Premise of the study:Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada.Methods:Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%). For 98% of the specimens, at least one of the DNA barcode regions was recovered from the plastid loci rbcL and matK and from the nuclear ITS2 region. We used beta regression to quantify the effects of age, type of preservation, and taxonomic affiliation (family) on DNA sequence recovery.Results:Specimen age and method of preservation had significant effects on sequence recovery for all markers, but influenced some families more (e.g., Boraginaceae) than others (e.g., Asteraceae).Discussion:Our DNA barcode library represents an unparalleled resource for metagenomic and ecological genetic research working on temperate and arctic biomes. An observed decline in sequence recovery with specimen age may be associated with poor primer matches, intragenomic variation (for ITS2), or inhibitory secondary compounds in some taxa.

BackgroundComprehensive biotic surveys, or ‘all taxon biodiversity inventories’ (ATBI), have traditionally been limited in scale or scope due to the complications surrounding specimen sorting and species identification. To circumvent these issues, several ATBI projects have successfully integrated DNA barcoding into their identification procedures and witnessed acceleration in their surveys and subsequent increase in project scope and scale. The Biodiversity Institute of Ontario partnered with the rare Charitable Research Reserve and delegates of the 6th International Barcode of Life Conference to complete its own rapid, barcode-assisted ATBI of an established land trust in Cambridge, Ontario, Canada.New informationThe existing species inventory for the rare Charitable Research Reserve was rapidly expanded by integrating a DNA barcoding workflow with two surveying strategies – a comprehensive sampling scheme over four months, followed by a one-day bioblitz involving international taxonomic experts. The two surveys resulted in 25,287 and 3,502 specimens barcoded, respectively, as well as 127 human observations. This barcoded material, all vouchered at the Biodiversity Institute of Ontario collection, covers 14 phyla, 29 classes, 117 orders, and 531 families of animals, plants, fungi, and lichens. Overall, the ATBI documented 1,102 new species records for the nature reserve, expanding the existing long-term inventory by 49%. In addition, 2,793 distinct Barcode Index Numbers (BINs) were assigned to genus or higher level taxonomy, and represent additional species that will be added once their taxonomy is resolved. For the 3,502 specimens, the collection, sequence analysis, taxonomic assignment, data release and manuscript submission by 100+ co-authors all occurred in less than one week. This demonstrates the speed at which barcode-assisted inventories can be completed and the utility that barcoding provides in minimizing and guiding valuable taxonomic specialist time. The final product is more than a comprehensive biotic inventory – it is also a rich dataset of fine-scale occurrence and sequence data, all archived and cross-linked in the major biodiversity data repositories. This model of rapid generation and dissemination of essential biodiversity data could be followed to conduct regional assessments of biodiversity status and change, and potentially be employed for evaluating progress towards the Aichi Targets of the Strategic Plan for Biodiversity 2011–2020.

The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet’s land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.

Cloud forests are characterized by consistently low temperatures and high precipitation/humidity and tend to be inhabited by species that exhibit multiple adaptations related to abiotic conditions that are stressful for the generally thermophilic ants (Bruijnzeel & Proctor, 1995; Gentry, 1992; Still et al., 1999). Climate change is expected to cause dramatic biotic transformations in cloud forest (Hulshof & Powers, 2020; Nadkarni & Solano, 2002; Pounds et al., 1999) and surveys of cloud forest species over time aid our understanding of these changes. We sampled ant communities from a cloud forest at the top of 1,500 m tall Volcán Cacao within Área de Conservación Guanacaste (ACG) in northwestern Costa Rica (10.9329, −85.4530). This single location is part of an ongoing inventory project examining elevational and temporal structure of ants and other leaf-litter arthropods

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Climate change continues to diminish ice cover duration for Northern Hemisphere lakes. However, the differential loss of lake ice duration for various types of lakes across the globe is not well established. In this study, we used time series of ice duration data (average length = 51 years) for 220 globally distributed Northern Hemisphere lakes to determine how local climate trends, geographical location, and physical properties of lakes affect their ice cover trends. Ice duration dynamics were influenced by surface air temperature trends, lake geography, and morphology. Deeper lakes, located at lower elevations, western longitudes, and lower latitudes, experienced the greatest reductions in ice cover over their time series. These results indicate that despite widespread patterns of warming, the individual features of lakes can determine how rapidly they are losing ice cover and may prove informative for future modeling and conservation efforts. Plain Language Summary Citizen scientists and researchers alike have been visually logging the freezing and breakup dates of lake ice for hundreds of years. Studies have shown that lake ice duration (the number of days between freezing and breakup) has decreased over time due to human-induced climate change. We have used this type of data to determine how the size and geographic location of a lake influence how its ice cover length in winter has changed over time. We found that deep lakes, at lower elevations, western longitudes, and lower latitudes, are losing ice cover at relatively fast rates. Our results demonstrate that even though warming is a general pattern on our planet, these specific types of lakes are being affected disproportionately, which may help to prioritize conservation efforts to preserve freshwater biodiversity and drinking water resources.

Global identification and monitoring programs for invasive species aim to reduce imminent impacts to biodiversity, ecosystem services, agriculture, and human health. This study employs a 658 base pair fragment of the cytochrome c oxidase subunit I (COI) gene to identify and categorize clades of the banded grove snail (Cepaea nemoralis (Linnaeus, 1758)) from native (European) and introduced (North American) ranges using a maximum-likelihood phylogeny and haplotype networks. This work corroborates the existence of eight clades within C. nemoralis and further identified three clades that were common to both Europe and North America (A, D, O). Clades A and D were found in eastern Canada, Ontario (Canada), and British Columbia (Canada), whereas clade O was restricted to Ontario, possibly introduced from Poland or central Europe. Haplotype networks suggest clade A was introduced from northern Europe, whereas clade D was introduced from western and central Europe. Networks contained many private haplotypes and a lack of haplotype sharing, suggesting strong genetic structure in this system, possibly resulting from reduced dispersal in this species. This study describes the contemporary distribution of C. nemoralis in Canada and demonstrates the efficacy of DNA barcoding for monitoring the spread of invasive species, warranting its widespread adoption in management policies.