Monitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological ...approaches. The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly decline as high-throughput sequencing technologies advance. Aside from detailing protocols from specimen sorting to data release, this paper describes their use in a survey of arthropod diversity in a national park that examined 21 194 specimens representing 2255 species. These protocols can support arthropod monitoring programs at regional, national, and continental scales.
Accurate and cost-effective methods for tracking changes in arthropod communities are needed to develop integrative environmental monitoring programs in the Arctic. To date, even baseline data on ...their species composition at established ecological monitoring sites are severely lacking. We present the results of a pilot assessment of non-marine arthropod diversity in a middle arctic tundra area near Ikaluktutiak (Cambridge Bay), Victoria Island, Nunavut, undertaken in 2018 using DNA barcodes. A total of 1264 Barcode Index Number (BIN) clusters, used as a proxy for species, were recorded. The efficacy of widely used sampling methods was assessed. Yellow pan traps captured 62% of the entire BIN diversity at the study sites. When complemented with soil and leaf litter sifting, the coverage rose up to 74.6%. Combining community-based data collection with high-throughput DNA barcoding has the potential to overcome many of the logistic, financial, and taxonomic obstacles for large-scale monitoring of the Arctic arthropod fauna.
Display omitted
•The Hyalella amphipod species cloud of ancient Lake Titicaca is polyphyletic.•Lake Titicaca was colonized at least 5 times independently.•Evolutionary radiation occurred within Lake ...Titicaca in two primarily endemic clades.•The dispersal history is complex, including migrations out of the lake.
Ancient lakes are renowned for their exceptional diversity of endemic species. As model systems for the study of sympatric speciation, it is necessary to understand whether a given hypothesized species flock is of monophyletic or polyphyletic origin. Here, we present the first molecular characterization of the Hyalella (Crustacea: Amphipoda) species complex of Lake Titicaca, using COI and 28S DNA sequences, including samples from the connected Small and Large Lakes that comprise Lake Titicaca as well as from a broader survey of southern South American sites. At least five evolutionarily distant lineages are present within Lake Titicaca, which were estimated to have diverged from one another 12–20 MYA. These major lineages are dispersed throughout the broader South American Hyalella phylogeny, with each lineage representing at least one independent colonization of the lake. Moreover, complex genetic relationships are revealed between Lake Titicaca individuals and those from surrounding water bodies, which may be explained by repeated dispersal into and out of the lake, combined with parallel intralacustrine diversification within two separate clades. Although further work in deeper waters will be required to determine the number of species present and modes of diversification, our results strongly indicate that this amphipod species cloud is polyphyletic with a complex geographic history.
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.
Global biodiversity gradients are generally expected to reflect greater species replacement closer to the equator. However, empirical validation of global biodiversity gradients largely relies on ...vertebrates, plants, and other less diverse taxa. Here we assess the temporal and spatial dynamics of global arthropod biodiversity dynamics using a beta-diversity framework. Sampling includes 129 sampling sites whereby malaise traps are deployed to monitor temporal changes in arthropod communities. Overall, we encountered more than 150,000 unique barcode index numbers (BINs) (i.e. species proxies). We assess between site differences in community diversity using beta-diversity and the partitioned components of species replacement and richness difference. Global total beta-diversity (dissimilarity) increases with decreasing latitude, greater spatial distance and greater temporal distance. Species replacement and richness difference patterns vary across biogeographic regions. Our findings support long-standing, general expectations of global biodiversity patterns. However, we also show that the underlying processes driving patterns may be regionally linked.
BACKGROUND: Arctic ecosystems, especially those near transition zones, are expected to be strongly impacted by climate change. Because it is positioned on the ecotone between tundra and boreal ...forest, the Churchill area is a strategic locality for the analysis of shifts in faunal composition. This fact has motivated the effort to develop a comprehensive biodiversity inventory for the Churchill region by coupling DNA barcoding with morphological studies. The present study represents one element of this effort; it focuses on analysis of the spider fauna at Churchill. RESULTS: 198 species were detected among 2704 spiders analyzed, tripling the count for the Churchill region. Estimates of overall diversity suggest that another 10–20 species await detection. Most species displayed little intraspecific sequence variation (maximum <1%) in the barcode region of the cytochrome c oxidase subunit I (COI) gene, but four species showed considerably higher values (maximum = 4.1-6.2%), suggesting cryptic species. All recognized species possessed a distinct haplotype array at COI with nearest-neighbour interspecific distances averaging 8.57%. Three species new to Canada were detected: Robertus lyrifer (Theridiidae), Baryphyma trifrons (Linyphiidae), and Satilatlas monticola (Linyphiidae). The first two species may represent human-mediated introductions linked to the port in Churchill, but the other species represents a range extension from the USA. The first description of the female of S. monticola was also presented. As well, one probable new species of Alopecosa (Lycosidae) was recognized. CONCLUSIONS: This study provides the first comprehensive DNA barcode reference library for the spider fauna of any region. Few cryptic species of spiders were detected, a result contrasting with the prevalence of undescribed species in several other terrestrial arthropod groups at Churchill. Because most (97.5%) sequence clusters at COI corresponded with a named taxon, DNA barcoding reliably identifies spiders in the Churchill fauna. The capacity of DNA barcoding to enable the identification of otherwise taxonomically ambiguous specimens (juveniles, females) also represents a major advance for future monitoring efforts on this group.
Comprehensive 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.
The 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.
Background: The ability to rapidly measure the health of an ecosystem is becoming increasingly important with respect to effects of global climate change and human activity on the environment. ...Invertebrate diversity assessments facilitated by genetic analysis show promise as a rapid and effective approach to measure baseline data and subsequently monitor changes in local communities over time. However, many methods of capturing this diversity prior to genetic analysis are available, which can vary greatly in the amount of time, effort, and cost required. In this study, we assess the effectiveness of three collecting strategies (a 24 h bioblitz, a week of standardized sampling, and 20 weeks of Malaise trapping) employed within the Rouge National Urban Park in the summer of 2013. Results: In total, 43 924 individual specimens were sequenced for the barcode region of COI. Of these records, 38 145 met minimum sequence quality criteria, representing 4422 putative species or Barcode Index Numbers (BINs). Despite temporal and spatial overlap between the three approaches, only 183 BINs were found using all three methods. One week of standardized sampling resulted in the highest capture abundance (21 443) and second-highest BIN richness (2091) but required the maximum collecting effort (612 min). Conversely, the maximum richness (2225) and similar capture abundance (18 118) was detected with just 60 min of effort using 20 weeks of Malaise trapping. In comparison, 610 min of collector effort was employed during the 24 h bioblitz but resulted in the lowest capture abundance (4363) and BIN richness detection (1215). Significance: Our results indicate that while each DNA barcode-based biotic survey approach captured unique diversity of the invertebrate community, Malaise trapping presents the most valuable method for invertebrate surveys with potential for long-term site monitoring.
Background: In 2015 a rapid, barcode-assisted all taxon biodiversity inventory was completed at the rare Charitable Research Reserve in Cambridge, Canada. Two approaches were used -- a 7-month ...sampling program and a 24 h bioblitz, each employing a variety of collecting techniques. Delegates from the 6th International Barcode of Life Conference took part in the bioblitz, expanding the species inventory through collection and identification of animals, plants, and fungi. During the single week of the conference, 3502 bioblitz specimens were collected, analyzed, and their data released in a published manuscript, demonstrating how swift a barcode-assisted inventory can be. Results: Mass sampling using six standardized collection methods was implemented at rare from April-October 2015. Overall, 5577 Barcode Index Numbers (BINs, a proxy for species) were determined from barcoding nearly 50 000 specimens. In total, 3332 BINs were released with the first publication, and the subsequent two months of collecting resulted in 2245 additional BINs. Insects dominated the inventory with 4554 BINs, mainly Diptera (49%) and Hymenoptera (23%). Adding the BINs that were assigned to species using the Barcode of Life Data System (BOLD) resulted in a species checklist of 3348 animals, plants, and fungi. Using public data on BOLD, a near complete BIN reference library was created to represent all animal species known from the reserve. Significance: Standardized methods of sampling are easy to implement and gather large and diverse quantities of specimens. Coupling this mass sampling with DNA barcoding can provide a rapid taxon inventory, even in the absence of taxonomic specialists. One season of this approach can result in an impressive local checklist -- this study has now made rare one the best-inventoried reserves in North America. Furthermore, this approach complements traditional surveys and provides valuable occurrence data for difficult and small-bodied groups often disregarded.
Background: Large natural history collections are a crucial resource of diverse and rare specimens, but their genetic reserves are underutilized. For the last decade, the Centre for Biodiversity ...Genomics (CBG) has worked to reverse this trend and has set the standard for DNA barcode-based museum processing pipelines. Past efforts were often limited by specimen age, preservation method, and ultimately DNA quality. However, recent advances in high-throughput sequencing (HTS) technologies have made it possible to amplify and sequence DNA from old and rare specimens, even with very limited quantities of DNA. CBG's partnership with the National Museum of Natural History (NMNH) in Washington DC is an exemplar of this system, which incorporates both Sanger- and HTS-based methods to maximize sequencing success rates based on predicted DNA quality. Results: To date, over 120 000 specimens from the NMNH have been DNA barcoded and deposited in the Barcode of Life Data System (BOLD). The current focus of this partnership remains on building the barcode reference library of North American Lepidoptera, which is nearing completion. However, efforts have recently expanded to include barcoding the world genera of Lepidoptera, where significant progress can be made at the NMNH due to its vast archives of authoritatively identified material from around the globe. In parallel, the CBG is also working towards completing barcode coverage for every insect family with the assistance of the NMNH. Significance: While contributing valuable digitization services to participating institutions, the CBG's museum harvesting pipeline is also producing an invaluable reference barcode library for BOLD, and for the community as a whole. This resource is of critical importance for parameterizing the BOLD Identification Engine, and it will undoubtedly assist its users with the discovery of new, rare, and exciting taxa.
PDF
