Evgeny V. Zakharov

Evgeny V. Zakharov
University of Guelph | UOGuelph · Centre for Biodiversity Genomics

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300
Publications
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Publications

Publications (300)
Article
Full-text available
According to COI DNA barcoding testing, the marine bivalve mollusc Mactra chinensis , which is native to the Asia-Pacific region, diverged into three species. These species were preliminary characterized as M. chinensis COI clade I, M. chinensis COI clade II and M. chinensis COI clade III. To find out whether it is possible to morphologically disti...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Preprint
Full-text available
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...
Article
Full-text available
The kingdom Fungi is a megadiverse group represented in all ecosystem types. The global diversity and distribution of fungal taxa are poorly known, in part due to the limitations related to traditional fruit-body survey methods. These previous hurdles are now being overcome by rapidly developing DNA-based surveys. Past fungal DNA surveys have predo...
Article
Full-text available
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...
Article
Full-text available
Metabarcoding can rapidly determine the species composition of bulk samples and thus aids biodiversity and ecosystem assessment. However, it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has...
Preprint
Full-text available
Metabarcoding can rapidly determine the species composition of bulk samples and thus aids ecosystem assessment. However , it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been suffic...
Preprint
Full-text available
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...
Preprint
Full-text available
Metabarcoding can rapidly determine the species composition of bulk samples and thus aids ecosystem assessment. However , it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been suffic...
Preprint
Full-text available
Metabarcoding can rapidly determine the species composition of bulk samples and thus aids ecosystem assessment. However , it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been suffic...
Article
Full-text available
Biodiversity research in tropical ecosystems - popularized as the most biodiverse habitats on Earth - often neglects invertebrates, yet representing the bulk of local species richness. Insect communities in particular remain strongly impeded by both Linnaean and Wallacean shortfalls, and identifying species often remains a formidable challenge inhi...
Article
Full-text available
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...
Preprint
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
According to recent reports, shell morphology is unreliable for the identification of oysters because of the high phenotypic plasticity of these bivalves. Using COI DNA barcoding and sperm morphology, we reinvestigated the species validity of wild Pacific oyster Crassostrea gigas habituating the Peter the Great Bay (Sea of Japan). DNA barcoding con...
Article
Full-text available
Premise of the Study The detection of environmental DNA (eDNA) using high‐throughput sequencing has rapidly emerged as a method to detect organisms from environmental samples. However, eDNA studies of aquatic biomes have focused on surveillance of animal species with less emphasis on plants. Pondweeds are important bioindicators of freshwater ecosy...
Article
Full-text available
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...
Article
Full-text available
Premise of the study Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada. Methods Our study examined 20,816 speci...
Preprint
Full-text available
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...
Preprint
Full-text available
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...
Article
The genetic barcode ITS2 (ITS: internal transcribed spacer) and pollen morphology were used for the identification of the pharmacologically valuable wild Araliaceae species Panax ginseng, Oplopanax elatus, Aralia elata, Aralia continentalis, Eleutherococcus senticosus, and Eleutherococcus sessiliflorus inhabiting the natural forests of Primorye, Ru...
Article
Full-text available
This study reports the assembly of a DNA barcode reference library for species in the lepi-dopteran superfamily Noctuoidea from Canada and the USA. Based on the analysis of 69,378 specimens, the library provides coverage for 97.3% of the noctuoid fauna (3565 of 3664 species). In addition to verifying the strong performance of DNA barcodes in the di...
Data
Introduced species into North America. List of introduced species of noctuoids in North America with the approximate date of their arrival. (XLS)
Data
Two-way presence-absence data for 3252 North American noctuoid species in 12 ecoregions of North America. Each region designated by a numeric code: 1 Arctic (Arctic Cordillera + Tundra); 2 Boreal (Taiga + Hudson plain + Northern forests); 3 Northwestern forested mountains; 4 Marine west coast forests; 5 Eastern temperate forests; 6 Great plains; 7...
Data
Barcode performance among ecoregions of North America. Data set for the analysis of barcode performance in the discrimination of noctuoid species from the 12 ecoregions of North America. (XLS)
Data
Data set for the analysis of BIN overlap among zoogeographical regions. (XLS)
Data
Barcode coverage. List of North American noctuoid species without barcode coverage. (XLS)
Data
Noctuidae-3. NJ tree based on sequence variation in the barcode region of the cytochrome c oxidase I gene for North American species in the family Noctuidae-3. (PDF)
Data
Checklist for North American noctuoids. The table represents barcode coverage in terms of the number of specimens analyzed and geographic coverage. Species lacking barcode data are in red. (XLS)
Data
Species with extraterritorial barcode records. Forty-eight species barcoded from other nations likely share the same barcode as specimens collected in the USA. For species collected in Texas and Arizona—barcodes from Mexican specimens are the best proxy, followed by Guatemala. For species collected in Florida—barcodes from Cuban specimens are best,...
Data
Low sequence divergence. List of North American noctuoid species with low sequence divergence from another taxon. (XLS)
Data
Noctuidae-1. NJ tree based on sequence variation in the barcode region of the cytochrome c oxidase I gene for North American species in the family Noctuidae-1. (PDF)
Data
Noctuidae-2. NJ tree based on sequence variation in the barcode region of the cytochrome c oxidase I gene for North American species in the family Noctuidae-2. (PDF)
Data
Barcode sharing. List of North American noctuoid species sharing a barcode haplotype. (XLS)
Data
Deep split. List of North American noctuoid species with deep intraspecific sequence divergence. (XLS)
Data
List of all noctuoid species known from North America with number of BINs, mean intra-specific divergence, and number of specimens per species. (XLS)
Data
Euteliidae. NJ tree based on sequence variation in the barcode region of the cytochrome c oxidase I gene for North American species in the family Euteliidae. (PDF)
Data
Nolidae. NJ tree based on sequence variation in the barcode region of the cytochrome c oxidase I gene for North American species in the family Nolidae. (PDF)
Data
Erebidae (rest). NJ tree based on sequence variation in the barcode region of the cytochrome c oxidase I gene for North American species in the family Erebidae (rest). (PDF)
Data
Notodontidae and Doidae. NJ tree based on sequence variation in the barcode region of the cytochrome c oxidase I gene for North American species in the families Notodontidae and Doidae. (PDF)
Data
Erebidae (Arctiinae). NJ tree based on sequence variation in the barcode region of the cytochrome c oxidase I gene for North American species in the family Erebidae (Arctiinae). (PDF)
Article
Full-text available
Their relatively slow rates of molecular evolution, as well as frequent exposure to hybridization and introgression, often make it difficult to discriminate species of vascular plants with the standard barcode markers (rbcL, matK, ITS2). Previous studies have examined these constraints in narrow geographic or taxonomic contexts, but the present inv...
Data
A supplemental file containing four tables. Raw MPD and MNTD values for the vascular plant families of Canada (Table A). Raw MPD and MNTD values for the vascular plant genera of Canada (Table B). The biogeographic region, number of families, MPD, and MNTD for the 28 Canadian localities employed as a basis to test barcode resolution (Table C). The m...
Data
MNTD values for the three barcodes for genera. Comparison of MNTD values for the three barcode regions for genera of Canadian vascular plants. A) Three- dimensional scatter plot of 243 genera; B) Three-dimensional scatter plot of a subset of 171 genera with low MNTD values. The r2 is less than 0.007 for all comparisons. (PDF)
Data
The percentage of congeners for the six most species-rich families with low MNTD. The percentage of congeners for the six most species-rich families with low MNTD by barcode and region. (PDF)
Article
Full-text available
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...
Article
Full-text available
Numerous studies have demonstrated that DNA barcoding is an effective tool for detecting DNA clusters, which can be viewed as operational taxonomic units (OTUs), useful for biodiversity research. Frequently, the OTUs in these studies remained unnamed, not connected with pre-existing taxonomic hypotheses, and thus did not really contribute to feasib...
Article
Full-text available
Background: DNA-based testing has been gaining acceptance as a tool for authentication of a wide range of food products; however, its applicability for testing of herbal supplements remains contentious. Methods: We utilized Sanger and Next-Generation Sequencing (NGS) for taxonomic authentication of fifteen herbal supplements representing three d...
Data
Fungal taxa found in herbal supplements. Read coverage for fungal OTUs. (XLSX)
Data
Plant taxa found in herbal supplements. Read coverage for plant OTUs. (XLSX)