Robert Hanner

University of Guelph | UOGuelph · Department of Integrative Biology

The utility of eDNA for fish species and community monitoring is well-established using targeted amplification (i.e., qPCR and ddPCR) and passive sequencing approaches (i.e., metabarcoding). However, the lack of optimized and standardized methods reduces the sensitivity of this approach and precludes the reliable comparison of findings across studi...

Accurately determining the diet of wild animals can be challenging if food items are small, visible only briefly, or rendered visually unidentifiable in the digestive system. In some food caching species, an additional challenge is determining whether consumed diet items have been previously stored or are fresh. The Canada jay ( Perisoreus canadens...

The abundance of environmental DNA (eDNA) in water samples has been proposed as a sensitive, cost‐efficient, and non‐invasive alternative to infer population abundance and biomass, regardless of the acknowledgment that a number of biotic and abiotic factors can lead to substantially varying rates of eDNA deposition among organisms in a population....

Here, we introduce VLF , an R package to determine the distribution of very low frequency variants (VLFs) in nucleotide and amino acid sequences for the analysis of errors in DNA sequence records. The package allows users to assess VLFs in aligned and trimmed protein-coding sequences by automatically calculating the frequency of nucleotides or amin...

Biological soil crusts (BSCs) are communities of bryophytes, lichens, bacteria, and fungi and are the primary colonizing communities in early successional landscapes. In early ecosystem development BSCs often improve the physical and chemical conditions while also promoting soil microbial communities. Although BSCs are considered ecosystem engineer...

Background Mitochondrial genomes are the most sequenced genomes after bacterial and fungal genomic DNA. However, little information on mitogenomes is available for multiple metazoan taxa, such as Culicoides , a globally distributed, megadiverse genus containing 1,347 species. Aim Generating novel mitogenomic information from single Culicoides sono...

Environmental DNA (eDNA) holds notable potential for biomonitoring and ecological research. However, its utility for quantifying temporal changes in abundance, biomass, and diversity remains contentious. We investigated biotic and abiotic factors influencing temporal variation in eDNA concentration in large, 28,000 L experimental mesocosms. Time se...

Environmental DNA (eDNA) monitoring methods have played a significant role in improving fisheries management decisions. Yet, their impact to date has been rather limited in Canada, where eDNA sampling and analyses are only beginning to be used to inform management and conservation decisions, practices, and policies. Studies investigating hurdles to...

Increased use of environmental DNA (eDNA) analysis for indirect species detection has spurred the need to understand eDNA persistence in the environment. Understanding the persistence of eDNA is complex because it exists in a mixture of different states (e.g., dissolved, particle adsorbed, intracellular, and intraorganellar), and each state is expe...

DNA barcoding has been largely successful in satisfactorily exposing levels of standing genetic diversity for a wide range of taxonomic groups through the employment of only one or a few universal gene markers. However, sufficient coverage of geographically-broad intra-specific haplotype variation within genomic databases like the Barcode of Life D...

Freshwater ecosystems, such as streams, are facing increasing pressures from agricultural land use. Aquatic insects and other macroinvertebrates have historically been used as indicators of ecological condition and water quality in freshwater biomonitoring programs; however, many of these protocols use coarse taxonomic resolution (e.g., family) whe...

Early life stage (ELS) fishes provide a valuable metric for species, population, and ecosystem monitoring. Industrial, manufacturing, and power generating facilities in the U.S. can be required to monitor ELS fishes to assess impacts of facility intake waters. Traditional methods for collecting, identifying and enumerating ELS fishes includes ichth...

Background Grapevine, as an essential fruit crop with high economic values, has been the focus of molecular studies in diverse areas. Two challenges exist in the grapevine research field: (i) the lack of a rapid, user-friendly and effective RNA isolation protocol for mature dark-skinned berries and, (ii) the lack of validated reference genes that a...

Molecular sequence data is an essential component for many biological fields of study. The strength of these data is in their ability to be centralised and compared across research studies. There are many online repositories for molecular sequence data, some of which are very large accumulations of varying data types like NCBI’s GenBank. Due to the...

The COVID-19 pandemic has generated increased interest in potential transmission routes. In food retail settings, transmission from infected customers and workers and customers through surfaces has been deemed plausible. However, limited information exists on the presence and survival of SARS-CoV-2 on surfaces, particularly outside laboratory setti...

Conservation and long-term management plans of marine species need to be based upon the universally recognized key-feature of species identity. This important assignment is particularly challenging in skates (Rajiformes) in which the phenotypic similarity between some taxa and the individual variability in others, hampers accurate species identific...

Citation: Rapai, S.B.; Collis, B.; Henry, T.; Lyle, K.; Newmaster, S.G.; Raizman, V.; Hanner, R.H. Plant Community Structure within a Reclamation Field Trial and Forested Reference Sites in a Post-Mine Environment. Forests 2021, 12, 776.

eDNA metabarcoding is an effective molecular-based identification method for the biosurveillance of flighted insects. An eDNA surveillance approach maintains specimens for secondary morphological identification useful for regulatory applications. This study identified Culicoides species using eDNA metabarcoding and compared these results to morphol...

Grapevine leafroll is one of the most widespread and highly destructive grapevine diseases that is responsible for great economic losses to the grape and wine industries throughout the world. Six distinct viruses have been implicated in this disease complex. They belong to three genera, all in the family Closteroviridae. For the sake of convenience...

Building the capacity of efficiently determining the provenance of food products represents a crucial step towards the sustainability of the global food system. Despite species specific empirical examples of multi-tracer approaches to provenance, the precise benefit and efficacy of multi-tracers remains poorly understood. Here we show why, and when...

Despite the expressed interest of Canadians in sustainable and comprehensively labelled seafood, the country’s seafood labelling requirements remain scant and naming conventions in the Canadian Food Inspection Agency (CFIA) ‘fish list’ allow the grouping of multiple species under single ‘umbrella’ terms. Here, we test the extent to which CFIA listi...

Environmental DNA (eDNA) metabarcoding has revolutionized biodiversity monitoring and invasive pest biosurveillance programs. The introduction of insect pests considered invasive alien species (IAS) into a non-native range poses a threat to native plant health. The early detection of IAS can allow for prompt actions by regulating authorities, there...

Environmental DNA (eDNA) is gaining traction in conservation ecology as a powerful tool for detecting species at risk. We developed a quantitative polymerase chain reaction assay to detect a DNA amplicon fragment of the mitochondrial nicotinamide adenine dinucleotide locus of the Blanding’s turtle (Emydoidea blandingii) for detecting overwintering...

• With the increase in global trade and warming patterns, the movement, introduction, and establishment of non‐native insect species has increased. A rapid and effective early detection biosurveillance program to identify species of concern is needed to reduce future impacts and costs associated with introduced non‐native species. One of the challe...

Seafood represents up to 20% of animal protein consumption in global food consumption and is a critical dietary and income resource for the world’s population. Currently, over 30% of marine fish stocks are harvested at unsustainable levels, and the industry faces challenges related to Illegal, Unregulated and Unreported (IUU) fishing. Accurate spec...

This study represents a continuation of a backcrossing experi�ment initiated in 1982 and reported on earlier after seven generations of backcrossing (Gyllensten et al. 1985) and again after 26 generations (Gyllensten et al. 1991). For the better part of 50 years, it has been demonstrated that mito�chondrial DNA (mtDNA) has a largely, if not exclusi...

Seafood is an important source of protein worldwide. However, it is susceptible to a variety of fraudulent practices, including species substitution, illegal transshipment, and short-weighting. This chapter describes the global seafood industry and the ways in which it is vulnerable to fraud. Common categories of seafood fraud are discussed, along...

The use of environmental DNA (eDNA) allows the early detection of aquatic species at low densities (e.g. elusive and invasive species), which otherwise could be challenging to monitor using conventional techniques. Here, we assess the ability of eDNA sampling to detect the presence/absence of one species-at-risk (Blanding’s Turtle) and two invasive...

Quantitative polymerase chain reaction (qPCR) has been used as a standard molecular detection tool in many scientific fields. Unfortunately, there is no standard method for managing published qPCR data, and those currently used generally focus on only managing raw fluorescence data. However, associated with qPCR experiments are extensive sample and...

Building the capacity of efficiently determining the provenance of food products represents a crucial step towards the sustainability of the global food system. Whether it is for enforcing existing egislation or providing reliable information to consumers, technologies to verify geographical origin of food are being actively developed. Biological t...

Environmental DNA (eDNA) methods and technologies are increasingly being explored and applied in research studies and environmental monitoring. Although eDNA has some limitations, there is the potential for major advantages to using this method within a regulatory context for characterizing and assessing species, populations, communities, and whole...

Freshwater bio‐monitoring programs routinely sample aquatic macroinvertebrates. These samples are time‐consuming to collect, as well as challenging and costly to identify reliably to genus or species. Environmental DNA (eDNA) metabarcoding has emerged as a surrogate to traditional collection techniques and has been used in whole‐community approache...

This special issue features eleven articles presented at the Pathway to Increase Standards and Competency of eDNA Surveys (PISCeS) conference in October 2018. The prominent theme in this special issue is methodological developments to enhance species and community characterization using eDNA, covering tree main scientific trends: validation of eDNA...

Modern taxonomy requires the preservation of biospecimens for both morphological and molecular applications. The utility of a previously identified preservative, dimethyldimethylhydantoin hydantoin (Dekafald®), to retain both physical diagnostic traits and the DNA integrity of biological specimens remains unknown. Using 439 eggs and 414 larvae from...

The profile of human gut microbiota is known to be affected by diet and is linked to human health. Seafood is a highly consumed food and it accounts for a large proportion of food-borne illness. The objective of this study is to characterise the microbiota of fish fillets of various species sold in the Canadian market. We test 19 fish fillet sample...

Citation: Young RG, Yu J, Cote M-J, Hanner RH (2020) The Molecular Data Organization for Publication (MDOP) R package to aid the upload of data to shared databases. Biodiversity Data Journal 8: e50630. Abstract Molecular identification methods, such as DNA barcoding, rely on centralized databases populated with morphologically identified individual...

Biodiversity informatics depends on digital access to credible information about species. Many online resources host species’ data, but the lack of categorisation for these resources inhibits the growth of this entire field. To explore possible solutions, we examined the (now retired) Biodiversity Information Projects of the World (BIPW) dataset cr...

As environmental DNA (eDNA) becomes more widely used in research, it becomes increasingly important to have a standard set of reporting guidelines for metadata. The unique properties of eDNA combined with the physical characteristics of the surrounding environment produce highly varied sampling conditions which can influence how an organism is dete...

Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constr...

Abstract Environmental DNA metabarcoding has been widely touted as a powerful tool for monitoring biodiversity in marine ecosystems. However, this method still requires thorough validation and standardization before it can be widely applied for ecological monitoring. The potential utility of environmental DNA metabarcoding is greatest in systems wi...

Entrainment studies, mandated by The Final Rule, require facilities to identify entrained organisms to “the lowest taxon possible”, usually species. The life stages most commonly captured present challenges to traditional taxonomic approaches, and DNA barcoding also presents time- and cost-related barriers to routine screening. Real-time PCR offers...

Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constr...

DNA barcoding opens new perspectives on the way we document biodiversity. Initially proposed to circumvent the limits of morphological characters to assign unknown individuals to known species, DNA barcoding has been used in a wide array of studies where collecting species identity constitutes a crucial step. The assignment of unknowns to knowns as...

Abstract Environmental DNA (eDNA) methods are being developed for use in conservation biology to improve upon conventional species survey techniques. Validation of eDNA methods in different environmental contexts is required if they are to be widely adopted. One potential application of eDNA methods is for the detection of freshwater mussels (Bival...

Larval fishes provide a valuable metric for assessing and monitoring species, populations, and ecosystem trends and condition. However, taxonomic resolution for this life stage is inherently problematic because of their individual sizes, limited morphological characteristics and high tissue degradation rates. There is little research on methods tha...

This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. Abstract Environmental effects monitoring in marine ecosystems are...

Assessing levels of standing genetic variation within species requires a robust sampling for the purpose of accurate specimen identification using molecular techniques such as DNA barcoding; however, statistical estimators for what constitutes a robust sample are currently lacking. Moreover, such estimates are needed because most species are curren...

Species proliferate through evolutionary mechanisms but coexist through ecological dynamics. As such, it might be expected that mechanisms of speciation and species maintenance jointly influence the settlement of ecological communities, a process called community assembly. Disentangling the relative contribution of evolutionary and ecological dynam...

Rose gall wasps, Diplolepis Geoffroy (Hymenoptera: Cynipidae), induce structurally distinct galls on wild roses (Rosa Linnaeus; Rosaceae), which provide gallers with food and shelter. These galls are attacked by a wide variety of micro-hymenopterans, including Periclistus Förster (Hymenoptera: Cynipidae), which act as inquilines. Both Diplolepis an...

Interception of potential invasive species at ports-of-entry is essential for effective biosecurity and biosurveillance programs. However, taxonomic assessment of the immature stages of most arthropods is challenging; characters for identification are often dependent on adult morphology and reproductive structures. This study aims to strengthen the...

Protecting the seafood supply chain from species substitution is critical for economic, health, and conservation reasons. DNA-based methods represent an effective means to detect species substitution, but current methods can be time consuming or costly, and require specialized instruments and operators. Real-time PCR provides an alternative that ca...

Meat and poultry are major protein sources for humans worldwide. Undeclared ingredients in processed meat products, like sausage, continue to be identified in retail products all over the world. In collaboration with the Canadian Food Inspection Agency, a previous study of products purchased in Canada showed 20% mislabelling rate in sausage meats w...

The global seafood market places humans as apex predators within the marine food web, linking species and ecosystems around the world. Here, we argue that the structure of these seafood systems is in opposition to nature’s common stabilizing structures. We first describe a remarkably repeated structure in nature’s food webs: generalist foraging by...

DNA barcoding has greatly accelerated the pace of specimen identification to the species level, as well as species delineation. Whereas the application of DNA barcoding to the matching of unknown specimens to known species is straightforward, its use for species delimitation is more controversial, as species discovery hinges critically on present l...

PCR methods are the most commonly used DNA-based identity tool in the commercial food, beverage, and natural health product markets. These methods are routinely used to identify foodborne pathogens and allergens in food. Proper validation methods for some sectors have been established, while there are none in other markets, such as botanicals. Resu...

Background: PCR methods are the most commonly used DNA-based identity tool in the commercial food, beverage, and natural health product markets. These methods are routinely used to identify foodborne pathogens and allergens in food. Proper validation methods for some sectors have been established, while there are none in other markets, such as bota...

Climate change is rewiring the food webs that determine the fate of diverse ecosystems. Mobile generalist consumers are responding to climate change by rapidly shifting their behaviour and foraging, driving food webs to flex. Although these responsive generalists form a key stabilizing module in food web structure, the extent to which they are pres...

Seafood has become one of the most heavily traded food commodities in the era of globalization. International seafood supply chains are complex and contend with many difficulties in bringing an enormous variety of products to market. A major challenge involves accurately labelling products such that they comply with a diverse set of regulatory fram...

Sustainably feeding the next generation is often described as one of the most pressing "grand challenges" facing the 21 st century. Generally, scholars propose addressing this problem by increasing agricultural production, investing in technology to boost yields, changing diets, or reducing food waste. In this paper, we explore whether global food...

Available Kilocalories and their equivalent servings from the FAO’s Food balance sheets for agricultural year 2011. Serving calculations were based on Canada’s Food Guide serving sizes and USDA guidelines. (PDF)

The amount of food produced, their uses for human food and livestock feed and arable land area under each food group based on FAO 2011 data. (PDF)

Breakdown of greenhouse gas emissions by food category. (PDF)

The woodland caribou (Rangifer tarandus caribou) boreal population is listed on Schedule 1 of the Federal Species at Risk Act as Threatened. During critical winter months, boreal caribou rely on Cladonia subgenus Cladina as their primary food source. To better understand how to rehabilitate winter habitat for caribou in a post mine environment in n...

Lampricides are currently being applied to streams and rivers to control the population of sea lamprey, an invasive species, in the Great Lakes. The most commonly used lampricide agent used in the field is 3-trifluoromethyl-4-nitrophenol (TFM), which targets larval sea lamprey in lamprey-infested rivers and streams. The specificity of TFM is due to...

The complexity of seafood supply chains and fish naming systems has rendered the traceability of a seafood product challenging if not impossible, creating loopholes for intentional or unintentional illicit practices that erode the market transparency and integrity. DNA barcoding has been extensively applied to evaluate the integrity of seafood mark...

Since 2013, DNA barcoding has been in use by the Canadian Food Inspection Agency (CFIA) to speciate finfish fillets sold and consumed in Canada. We retrospectively assessed both the usefulness of DNA barcoding technology as a regulatory tool and the usefulness of the publicly available Barcode of Life Database (BOLD) in supporting the application o...

Continuously increasing demand for plant and animal products causes unsustainable depletion of biological resources. It is estimated that one-quarter of sharks and rays are threatened worldwide and although the global fin trade is widely recognized as a major driver, demand for meat, liver oil, and gill plates also represents a significant threat....

Delineating Evolutionary Significant Units for conservation purposes is a crucial step in conservation. Across a distribution range, species frequently display population structure that drives the distribution of genetic diversity. These patterns of genetic structure and diversity result from intricate interactions between biogeographic history and...

Managing the biodiversity crisis requires access to credible information on species, as well as their changing abundance and spatio-temporal distributions, among other variables. Technological advances are expanding both the variety and volume of data available, resulting in the emergence of biodiversity informatics as a rapidly growing research pa...

Food adulteration and feed contamination are significant issues in the food/feed industry, especially for meat products. Reliable techniques are needed to monitor these issues. Droplet Digital PCR (ddPCR) assays were developed and evaluated for detection and quantification of bovine, porcine, chicken and turkey DNA in food and feed samples. The ddP...

Evaluating the repeatability of the ddPCR assay for the internal control (IC). IC was tested 16 times. The RSD% was 5.53. (TIFF)

Evaluating the effect of normalizing the ddPCR output using the internal control (IC). ddPCR results were obtained from testing fortified heat-processed beef in poultry meal without normalization to IC (A) and after normalization to IC (B). (TIFF)

Optimizing the concentration of internal control used in ddPCR assays. (PDF)

Results of robustness study. (PDF)

Example illustrating how the limit/range of quantification of the bovine ddPCR assay was determined. (A) ddPCR results for fortified beef in poultry meal at 0, 0.005, 0.01, 0.05, 0.1, 0.5, 1.0, 3.0, 5.0, and 10.0% (wt/wt). The curve exhibited a plateau when beef content was over 3.0%. (B-C) are subset data of (A) where (B) shows beef in poultry mea...

Accurate food labelling is of utmost importance for food safety and consumer choice in the food chain. Complete or partial substitution, whether intentional or unintentional, may introduce food pathogens or allergens to a product or affect personal or religious beliefs. Several studies around the world have reported different degrees of species sub...

Recently, Stawitz et al. (2016) collated existing primary literature on DNA identification of finfish products and conducted a series of analyses to explore the environmental and economic ripples of species substitution. While we agree that the assessment of the impacts of seafood mislabelling is paramount, we show that the main conclusion of the s...

Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or i...

Summary of all barcoded Mediterranean Chondrichthyans generated by the integration of data from the three main barcoding initiatives by Moftah et al. (2011), Landi et al. (2014) and ELASMOMED, as well as other available studies (reported under the column OTHER). Both the number of barcode records obtained from Mediterranean and non-Mediterranean sp...

The GenBank Accession Numbers, BIN, Sample ID and Process ID of the 882 Mediterranean chondrichthyan individuals successfully barcoded by ELASMOMED. (XLSX)

Haplotype parsimony networks of Dasyatis pastinaca reconstructed using ELASMOMED COI barcode sequences. Each circle represents one haplotype and its size is proportional to frequency. Colours indicate the origin of samples according to FAO fishing divisions. (TIF)

Complete list of mutations and positions characterizing each haplotype displayed in Fig 4. For each species, the number of sequences used and the length of the alignment are reported. (XLSX)

Summary of taxa and individuals collected and barcoded for the ELASMOMED initiative. The number of collected and barcoded individuals are reported for each chondrichthyan species and each FAO division as well as in total. (XLSX)

Lake Whitefish Coregonus clupeaformis is the most commercially valuable species in Lake Huron. The fishery for this species has historically been managed based on 25 management units (17 in Canada, 8 in the USA). However, congruence between the contemporary population structure of Lake Whitefish and management units is poorly understood. We used st...

Given long generation times and relatively slow reproductive rates, elasmobranchs (sharks and rays) are particularly prone to overexploitation. The unrelenting demand for shark products is unsustainable and many shark fisheries are collapsing. Because of the urgency of addressing this situation, this book concludes with an overview of how DNA-based...