Cory S. Sheffield

DNA barcoding and the mediocrity of morphology

A small but vocal community of critics has questioned the epistemological value of DNA barcoding by suggesting that either it ‘cannot work’ for the identification or discovery of species or that it ignores the ‘richness’ inherent in traditional approaches. We re‐examine these arguments through a comparison of DNA barcoding and morphological taxonomy in terms of their accuracy and diversity of characters employed. We conclude that morphology often does not work and that it is often nowhere near as ‘rich’ as has been argued. Morphology is particularly poor in numerous important situations, such as the association of larvae with adults and discrimination among cryptic species. The vehemence of some of the criticisms is surprising given that morphology alone is known to be inadequate to the task of species‐level identification in many instances.

DNA barcoding a regional bee (Hymenoptera: Apoidea) fauna and its potential for ecological studies

DNA barcoding has been evaluated for many animal taxa and is now advocated as a reliable and rapid means for species‐level identification. The coming‐to‐light of this identification tool is timely as we are now facing perhaps the greatest rate of species loss in recent millennia. This study contributes to an ever‐increasing number of published accounts of DNA barcoding successfully and accurately distinguishing animal taxa, in this instance, the bee fauna of Nova Scotia, Canada. Most members of this well‐known fauna were resolved with particular clarity; the average intraspecific divergence was less than 0.5%, and COI sequences from over 75% of the provinces species are now in the Barcodes of Life Data System. DNA barcoding also revealed some surprises within this fauna, including the possible recognition of two undescribed genetically unique species, one in the genus Ceratina (subgenus Zadontomerus), the second in the genus Andrena (subgenus Larandrena); both are presently receiving further taxonomic study. In addition, DNA barcoding has allowed sex‐associations among two pairs of cleptoparasitic species. The resulting utility of DNA barcoding for ecological studies of bee communities is discussed.

Wolbachia and DNA barcoding insects: Patterns, potential, and problems

Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein – wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor – for which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region.

Unveiling cryptic species of the bumblebee subgenus Bombus s. str. worldwide with COI barcodes (Hymenoptera: Apidae)

Bumblebees of the subgenus Bombus s. str. dominate (or used to dominate) many north temperate pollinator assemblages and include most of the commercial bumblebee pollinator species. Several species are now in serious decline, so conservationists need to know precisely which ones are involved. The problem is that many Bombus s. str. species are cryptic, so that species identification from morphology may be impossible for some individuals and is frequently misleading according to recent molecular studies. This is the first review of the entire subgenus to: (1) avoid fixed a priori assumptions concerning the limits of the problematic species; and (2) sample multiple sites from across the entire geographic ranges of all of the principal named taxa worldwide; and (3) fit an explicit model for how characters change within an evolutionary framework; and (4) apply explicit and consistent criteria within this evolutionary framework for recognising species. We analyse easily-obtained DNA (COI-barcode) data for 559 sequences from 279 localities in 33 countries using general mixed Yule-coalescent (GMYC) models, assuming only the morphologically distinctive species B. affinis Cresson, B. franklini (Frison), B. ignitus Smith and B. tunicatus Smith, and then recognise other comparable COI-barcode groups as putative species. These species correspond to modified concepts of the taxa B. cryptarum (Fabricius), B. hypocrita Pérez, B. jacobsoni Skorikov, B. lantschouensis Vogt n. stat., B. longipennis Friese, B. lucorum (Linnaeus), B. magnus Vogt, B. minshanensis Bischoff n. stat., B. occidentalis Greene, B. patagiatus Nylander, B. sporadicus Nylander, B. terrestris (Linnaeus) and B. terricola Kirby (a total of 17 species). Seven lectotypes are designated. Our results allow us for the first time to diagnose all of the putative species throughout their global ranges and to map the extent of these geographic ranges.

The potential of cleptoparasitic bees as indicator taxa for assessing bee communities

Many factors affect bee diversity and abundance, and knowledge of these is crucial for maintaining healthy bee communities. However, there are few means to fully evaluate the status of bee communities; most are based on monitoring species richness and abundance and do not consider the diverse life histories of bees. We propose that functional diversity of bee communities offers a more consistent means of evaluation and suggest that cleptoparasitic bees in particular show much promise as indicator taxa. Cleptoparasitic bees play a stabilising role within bee communities. They represent the apex of bee communities and are the first guild to respond to disturbances, are easily distinguished as such and are diverse enough to be representative of entire bee communities. The diversity and abundance of cleptoparasites in relation to all bees is indicative of the status of the total bee community, and monitoring them should form an integral part of assessing bee communities.

Potential of bigleaf lupine for building and sustaining Osmia lignaria populations for pollination of apple

Bees of the genus Osmia Panzer (Hymenoptera: Megachilidae) are among the contenders to replace honey bees, Apis mellifera L. (Apidae), for pollinating tree-fruit crops. One species, Osmia lignaria Say, has shown great potential in western North America and was recently introduced into Nova Scotia for evaluation as a pollinator of apple, Malus Mill. (Rosaceae). A major component of that study was to develop management options for O. lignaria, including methods of sustaining nesting females following crop flowering to maximize population recovery for pollination in subsequent seasons. The objective of this study was to evaluate bigleaf lupine, Lupinus polyphyllus Lindl. (Fabaceae), as a secondary food plant for nesting female O. lignaria by investigating nesting activity, pollen-use patterns, and fecundity. During 2002–2003, female O. lignaria collected high proportions of apple pollen (>70%) during mid and late flowering; after then, most pollen (>90%) was collected from bigleaf lupine. The flowering perio...

DNA barcoding reveals diversity of Hymenoptera and the dominance of parasitoids in a sub-arctic environment.

BackgroundInsect 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.ResultsWe 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.ConclusionsThe 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.

Bee diversity in naturalizing patches of Carolinian grasslands in southern Ontario, Canada

Abstract The bee fauna (Hymenoptera: Apoidea) of the Niagara Peninsula, at the eastern end of the Carolinian Zone in Ontario, Canada, is poorly known. From April to October 2003, we studied bee abundance and diversity in set-aside grasslands at Brock University and the Glenridge Quarry Naturalization Site in southern St. Catharines, Ontario. Using three sampling methods (pan traps, sweep nets, and aerial nets), we collected and identified 15 733 specimens of 124 species and morphospecies representing all bee families, except Melittidae, found in North America. Abundance-based diversity estimators suggested bee species richness to be as high as 148 species. There were three seasonal peaks in bee abundance (early spring, late spring, and midsummer) with a lull in activity shortly after the summer solstice. Several indicators suggested substantial impacts of disturbance on the Niagara bee community, including evidence of high dominance by the most abundant species. Comparison of the sampling methods indicated considerable catch variation among taxa; Halictidae and Apidae were dominant in pan trap samples and in sweep—aerial net samples, respectively. However, bee abundances in pan traps and sweep nets were highly correlated, suggesting that both methods fairly sample local bee abundances.

Rapid Range Expansion of the Wool-Carder Bee, Anthidium manicatum (Linnaeus) (Hymenoptera: Megachilidae), in North America

Abstract Anthidium manicatum (L.) is an adventive species of European origin first recorded in North America in the late 1960s; from that point until 2001 its range on the continent was restricted to the northeast-central USA and central Canada (Ontario, more recently Québec). In 2005, this species was reported from Nova Scotia, a rapid and wide increase in its distribution. In this paper, we document a similar rapid spread of A. manicatum into western North America, including British Columbia and Idaho, and discuss the potential risks of this species in eastern Canada. In addition, the potential of DNA barcoding as a rapid and reliable means of recognizing adventive bee species is advocated.

Nesting Biology and DNA Barcode Analysis of Ceratina dupla and C. mikmaqi, and Comparisons with C. calcarata (Hymenoptera: Apidae: Xylocopinae)

Abstract Using DNA barcode analysis, nest collections, and pan-trapping we compared molecular differences, nesting behaviour, and phenology of three of the four species of Ceratina Latreille present in the Niagara Region of southern Ontario, Canada: C. dupla Say, C. calcarata Robertson, and C. mikmaqi Rehan and Sheffield. Ceratina dupla and C. mikmaqi were separated by five fixed nucleotide differences and an average sequence divergence of 1.86%. In our population, C. mikmaqi and C. calcarata were common and C. dupla was rare. Ceratina dupla nested earlier than C. mikmaqi and C. calcarata, and sometimes produced a second brood in late July – early August. Each species constructed linear nests in the pith of dead twigs, C. mikmaqi and C. dupla usually in Fullers teasel (Dipsacus fullonum L.; Dipsacaceae) and C. calcarata usually in raspberry (Rubus L.; Rosaceae). Genetically distinct, each species occupies a slightly different niche in the Niagara bee assemblage.