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Biological conclusions based on DNAbarcoding 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 for animals, with conserved structure and function that allows for biologically informed error identification. Here, we present coil (https://CRAN.R-project.org/package=coil), an R package for the preprocessing and frameshift error assessment of COI-5P animal barcode and metabarcode sequence data. The package contains functions for placement of barcodes into a common reading frame, accurate translation of sequences to amino acids, and highlighting insertion and deletion errors. The analysis of10 000 barcode sequences of varying quality demonstrated how coil can place barcode sequences in reading frame and distinguish sequences containing indel errors from error-free sequences with greater than 97.5% accuracy. Package limitations were tested through the analysis of COI-5P sequences from the plant and fungal kingdoms as well as the analysis of potential contaminants: nuclear mitochondrial pseudogenes and Wolbachia COI-5P sequences. Results demonstrated that coil is a strong technical error identification method but is not reliable for detecting all biological contaminants. Key words: COI, DNA barcoding, error identification, translation. Les conclusions biologiques fondees sur les analyses de codage ou meta-codage a barres de l'ADN peuvent etre influencees fortement par les methodes employees pour generer et traiter les donnees, ce qui peut mener a des succes variables dans la distinction entre la variation biologique et l'erreur experimentale. La region 5= de la sous-unite I de la cytochrome c oxydase (COI-5P) est le code a barres le plus largement employe chez les animaux, grace a leurs structure et fonction conservees qui permettent d'identifier les erreurs sur des bases biologiques. Dans ce travail, les auteurs presentent coil (https://CRAN.R-project.org/package=coil), un paquet R pour le pretraitement et l'identification des erreurs causant des changements de cadre de lecture chez les donnees de sequences au sein du code a barres COI-5P chez les animaux. Le paquet contient des fonctions permettant de positionner les codes a barres dans un meme cadre de lecture, de traduire correctement la sequence en acides amines et de mettre en lumiere les erreurs de type insertion et deletion. L'analyse de 10 000 sequences de codes a barres de diverses qualites ont demontre comment coil permet de situer les sequences dans le bon cadre de lecture et de distinguer les sequences contenant des erreurs indel de celles depourvues de telles erreurs avec une justesse de plus de 97,5 %. Les limitations du paquet ont ete testees en analysant des sequences COI-5P provenant de plantes et de champignons, de meme qu'en analysant des contaminants potentiels : des pseudogenes nucleaires d'origine mitochondriale et des sequences COI-5P du genre Wolbachia. Les resultats montrent que coil offre une methode puissante pour l'identification d'erreurs techniques mais qu'il n'est pas en mesure de detecter tous les contaminants biologiques. [Traduit par la Redaction] Mots-cles : COI, codage a barres de l'ADN, identification d'erreurs, traduction., Introduction DNA barcoding leverages sequence diversity within standardized gene regions for the identification and classification of organisms (Hebert et al. 2003; Ratnasingham and Hebert 2007). Answering questions about biodiversity through [...]

Divergence times for species assemblages of Arctic marine invertebrates have often been estimated using a standard rate (1.4%/MY) of molecular evolution calibrated using a single sister pair of tropical crustaceans. Because rates of molecular evolution vary among taxa and environments, it is essential to obtain clock calibrations from northern lineages. The recurrent opening and closure of the Bering Strait provide an exceptional opportunity for clock calibration. Here, we apply the iterative calibration approach to investigate patterns of molecular divergence among lineages of northern marine molluscs and arthropods using publicly available sequences of the cytochrome c oxidase subunit I (COI) gene and compare these results with previous estimates of trans-Bering divergences for echinoderms and polychaetes. The wide range of Kimura two-parameter (K2P) divergences among 73 trans-Bering sister pairs (0.12%-16.89%) supports multiple pulses of migration through the Strait. Overall, the results indicate a rate of K2P divergence of 3.2%/MY in molluscs, 5%-5.2%/MY in arthropods, and 3.5%-4.7%/MY in polychaetes. While these rates are considerably higher than the often-adopted 1.4%/MY rate, they are similar to calibrations (3%-5%/MY) in several other studies of marine invertebrates. This upward revision in rates means there is a need both to reevaluate the evolutionary history of marine lineages and to reexamine the impact of prior climatic changes upon the diversification of marine life. Key words: clock dating, molecular rates, trans-Arctic, biogeographic clock calibration, DNA barcoding. Les temps de divergence au sein d'especes d'invertebres marins arctiques ont souvent ete estimes a l'aide d'un taux standard d'evolution moleculaire (1,4 %/million d'annees) calibre au moyen d'une seule paire de crustaces tropicaux. Puisque les taux d'evolution moleculaire peuvent varier entre taxons et environnements, il est essentiel d'obtenir une calibration de l'horloge pour les especes nordiques. L'ouverture et la fermeture recurrente du detroit de Bering fournit une opportunite exceptionnelle de calibrer l'horloge. Dans ce travail, les auteurs ont employe une approche iterative de calibration pour etudier la divergence moleculaire au sein de groupes nordiques de mollusques et d'arthropodes marins a l'aide de donnees disponibles pour la sequence du gene codant pour la sous-unite I de la cytochrome c oxydase (COI) et pour comparer ces resultats avec des estimes anterieurs de divergence trans-Bering chez des echinodermes et des polychetes. La grande gamme de valeurs pour les divergences Kimura a deux parametres (K2P) parmi 73 paires d'especes soeurs trans-Bering (0,12-16,89 %) supporte l'hypothese de plusieurs poussees migratoires a travers le detroit. Globalement, les resultats indiquent un taux de divergence K2P de 3,2 %/MA chez les mollusques, de 5-5,2 %/MA chez les arthropodes et de 3,5-4,7 %/MA chez les polychetes. Bien que ces taux soient considerablement plus eleves que le taux souvent utilise (1,4 %/MA), ils sont semblables aux calibrations (3-5 %/MA) obtenues chez plusieurs autres etudes d'invertebres marins. La revision a la hausse de ces taux implique qu'il sera necessaire a la fois de reevaluer l'histoire evolutive des lignages marins et de reexaminer l'impact des changements climatiques anterieurs sur la diversification de la vie marine. [Traduit par la Redaction] Mots-cles : datation de l'horloge, taux moleculaires, trans-Arctique, calibration de l'horloge biogeographique, codage a barres de l'ADN., Introduction The molecular clock is a fundamental tool for establishing an absolute time scale for the tree of life. Traditionally, fossil evidence has provided the main source of dates for [...]

This open-access special issue features 12 full articles representing emerging trends from the international DNA barcoding community. Several articles highlight how DNA-based techniques are elucidating the species diversity, biogeography, and [...]

Chironomid flies (non-biting midges) are among the most abundant and diverse animals in Arctic regions, but detailed analyses of species distributions and biogeographical patterns are hampered by challenging taxonomy and reliance on morphology for species-level identification. Here we take advantage of available DNA barcode data of Arctic Chironomidae in BOLD to analyse similarities in species distributions across a northern Nearctic--West Palearctic gradient. Using more than 260 000 barcodes representing 4666 BINs (Barcode Index Numbers) and 826 named species (some with interim names) from a combination of public and novel data, we show that the Greenland chironomid fauna shows affinities to both the Nearctic and the West Palearctic regions. While raw taxon counts indicate a strong Greenland--North American affinity, comparisons using Chao's dissimilarity metric support a slightly higher similarity between Greenland and West Palearctic chironomid communities. Results were relatively consistent across different definitions of species taxonomic units, including morphologically determined species, BINs, and superBINs based on a ~4.5% threshold. While most taxa found in Greenland are shared with at least one other region, reflecting circum-Arctic dispersal, our results also reveal that Greenland harbours a small endemic biodiversity. Our exploratory study showcases how DNA barcoding efforts using standardized gene regions contribute to an understanding of broad-scale patterns in biogeography by enabling joint analysis of public DNA sequence data derived from diverse prior studies.Key words: Diptera, zoogeography, biogeography, Canada, Norway, Svalbard.Les chironomides (moucherons non-piqueurs) sont parmi les animaux les plus abondants et diversifies dans les regions arctiques, mais des analyses detaillees des distributions de ces especes et de leur repartition biogeographique sont entravees par une taxonomie difficile et une dependance a la morphologie pour l'identification des especes. Ici, les auteurs tirent profit des donnees disponibles en matiere de codes a barres de l'ADN pour les chironomides arctiques au sein de la base de donnees BOLD pour analyser les similarites pour ce qui est des distributions des especes au long d'un gradient nordique Nearctique-Palearctique occidental. Au moyen de plus de 260 000 codes a barres representant 4666 BIN (<< Barcode Index Numbers >>) et 826 especes nommees (dont certaines de maniere interimaire) a partir d'une combinaison de donnees publiques et inedites, les auteurs montrent que la faune des chironomides du Groenland montre des ressemblances a la fois avec celles des regions Nearctique et Palearctique occidentale. Bien que des decomptes bruts indiquent une grande affinite Groenland--Amerique du Nord, des comparaisons a l'aide de l'indice de dissimilarite de Chao suggerent une similarite legerement plus elevee entre les communautes du Groenland et du Palearctique occidental. Les resultats etaient relativement coherents en faisant appel a diverses definitions des unites taxonomiques specifiques, incluant les especes definies sur une base morphologique, des BIN et des superBIN a un seuil de 4,5%. Bien que la plupart des taxons du Groenland soient partages avec au moins une autre region, ce qui reflete une distribution circum-arctique, les resultats revelent aussi que le Groenland recele une petite biodiversite endemique. Cette etude exploratoire demontre comment les efforts en matiere de codage a barres au moyen de regions geniques standardisees contribuent a la comprehension de la biogeographie a grande echelle en rendant possible l'analyse conjointe de donnees moleculaires publiques derivees de diverses etudes anterieures. [Traduit par la Redaction]Mots-cles: Diptera, zoogeographie, biogeographie, Canada, Norvege, Svalbard., IntroductionThe Arctic is home to about 21000 described species, many of which are specifically adapted to a cold climate (CAFF 2013). As this diversity is under pressure from several sources, [...]

Abstract: DNA barcoding has been used successfully for identifying specimens belonging to marine planktonic groups. However, the ability to delineate species within taxonomically diverse and widely distributed marine groups, such [...]

Abstract: Additive diversity partitioning (α, β, and 7) is commonly used to study the distribution of species-level diversity across spatial scales. Here, we first investigate whether published studies of additive [...]

The two special issues--Barcodes to Biomes--mark the one-year anniversary of the 6th International Barcode of Life Conference held in Guelph, Canada. The 6th Conference brought together 601 delegates from 51 [...]

Abstract: Insect lineages have crossed between terrestrial and aquatic habitats many times, for both immature and adult life stages. We explore patterns in molecular evolutionary rates between 42 sister pairs [...]

DNA barcoding--the sequencing of short, standardized DNA regions for specimen identification and species discovery--has promised to facilitate rapid access to biodiversity knowledge by diverse users. Here, we advance our opinion that increased global participation in genetics research is beneficial, both to scientists and for science, and explore the premise that DNA barcoding can help to democratize participation in genetics research. We examine publication patterns (2003-2014) in the DNA barcoding literature and compare trends with those in the broader, related domain of genomics. While genomics is the older and much larger field, the number of nations contributing to the published literature is similar between disciplines. Meanwhile, DNA barcoding exhibits a higher pace of growth in the number of publications as well as greater evenness among nations in their proportional contribution to total authorships. This exploration revealed DNA barcoding to be a highly international discipline, with growing participation by researchers in especially biodiverse nations. We briefly consider several of the challenges that may hinder further participation in genetics research, including access to training and molecular facilities as well as policy relating to the movement of genetic resources. Keywords: DNA barcoding, International Barcode of Life, genomics, research trends, collaboration. Le codage a barres de l'ADN, soit le sequencage de courtes regions d'ADN standardisees pour des fins d'identification de specimens et la decouverte d'especes, promettait de faciliter un acces rapide aux connaissances sur la biodiversite par divers utilisateurs. Dans cet article, les auteurs mettent de l'avant qu'une participation internationale accrue a la recherche en genetique est benefique tant pour les chercheurs que pour la science et ils explorent l'hypothese que le codage a barres de l'ADN peut aider a democratiser la participation a la recherche en genetique. Les auteurs ont examine l'evolution des publications (2003-2014) dans le domaine du codage a barres de l'ADN et ont compare les tendances avec celles observees dans le domaine plus large mais apparente de la recherche en genomique. Bien que la genomique soit un champ de recherche plus ancien et beaucoup plus vaste, le nombre de pays ayant contribue a la litterature est semblable entre ces deux champs. De plus, le codage a barres de l'ADN presente une croissance plus rapide du nombre de publications ainsi qu'une plus grande uniformite entre pays en ce qui a trait a la contribution proportionnelle des auteurs. Cette exploration a revele que le codage a barres de l'ADN est une discipline hautement internationale, avec une participation croissante des chercheurs de pays presentant une biodiversite particulierement grande. Les auteurs discutent brievement de plusieurs des defis qui pourraient restreindre une participation accrue a la recherche en genetique, incluant l'acces a la formation et aux laboratoires d'analyse de meme que les politiques regissant le mouvement des ressources genetiques. [Traduit par la Redaction] Mots-cles: codage a barres de l'ADN, projet international du code barre du vivant, genomique, tendances en recherche, collaboration., The benefits of increasing global participation in genetics research The invitation to contribute an opinion piece to the special issue entitled 'Genomics: the Power and the Promise 2014' inspired us [...]

The 6th International Barcode of Life Conference (Guelph, Canada, 18-21 August 2015), themed Barcodes to Biomes, showcases the latest developments in DNA barcoding research and its diverse applications. The meeting also provides a venue for a global research community to share ideas and to initiate collaborations. All plenary and contributed abstracts are being published as an open-access special issue of Genome. Here, I use a comparison with the 3rd Conference (Mexico City, 2009) to highlight 10 recent and emerging trends that are apparent among the contributed abstracts. One of the outstanding trends is the rising proportion of abstracts that focus upon multiple socio-economically important applications of DNA barcoding, including studies of agricultural pests, quarantine and invasive species, wildlife forensics, disease vectors, biomonitoring of ecosystem health, and marketplace surveys evaluating the authenticity of seafood products and medicinal plants. Other key movements include the use of barcoding and metabarcoding approaches for dietary analyses--and for studies of food webs spanning three or more trophic levels--as well as the spread of next-generation sequencing methods in multiple contexts. In combination with the rising taxonomic and geographic scope of many barcoding iniatives, these developments suggest that several important questions in biology are becoming tractable. 'What is this specimen on an agricultural shipment?', 'Who eats whom in this whole food web?', and even 'How many species are there?' are questions that may be answered in time periods ranging from a few years to one or a few decades. The next phases of DNA barcoding may expand yet further into prediction of community shifts with climate change and improved management of biological resources. Keywords: DNA barcoding, conference, research trends, ecology, evolution, socio-economic applications, market substitution, next-generation sequencing, plant barcoding, ethnobotany genomics, marker selection. Resume : Le 6e congres international << Barcode of Life >>(Guelph, Canada, 18 au 21 aout 2015), dont le theme est << Des codes a barres aux biomes >>, permet de presenter les plus recents developpements en recherche sur les codes a barres de l'ADN et leurs diverses applications. Ce congres se veut egalement un lieu de rencontre pour une communaute internationale de chercheurs afin d'echanger des idees et d'initier des collaborations. Tous les resumes, tant des conferences plenieres que des autres contributions, sont reunis pour publication dans un numero special de Genome a acces libre. Dans ce qui suit, l'auteure dresse une comparaison avec le troisieme congres (Mexico, 2009) pour mettre en relief 10 tendances recentes et emergentes qui ressortent parmi les resumes soumis. L'une des tendances qui ressort est la proportion croissante de resumes qui portent sur des applications ayant des retombees socioeconomiques du codage ?i barres de l'ADN. Cela inclut des etudes sur des ravageurs en agriculture, des especes de quarantaine ou envahissantes, les causes de mortalite de la faune, des vecteurs de maladies, la biosurveillance de la sante des ecosystemes ainsi que des analyses de l'authenticite des produits de la mer ou des plantes medicinales qu'on retrouve sur le marche. D'autres tendances cles incluent l'emploi du codage a barres et du meta-codage a barres dans le cadre d'analyses nutritionnelles--dont des etudes de reseaux trophiques comprenant trois niveaux ou plus--ainsi que le deploiement de methodes de sequencage de nouvelle generation dans de nombreux contextes. Conjointement a la portee taxonomique et geographique croissante des initiatives de codage a barres, ces developpements suggerent qu'on peut maintenant s'attaquer a plusieurs questions importantes en biologie. << Quel est ce specimen de denree agricole ? >>, << Qui mange qui dans ce reseau trophique? >>, et meme << Combien existe-il d'especes ? >> sont des questions auxquelles il devient possible de repondre sur l'horizon de quelques annees a une ou plusieurs decennies. Les prochaines phases du codage a barres de l'ADN pourraient ouvrir de nouveaux chantiers dans la prediction de l'evolution des communautes biologiques liee aux changements climatiques et dans la gestion des ressources biologiques. [Traduit par la Redaction] Mots-cles : codage a barres de l'ADN, congres, tendances en recherche, ecologie, evolution, applications socioeconomiques, substitution de produits, sequencage de nouvelle generation, codage a barres chez les plantes, ethnobotanique, genomique, selection de marqueurs., Introduction The 6th International Barcode of Life Conference, held 18-21 August 2015 in Guelph, Ontario, Canada--themed Barcodes to Biomes--highlights key recent expansions to the DNA barcoding research program, including large-scale [...]

Daphnia ambigua, one of the most broadly distributed members of its genus, occurs in Europe as well as in North and South America. This investigation examines diversity in two mitochondrial genes, COI and 12S rDNA, to ascertain the geographical distribution of variation in this species. The results establish that North American D. ambigua are separable into four phylogroups with an average of 4% mtDNA sequence divergence. One of these groups is dominant, occupying Mexico and the central United States, whereas the other groups are restricted to the Atlantic or Pacific coasts. Their distributional centroids coincide with refugial areas identified in prior studies, reinforcing evidence that the Appalachian and West Coast ranges have been important in the isolation of zooplankton lineages. Gene exchange, mediated by migratory birds whose flyways are structured by these mountains, is likely instrumental in maintaining north-south cohesion within each phylogroup. European populations of D. ambigua are closely allied to those from the eastern United States, a result concordant with their presumed recent introduction from North America. By contrast, South American populations last shared an ancestor with North American lineages approximately 2 million yr ago. The phylogeographic information now available suggests that topographic barriers generate predictable patterns of population divergence in zooplankton species and that allopatric speciation has played an important role in their diversification.

Knowledge of global patterns of genetic diversity is essential for biodiversity conservation as this parameter describes the ability of a species to respond to environmental changes. Ichneumonoids parasitoid wasps are among the few taxa showing an anomalous latitudinal diversity gradient. Using the largest georeferenced molecular dataset for this group, we used a macrogenetics approach to examine latitudinal patterns and predictors of intraspecific genetic diversity. We calculated the mean nucleotide diversity of mitochondrial DNA barcode sequences at three geographic levels: grid cells, latitudinal bands and climatic zones. Nucleotide diversity values were consistently higher at northern temperate latitudes, peaking at 50°. We found a positive but weak relationship between intraspecific diversity and the latitude, between intra‐ and interspecific diversity, and a positive effect of the temperature range. Examining the spatial relationship between different levels of biodiversity and its drivers is particularly relevant considering climate change and its impact on species distribution. Yet, in insects, it has been challenging to integrate ecological, evolutionary and geographical components when analysing the processes leading to species richness gradients. [ABSTRACT FROM AUTHOR]

Abstract Background Insect diversity typically declines with increasing latitude, but previous studies have shown conflicting latitude-richness gradients for some hymenopteran parasitoids. However, historical estimates of insect diversity and species richness can be difficult to confirm or compare, because they may be based upon dissimilar methods. As a proxy for species identification, we used DNA barcoding to identify molecular operational taxonomic units (MOTUs) for 7870 Hymenoptera specimens collected near Churchill, Manitoba, from 2004 through 2010. Results We resolved 1630 MOTUs for this collection, of which 75% (1228) were ichneumonoids (Ichneumonidae + Braconidae) and 91% (1484) were parasitoids. We estimate the total number of Hymenoptera MOTUs in this region at 2624-2840. Conclusions The diversity of parasitoids in this sub-Arctic environment implies a high diversity of potential host species throughout the same range. We discuss these results in the contexts of resolving interspecific interactions that may include cryptic species, and developing reproducible methods to estimate and compare species richness across sites and between surveys, especially when morphological specialists are not available to identify every specimen.

Background: Divergence times for Arctic marine lineages have commonly been estimated using calibrations from geographically distant taxa. However, due to evidence of rate heterogeneity among taxa and environments, it is [...]

Abstract Background Various methods have been proposed to assign unknown specimens to known species using their DNA barcodes, while others have focused on using genetic divergence thresholds to estimate “species” diversity for a taxon, without a well-developed taxonomy and/or an extensive reference library of DNA barcodes. The major goals of the present work were to: a) conduct the largest species-level barcoding study of the Muscidae to date and characterize the range of genetic divergence values in the northern Nearctic fauna; b) evaluate the correspondence between morphospecies and barcode groupings defined using both clustering-based and threshold-based approaches; and c) use the reference library produced to address taxonomic issues. Results Our data set included 1114 individuals and their COI sequences (951 from Churchill, Manitoba), representing 160 morphologically-determined species from 25 genera, covering 89% of the known fauna of Churchill and 23% of the Nearctic fauna. Following an iterative process through which all specimens belonging to taxa with anomalous divergence values and/or monophyly issues were re-examined, identity was modified for 9 taxa, including the reinstatement of Phaonia luteva (Walker) stat. nov. as a species distinct from Phaonia errans (Meigen). In the post-reassessment data set, no distinct gap was found between maximum pairwise intraspecific distances (range 0.00-3.01%) and minimum interspecific distances (range: 0.77-11.33%). Nevertheless, using a clustering-based approach, all individuals within 98% of species grouped with their conspecifics with high (>95%) bootstrap support; in contrast, a maximum species discrimination rate of 90% was obtained at the optimal threshold of 1.2%. DNA barcoding enabled the determination of females from 5 ambiguous species pairs and confirmed that 16 morphospecies were genetically distinct from named taxa. There were morphological differences among all distinct genetic clusters; thus, no cases of cryptic species were detected. Conclusions Our findings reveal the great utility of building a well-populated, species-level reference barcode database against which to compare unknowns. When such a library is unavailable, it is still possible to obtain a fairly accurate (within ~10%) rapid assessment of species richness based upon a barcode divergence threshold alone, but this approach is most accurate when the threshold is tuned to a particular taxon.