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To assess the recent history of taxonomy in Canada and the impact of DNA barcoding upon the field, we performed a survey of various indicators of taxonomic research over the past 30 years and also assessed the current direct impact of funds made available for taxonomy through the DNA barcoding NSERC (Natural Sciences and Engineering Research Council of Canada) network grant. Based on results from surveys of three Canadian journals, we find that between 1980 and 2000 there was a 74% decline in the number of new species described and a 70% reduction in the number of revisionary studies published by researchers based in Canada, but there was no similar decline for non-Canadian- authored research in the same journals. Between 1991 and 2007 there was a 55% decline in the total amount of inflation-corrected funds spent upon taxonomic research by NSERC's GSC18 (Grant Selection Committee 18); this was a result of both a decrease in the number of funded taxonomists and a decrease in mean grant size. Similarly, by 2000, the number of entomologists employed at the Canadian National Collection (CNC) had decreased to almost half their 1980 complement. There was also a significant reduction in the number of active arthropod taxonomists in universities across the country between 1989 and 1996. If these declines had continued unabated, it seems possible that taxonomy would have ceased to exist in Canada by the year 2020. While slight increases in personnel have occurred recently at the CNC, the decline in financial assistance for taxonomists has been largely reversed through funds associated with DNA barcoding. These moneys have increased the financial resources available for taxonomy overall to somewhere close to NSERC's 1980 expenditures and have also substantially increased the number of HQP (highly qualified personnel) currently being trained in taxonomy. We conclude that the criticism 'DNA barcoding has taken funds away from traditional approaches to taxonomy' is false and that, in Canada at least, the advent of DNA barcoding has reversed the dramatic decline in taxonomy. We provide recommendations on how to foster the future health of taxonomy in Canada. Afin d'evaluer l'evolution recente de la taxonomie an Canada et l'impact de l'utilisation des codes a barres ADN sur la discipline, nous avons fait l'inventaire de divers indicateurs de la recherche taxonomisee an cours des 30 dernieres annees; nous avons aussi evalue l'impact direct actuel des fonds mis a la disposition de la taxonomie par la subvention de reseau de codage par codes a barres du CRSNG (Conseil de recherches en sciences naturelles et en genie du Canada). D'apres les resultats des inventaires faits dans trois revues canadiennes entre 1980 et 2000, il y a eu un declin de 74 % du nombre de nouvelles especes decrites et une reduction de 70 % du nombre de travaux de revision publies par des chercheurs bases an Canada, mais aucune reduction similaire des travaux de recherche provenant d'auteurs non canadiens dans les memes revues. Entre 1991 et 2007, il y a eu un declin de 55 % dans la quantite totale de fonds, apres correction pour l'inflation, consacres a la recherche taxonomisee par le comite CSS18 (Comites de selection des subventions 18) du CRSNG; c'est le resultat a la fois d'une diminution du nombre de taxonomistes subventionnes et une reduction de la subvention moyenne. De meme, en 2000, le nombre d'entomologistes a l'emploi de la Collection nationale du Canada (CNC) avait diminue de moitie par rapport a l'accompagnement dans les annees 1980 et il y avait une reduction significative du nombre de taxonomistes des arthropodes actifs dans les universites dans tout le pays entre 1989 et 1996. Si ces declins s'etaient poursuivis sans remede, il apparait possible que la taxonomie ait cesse d'exister an Canada avant l'annee 2020. Alors qu'il y a eu recemment une faible augmentation du personnel a la CNC, le declin de l'aide financiere aux taxono mistes a ete en grande partie contrecarre par les ressources financieres associees au codage par codes a barres. Ces argents ont augmente les ressources financieres disponibles a la taxonomie globalement a un niveau assez proche des ressources depensees par le CRSNG en 1980 et ont accru la quantite de personnes hautement qualifiees (HQP) actuellement en formation en taxonomie. Nous concluons que la critique qui veut que le codage par codes a barres ADN ait retire des fonds aux approches traditionnelles de la taxonomie est fausse et qu'au Canada au moins, 1'arrivee du codage par codes a barres ADN a renverse la tendance au declin de la taxonomie. Nous presentons des recommandations pour ameliorer la sante future de la taxonomie au Canada. [Traduit par la Redaction], Introduction Taxonomy is fundamental to all of biology, yet there have been numerous reports that the state of the discipline is in decline worldwide (e.g., Winston and Metzger 1998; Disney [...]

The soybean aphid ( Aphis glycines Matsumura) is an economically significant pest in North America, causing extensive damage to soybean crops through direct feeding damage and disease transmission. If unchecked, this pest could cause billions of dollars of damage to soybean crops. Identification of the soybean aphid can be difficult due to its small size, complex life cycle and morphological plasticity. Generally, an expert is required to identify a specimen. Additionally, identification of some life stages, such as eggs, is impossible. DNA barcoding has been successfully used to differentiate aphid species, including A. glycines, based on sequencing of a standardized gene region. Although this method represents an important step towards accurate identification, samples must still be sent to specialized facilities for analysis. Using existing DNA barcode sequences in the publically accessible Barcode of Life Data System ( BOLD; ), species-specific differences were identified and used to develop a real-time PCR assay to identify soybean aphids. This assay can be run on portable systems for rapid, accurate and simple identification in the field. The use of a non-destructive DNA extraction protocol allows the original insect to be vouchered and therefore available for further study if necessary. This work represents an important step in soybean aphid management. [ABSTRACT FROM AUTHOR]

The green apple aphid ( Aphis pomi) and the spirea aphid ( Aphis spiraecola) are pests of apples in North America. Although management regimes exist to effectively control these pests, they differ significantly because of varying susceptibility of each species to common pesticides and differences in their life cycles. Therefore, accurate identification of the species present is essential for pest control. However, the identification process is complicated because of the morphological similarity between these two species. As a result, confusion between A. pomi and A. spiraecola often occurs. DNA barcoding has been proven to accurately identify species of Aphididae. A further study demonstrated that DNA barcodes could be used to accurately differentiate A. pomi and A. spiraecola. DNA barcoding represents an important step towards rapid identification of these pests as distinctions can be easily made between morphologically similar species as well as from eggs and immature individuals in addition to adults. However, samples must still be sent to specially equipped facilities for sequence analysis, which can take between several hours and days. Real-time PCR is emerging as a useful tool for more rapid pest identification. The purpose of this study was to develop a real-time PCR assay for differentiation of A.pomi from A. spiraecola based on DNA barcode sequences from the Barcode of Life Data System. This assay was designed on the portable SmartCycler II platform and can be used in field settings to differentiate these species quickly and accurately. It has the potential to be a valuable tool to improve pest management of A. pomi and A. spiraecola. [ABSTRACT FROM AUTHOR]

The review of the data on karyology and DNA content in Acipenseriformes shows that both extant families, the Polyodontidae and Acipenseridae, originated from a tetraploid ancestor which probably had a karyotype consisting of 120 macro- and microchromosomes and DNA content ofabout 3.2--3.8 pg per nucleus. The tetraploidization of the presumed60-chromosome ancestor seems to have occurred at an early time of evolution of the group. The divergence of the Acipenseridae into Scaphirhyninae and Acipenserinae occurred without polyploidization. Within the genus Acipenser, polyploidization was one of the main genetic mechanisms of speciation by which 8n and 16n-ploid species were formed. Individual gene trees constructed for sequenced partial fragments of the 18S rRNA (230 base pairs, bp), 12S rRNA (185 bp), 16S rRNA (316 bp), and cytochrome b (270 bp) genes of two Eurasian (A. baerii and A.ruthenus) and two American (A. transmontanus and A. medirostris) species of Acipenser, Huso dauricus, Pseudoscaphirhynchus kaufmanni, Scaphirhynchus albus, and Polyodon spathula showed a low level of resolution; the analysis of a combined set of data for the four genes, however, gave better resolution. Our phylogeny based on molecular analysis had two major departures from existing morphological hypotheses: Huso dauricus is a sister-species to Acipenser instead of being basal to all acipenseriforms, and Scaphirhynchus and Pseudoscaphirhynchus donot form a monophyletic group. The phylogenetic tree constructed forthe cytochrome b gene fragments (with inclusion of 7 additional species of Acipenser) supported the conclusion that octoploid species appeared at least three times within Acipenser. [ABSTRACT FROM AUTHOR]

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 canadensis) is a generalist resident of North American boreal and subalpine forests with anatomical and behavioural adaptations allowing it to make thousands of arboreal food caches in summer and fall that are presumably responsible for its high winter survival and late winter/early spring breeding. We used DNA fecal metabarcoding to obtain novel information on nestling diets and compiled a dataset of 662 published and unpublished direct observations or stomach contents identifications of natural foods consumed by Canada jays throughout the year. We then used detailed natural history information to make informed decisions on whether each item identified to species in the diets of winter adults and nestlings was best characterized as 'likely cached', 'likely fresh' (i.e., was available as a non-cached item when it appeared in a jay's feces or stomach), or 'either possible'. Of the 87 food items consumed by adults in the winter, 39% were classified as 'likely cached' and 6% were deemed to be 'likely fresh'. For nestlings, 29% of 125 food items identified to species were 'likely cached' and 38% were 'likely fresh'. Our results support both the indispensability of cached food for Canada jay winter survival and previous suggestions that cached food is important for late winter/early spring breeding. Our work highlights the value of combining metabarcoding, stomach contents analysis, and direct observations to determine the cached vs. non-cached origins of consumed food items and the identity of food caches, some of which could be especially vulnerable to degradation through climate change., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Sutton et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

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 identification. Here, 432 individual skate samples collected from four major ocean areas of the Atlantic were barcoded and taxonomically analysed. A BOLD project ELASMO ATL was implemented with the aim of establishing a new fully available and well curated barcode library containing both biological and molecular information. The evolutionary histories of the 38 skate taxa were estimated with two concatenated mitochondrial markers (COI and NADH2) through Maximum Likelihood and Bayesian inference. New evolutionary lineages within the genus Raja were discovered off Angola, where paleogeographic history coupled with oceanographic discontinuities could have contributed to the establishment of isolated refugia, playing a fundamental role among skates' speciation events. These data successfully resolved many taxonomic ambiguities, identified cryptic diversity within valid species and demonstrated a highly cohesive monophyletic clustering among the order, laying the background for further inference of evolutionary patterns suitable for addressing management and conservation issues.

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, data fusion of bio-tracers is an extremely powerful technique for geographical provenance discrimination. Specifically, we show using extensive simulations how, and under what conditions, geographical relationships between bio-tracers (e.g., spatial covariance) can act like a spatial fingerprint, in many naturally occurring applications likely allowing rapid identification with limited data. To highlight the theory, we outline several statistic methodologies, including artificial intelligence, and apply these methodologies as a proof of concept to a limited data set of 90 individuals of highly mobile Sockeye salmon that originate from 3 different areas. Using 17 measured bio-tracers, we demonstrate that increasing combined bio-tracers results in stronger discriminatory power. We argue such applications likely even work for such highly mobile and critical fisheries as tuna.

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 samples from nine species in five fish families, ten of which were previously determined to be mislabeled as different species. The microbiota profiles were characterized using 16S rRNA gene high-throughput sequencing. Despite the complexities of the supply chain to produce these fillets, the major microbial groups were fairly consistent across samples. Significant differences in microbial taxa were observed between species, families, and based on labelling accuracy. Several putative spoilage and putative pathogenic taxa were identified. Studying food-associated microbiota can provide comprehensive information on food safety, authenticity, and traceability., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

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 created by the Biodiversity Information Standards (TDWG); this project, which ran from 2007-2015 (officially removed from the TDWG website in 2018) was an attempt at organising the Web's biodiversity databases into an indexed list. To do this, we applied a simple classification scheme to score databases within BIPW based on nine data categories, to characterise trends and current compositions of this biodiversity e-infrastructure. Primarily, we found that of 600 databases investigated from BIPW, only 315 (~53%) were accessible at the time of this writing, underscoring the precarious nature of the biodiversity information landscape. Many of these databases are still available, but suffer accessibility issues such as link rot, thus putting the information they contain in danger of being lost. We propose that a community-driven database of biodiversity databases with an accompanying ontology could facilitate efficient discovery of relevant biodiversity databases and support smaller databases - which have the greatest risk of being lost., (Jarrett Blair, Rodger Gwiazdowski, Andrew Borrelli, Michelle Hotchkiss, Candace Park, Gleannan Perrett, Robert Hanner.)

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 that rapidly preserve larval tissues for later morphological and molecular identification. The goal of this study was to test methods of rapidly killing fish embryos that maintain both morphological and molecular integrity. Rapid cooling with dry ice successfully maintained morphological and molecular integrity and may offer a simple and cost-effective approach for larval fish identification., (© 2019 The Fisheries Society of the British Isles.)

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 constrained its use as a model in evolutionary studies. Here, we established a DNA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed.

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 assumes that species are already well identified and delineated, making the assignment performed reliable. Here, we used DNA-based species delimitation and specimen assignment methods iteratively to tackle the inventory of the Indo-Australian Archipelago grey mullets, a notorious case of taxonomic complexity that requires DNA-based identification methods considering that traditional morphological identifications are usually not repeatable and sequence mislabeling is common in international sequence repositories. We first revisited a DNA barcode reference library available at the global scale for Mugilidae through different DNA-based species delimitation methods to produce a robust consensus scheme of species delineation. We then used this curated library to assign unknown specimens collected throughout the Indo-Australian Archipelago to known species. A second iteration of OTU delimitation and specimen assignment was then performed. We show the benefits of using species delimitation and specimen assignment methods iteratively to improve the accuracy of specimen identification and propose a workflow to do so., Competing Interests: None declared., (© 2020 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

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 botanicals. Results: A survey of the literature indicates that some validation criteria are not addressed when developing PCR tests for botanicals. Objective: We provide recommendations for qualitative real-time PCR methods for validating identity tests for botanical ingredients. Methods: These include common criteria that underpin the development and validation of rigorous tests, including ( 1 ) the aim of the validation test, ( 2 ) the applicability of different matrix variants, ( 3 ) specificity in identifying the target species ingredient, ( 4 ) sensitivity in detecting the smallest amount of the target material, ( 5 ) repeatability of methods, ( 6 ) reproducibility in detecting the target species in both raw and processed materials, ( 7 ) practicability of the test in a commercial laboratory, and ( 8 ) comparison with alternative methods. In addition, we recommend additional criteria, according to which the practicability of the test method is evaluated by transferring the method to a second laboratory and by comparison with alternative methods. Conclusions and Highlights: We hope that these recommendations encourage further publication on the validation of PCR methods for many botanical ingredients. These properly validated PCR methods can be developed on small, real-time biotechnology that can be placed directly into the supply chain ledger in support of highly transparent data systems that support QC from the farm to the fork of the consumer.

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 frameworks, ranging from country-of-origin through to the final point of consumer sale. Thanks to DNA barcoding, seafood mislabelling is now recognized as a global problem, with potentially negative impacts on human health, economy and the environment. Mislabelling can result from species misidentification, use of inappropriate common names, incomplete and/or out-dated regulatory frameworks, or through market substitution. While prior studies have focused primarily on retail and food service establishments, this study used barcoding to assess rates of finfish mislabelling at multiple points in the supply chain within Ontario, Canada. A total of 203 specimens from 12 key targeted species were collected from varied importers, registered processing plants and retailers in Southern Ontario and identified using DNA barcoding. Species identity of samples was used to assess conformity of labelling against the Canadian Food Inspection Agency's (CFIA) Fish List, which revealed an overall mislabelling rate of 32.3% among targeted species. The mislabelling rate was significantly different between samples collected from importers and retailers. Among the mislabelled samples were seven samples that originated from US and were properly labelled according to US Food and Drug Administration (FDA) Seafood List. This study evaluated the integrity of chain of custody documents and identified discrepancies in 43 samples (21.4%). Implementing seafood traceability throughout the supply chain and harmonizing labelling regulations between countries can help to ensure industry compliance in a globalized market, while sampling at multiple points in the supply chain can help to reveal causes., (Copyright © 2018. Published by Elsevier Ltd.)

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 relative inability of sea lamprey to detoxify the agent relative to non-target fishes. There is increasing concern, however, about non-target effects on fishes, particularly threatened populations of juvenile lake sturgeon (LS; Acipenser fulvescens). There is therefore a need to develop models to better define lake sturgeon's response to TFM. Here we report the establishment of five LS cell lines derived from the liver, gill, skin and intestinal tract of juvenile LS and some of their cellular characteristics. All LS cell lines grew well at 25 °C in Leibovitz's (L)- 15 medium supplemented with 10% FBS. All cell lines demonstrated high senescence-associated β-galactosidase activity and varying levels of Periodic acid Schiff-positive polysaccharides, indicating substantial production of glycoproteins and mucosubstances by the cells. Comparative toxicity of TFM in the five LS cell lines was assessed by two fluorescent cell viability dyes, Alamar Blue and CFDA-AM, in conditions with and without serum and at 24 or 72 h exposure. Deduced EC 50 values were compared between the cell lines and to the reported in vivo LC 50 s. Tissues sensitive to the effects of TFM in vivo correlated with cell lines from the same tissues being most sensitive to TFM in vitro. EC 50 values for the LSliver-e cells was significantly lower than the EC 50 for the rainbow trout (RBT) liver cells RTL-W1, reaffirming the in vivo observation that LS was generally more TFM-sensitive than rainbow trout. Our data suggests that whole-fish sensitivity of LS to TFM is likely attributable to sensitivity at the cellular level. Thus, LS cell lines, as well as those of RBT, can be used to screen and evaluate the toxicity of the next generation of lampricides on non-target fish such as lake sturgeon., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Sustainably feeding the next generation is often described as one of the most pressing "grand challenges" facing the 21st 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 production is nutritionally balanced by comparing the diet that nutritionists recommend versus global agricultural production statistics. Results show that the global agricultural system currently overproduces grains, fats, and sugars while production of fruits and vegetables and protein is not sufficient to meet the nutritional needs of the current population. Correcting this imbalance could reduce the amount of arable land used by agriculture by 51 million ha globally but would increase total land used for agriculture by 407 million ha and increase greenhouse gas emissions. For a growing population, our calculations suggest that the only way to eat a nutritionally balanced diet, save land and reduce greenhouse gas emissions is to consume and produce more fruits and vegetables as well as transition to diets higher in plant-based protein. Such a move will help protect habitats and help meet the Sustainable Development Goals., Competing Interests: The authors have declared that no competing interests exist.

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. This study used DNA barcoding and 16 S rRNA sequencing as a method to identify shark and ray species from dried fins and gill plates, obtained in Canada, China, and Sri Lanka. 129 fins and gill plates were analysed and searches on BOLD produced matches to 20 species of sharks and five species of rays or - in two cases - to a species pair. Twelve of the species found are listed or have been approved for listing in 2017 in the appendices of the Convention on International Trade in Endangered Species of Fauna and Flora (CITES), including the whale shark (Rhincodon typus), which was surprisingly found among both shark fin and gill plate samples. More than half of identified species fall under the IUCN Red List categories 'Endangered' and 'Vulnerable', raising further concerns about the impacts of this trade on the sustainability of these low productivity species.

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 ddPCR methods were designed based on mitochondrial DNA sequences and integrated with an artificial recombinant plasmid DNA to control variabilities in PCR procedures. The specificity of the ddPCR assays was confirmed by testing both target species and additional 18 non-target species. Linear regression established a detection range between 79 and 33200 copies of the target molecule from 0.26 to 176 pg of fresh animal tissue DNA with a coefficient of determination (R2) of 0.997-0.999. The quantification ranges of the methods for testing fortified heat-processed food and feed samples were 0.05-3.0% (wt/wt) for the bovine and turkey targets, and 0.01-1.0% (wt/wt) for pork and chicken targets. Our methods demonstrated acceptable repeatability and reproducibility for the analytical process for food and feed samples. Internal validation of the PCR process was monitored using a control chart for 74 consecutive ddPCR runs for quantifying bovine DNA. A matrix effect was observed while establishing calibration curves with the matrix type under testing, and the inclusion of an internal control in DNA extraction provides a useful means to overcome this effect. DNA degradation caused by heating, sonication or Taq I restriction enzyme digestion was found to reduce ddPCR readings by as much as 4.5 fold. The results illustrated the applicability of the methods to quantify meat species in food and feed samples without the need for a standard curve, and to potentially support enforcement activities for food authentication and feed control. Standard reference materials matching typical manufacturing processes are needed for future validation of ddPCR assays for absolute quantification of meat species.

Among the 899 species of freshwater fishes reported from Sundaland biodiversity hotspot, nearly 50% are endemics. The functional integrity of aquatic ecosystems is currently jeopardized by human activities, and landscape conversion led to the decline of fish populations in several part of Sundaland, particularly in Java. The inventory of the Javanese ichthyofauna has been discontinuous, and the taxonomic knowledge is scattered in the literature. This study provides a DNA barcode reference library for the inland fishes of Java and Bali with the aim to streamline the inventory of fishes in this part of Sundaland. Owing to the lack of available checklist for estimating the taxonomic coverage of this study, a checklist was compiled based on online catalogues. A total of 95 sites were visited, and a library including 1046 DNA barcodes for 159 species was assembled. Nearest neighbour distance was 28-fold higher than maximum intraspecific distance on average, and a DNA barcoding gap was observed. The list of species with DNA barcodes displayed large discrepancies with the checklist compiled here as only 36% (i.e. 77 species) and 60% (i.e. 24 species) of the known species were sampled in Java and Bali, respectively. This result was contrasted by a high number of new occurrences and the ceiling of the accumulation curves for both species and genera. These results highlight the poor taxonomic knowledge of this ichthyofauna, and the apparent discrepancy between present and historical occurrence data is to be attributed to species extirpations, synonymy and misidentifications in previous studies., (© 2016 John Wiley & Sons Ltd.)

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 incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles. Here we present results generated by the ELASMOMED Consortium, a regional network aiming to sample and DNA-barcode the Mediterranean Chondrichthyans with the ultimate goal to provide a comprehensive DNA barcode reference library. This library will support and improve the molecular taxonomy of this group and the effectiveness of management and conservation measures. We successfully barcoded 882 individuals belonging to 42 species (17 sharks, 24 batoids and one chimaera), including four endemic and several threatened ones. Morphological misidentifications were found across most orders, further confirming the need for a comprehensive DNA barcoding library as a valuable tool for the reliable identification of specimens in support of taxonomist who are reviewing current identification keys. Despite low intraspecific variation among their barcode sequences and reduced samples size, five species showed preliminary evidence of phylogeographic structure. Overall, the ELASMOMED initiative further emphasizes the key role accurate DNA barcoding libraries play in establishing reliable diagnostic species specific features in otherwise taxonomically problematic groups for biodiversity management and conservation actions., Competing Interests: The authors have declared that no competing interests exist.

Mitogenome metadata are descriptive terms about the sequence, and its specimen description that allow both to be digitally discoverable and interoperable. Here, we review a sampling of mitogenome metadata published in the journal Mitochondrial DNA between 2005 and 2014. Specifically, we have focused on a subset of metadata fields that are available for GenBank records, and specified by the Genomics Standards Consortium (GSC) and other biodiversity metadata standards; and we assessed their presence across three main categories: collection, biological and taxonomic information. To do this we reviewed 146 mitogenome manuscripts, and their associated GenBank records, and scored them for 13 metadata fields. We also explored the potential for mitogenome misidentification using their sequence diversity, and taxonomic metadata on the Barcode of Life Datasystems (BOLD). For this, we focused on all Lepidoptera and Perciformes mitogenomes included in the review, along with additional mitogenome sequence data mined from Genbank. Overall, we found that none of 146 mitogenome projects provided all the metadata we looked for; and only 17 projects provided at least one category of metadata across the three main categories. Comparisons using mtDNA sequences from BOLD, suggest that some mitogenomes may be misidentified. Lastly, we appreciate the research potential of mitogenomes announced through this journal; and we conclude with a suggestion of 13 metadata fields, available on GenBank, that if provided in a mitogenomes's GenBank record, would increase their research value.

Mitochondrial DNA is routinely used to answer a variety of biological questions; and there is growing evidence suggesting that its accumulation of mutations is influenced by life history, effective population size and cellular energy requirements. This study examines the influence of phylogenetic patterns of metabolic activity on the evolution of mitochondrial DNA in fishes, given energy requirements associated with high performance versus sedentary life histories. It was determined that all 13 protein coding genes of the mitogenome experience a relaxation of purifying selection in sedentary fishes. This phenomenon was not detected in nuclear housekeeping genes, suggesting that it can be explained by the energy requirements of these groups, and possibly their effective population sizes. This study also examined the subunit binding sites of two subunits of cytochrome c oxidase (COXI and COXIII), and did not detect any differences in selection between these groups of fishes. These cytochrome c oxidase subunits interact with subunits that are encoded by the nuclear genome and it has been suggested that a unique form of coevolution occurs between these genomes in order to maintain function, and may have implications for speciation. Although this was not a main focus of this study, our preliminary results suggest that substitutions in subunit binding site regions are rare. The results from this study add to the growing literature on the complex relationship between mitochondrial DNA and the evolution of life histories across the tree of life., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Bemisia tabaci (Gennadius) is an economically important pest of agricultural and ornamental plants worldwide and is now widely recognized as a cryptic species complex. In North America, B. tabaci is a particularly important pest of greenhouse poinsettia. In poinsettia production, two cryptic species from the B. tabaci complex, Mediterranean and Middle East Minor 1, often infest crops simultaneously. Differences in pesticide susceptibility between these two cryptic species have the potential to influence growers' management decisions, including the use of biological control or insecticides, and the choice of insecticide active ingredient. However, the demographic behavior of mixed-species infestations in commercial greenhouses has yet to be investigated. We conducted a survey of B. tabaci populations in commercial greenhouses in Ontario, Canada, and provide evidence that under biological control-based management, Middle East Minor 1 can displace Mediterranean, whereas under insecticide-based management Mediterranean populations will persist. Furthermore, we comment on implications of this behavior on the management of B. tabaci, and comment on methods used to identify B. tabaci cryptic species.

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.

Background: The megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region., Results: Of the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence (<2%), application of a complementary character-based nucleotide diagnostic approach proved useful in discriminating them. Additionally, 14 species displayed high intra-specific genetic divergence (>2%), pointing to at least 23 strong candidates for new species., Conclusions: Our study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of reproductive isolation and putative cryptic speciation in some species (23 candidates for new species). Finally, our study constituted an important contribution to the international Barcoding of Life (iBOL.org) project, providing barcode sequences for use in identification of these species by experts and non-experts, and allowing them to be available for use in other applications.

Rapid and reliable toxicity assessment of oil sands process-affected waters (OSPW) is needed to support oil sands reclamation projects. Conventional toxicity tests using whole animals are relatively slow, costly, and often subjective, while at the same time requiring the sacrifice of test organisms as is the case with lethal dosage/concentration assays. A nonlethal alternative, using fish cell lines, has been developed for its potential use in supporting oil sands reclamation planning and to help predict the viability of aquatic reclamation models such as end-pit lakes. This study employed six fish cell lines (WF-2, GFSk-S1, RTL-W1, RTgill-W1, FHML, FHMT) in 24 h viability assays for rapid fluorometric assessment of cellular integrity and functionality. Forty-nine test water samples collected from the surface of oil sands developments in the Athabasca Oil Sands deposit, north of Fort McMurray, Alberta, Canada, were evaluated in blind. Small subsample volumes (8 ml) were mixed with 2 ml of 5× concentrated exposure media and used for direct cell exposures. All cell line responses in terms of viability as measured by Alamar blue assay, correlated well with the naphthenic acids (NA) content in the samples (R (2) between 0.4519 and 0.6171; p<0.0001) when data comparisons were performed after the bioassays. NA or total acid-extractable organics group has been shown to be responsible for most of the acute toxicity of OSPW and our results further corroborate this. The multifish cell line bioassay provides a strong degree of reproducibility among tested cell lines and good relative sensitivity of the cell line bioassay as compared to available in vivo data that could lead to cost effective, high-throughput screening assays.

Anthropogenic impacts are an increasing threat to the diversity of fishes, especially in areas around large urban centres, and many effective conservation actions depend on accurate species identification. Considering the utility of DNA barcoding as a global system for species identification and discovery, this study aims to assemble a DNA barcode reference sequence library for marine fishes from the coastal region of São Paulo State, Brazil. The standard 652 bp 'barcode' fragment of the cytochrome c oxidase subunit I (COI) gene was PCR amplified and bidirectionally sequenced from 678 individuals belonging to 135 species. A neighbour-joining analysis revealed that this approach can unambiguously discriminate 97% of the species surveyed. Most species exhibited low intraspecific genetic distances (0.31%), about 43-fold less than the distance among species within a genus. Four species showed higher intraspecific divergences ranging from 2.2% to 7.6%, suggesting overlooked diversity. Notably, just one species-pair exhibited barcode divergences of <1%. This library is a first step to better know the molecular diversity of marine fish species from São Paulo, providing a basis for further studies of this fauna - extending the ability to identify these species from all life stages and even fragmentary remains, setting the stage for a better understanding of interactions among species, calibrating the estimations about species composition and richness in an ecosystem, and providing tools for authenticating bioproducts and monitoring illegal species exploitation., (© 2012 Blackwell Publishing Ltd.)