughput sequencers (HTS) have largely displaced their Sanger counterparts, the short read lengths and high error rates of most platforms constrain their utility for amplicon sequencing. The present study tests the capacity of single molecule, real-time (SMRT) sequencing implemented on the SEQUEL platform to overcome these limitatio...

We present a series of key issues, challenges, and solutions associated with a classroom model of citizen science that engages a nationally distributed network of high school students (and other non-experts) in contributing professional quality biodiversity genomics data to the International Barcode of Life (iBOL) project. The successful implementa...

Recent estimates suggest that the global insect fauna includes fewer than six million species, but this projection is very uncertain because taxonomic work has been limited on some highly diverse groups. Validation of current estimates minimally requires the investigation of all lineages that are diverse enough to have a substantial impact on the f...

This study presents a machine learning method that increases the number of identified bases in Sanger Sequencing. The system post-processes a KB basecalled chromatogram. It selects a recoverable subset of N-labels in the KB-called chromatogram to replace with basecalls (A,C,G,T). An N-label correction is defined given an additional read of the same...

The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by sit...

Approximately 1460 species of spiders have been reported from Canada, 3% of the global fauna. This study provides a DNA barcode reference library for 1018 of these species based upon the analysis of more than 30,000 specimens. The sequence results show a clear barcode gap in most cases with a mean intraspecific divergence of 0.78% versus a minimum...

Approximately 1460 species of spiders have been reported from Canada, 3% of the global fauna. This study provides a DNA barcode reference library for 1018 of these species based upon the analysis of more than 30 000 specimens. The sequence results show a clear barcode gap in most cases with a mean intraspecific divergence of 0.78% vs. a minimum nea...

The study analyzes sequence variation of two mitochondrial genes (COI, cytb) in Pediculus humanus from three countries (Egypt, Pakistan, South Africa) that have received little prior attention, and integrates these results with prior data. Analysis indicates a maximum K2P distance of 10.3% among 960 COI sequences and 13.8% among 479 cytb sequences....

The Barcode of Life Data Systems (BOLD) is designed to support the generation and application of DNA barcode data, but it also provides a unique source of data with potential for many research uses. This paper explores the streamlining of BOLD specimen data to record species distributions - and its fast publication using the Biodiversity Data Journ...

Supplemental Appendix 4

Supplemental Appendix 1

Supplemental Appendix 3

Distribution of 10 Microgastrinae species based on BOLD records

Supplemental Appendix 2

The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of g...

The geometrid moths of Europe are one of the best investigated insect groups in traditional taxonomy making them an ideal model group to test the accuracy of the Barcode Index Number (BIN) system of BOLD (Barcode of Life Datasystems), a method that supports automated, rapid species delineation and identification. This study provides a DNA barcode l...

Because many animal species are undescribed, and because the identification of known species is often difficult, interim taxonomic nomenclature has often been used in biodiversity analysis. By assigning individuals to presumptive species, called operational taxonomic units (OTUs), these systems speed investigations into the patterning of biodiversi...

Cluster Accuracy Measure. A description of the F-Measure statistic which is used to produce a single measure of concordance between the prior taxonomy and the OTUs genera