Pollen DNA barcoding:Current applications and future prospects.

Identification of the species origin of pollen has many applications, including assessment of plant-pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.publishersversionPeer reviewe

The genetic structure of Aedes aegypti populations is driven by boat traffic in the Peruvian Amazon.

In the Americas, as in much of the rest of the world, the dengue virus vector Aedes aegypti is found in close association with human habitations, often leading to high population densities of mosquitoes in urban settings. In the Peruvian Amazon, this vector has been expanding to rural communities over the last 10-15 years, but to date, the population genetic structure of Ae. aegypti in this region has not been characterized. To investigate the relationship between Ae. aegypti gene flow and human transportation networks, we characterized mosquito population structure using a panel of 8 microsatellite markers and linked results to various potential mechanisms for long-distance dispersal. Adult and immature Ae. aegypti (>20 individuals per site) were collected from Iquitos city and from six neighboring riverine communities, i.e., Nauta, Indiana, Mazan, Barrio Florida, Tamshiaco, and Aucayo. FST statistics indicate significant, but low to moderate differentiation for the majority of study site pairs. Population structure of Ae. aegypti is not correlated with the geographic distance between towns, suggesting that human transportation networks provide a reasonable explanation for the high levels of population mixing. Our results indicate that Ae. aegypti gene flow among sub-populations is greatest between locations with heavy boat traffic, such as Iquitos-Tamshiaco and Iquitos-Indiana-Mazan, and lowest between locations with little or no boat/road traffic between them such as Barrio Florida-Iquitos. Bayesian clustering analysis showed ancestral admixture among three genetic clusters; no single cluster was exclusive to any site. Our results are consistent with the hypothesis that human transportation networks, particularly riverways, are responsible for the geographic spread of Ae. aegypti in the Peruvian Amazon. Our findings are applicable to other regions of the world characterized by networks of urban islands connected by fluvial transport routes

Generalisation and specialisation in hoverfly (Syrphidae) grassland pollen transport networks revealed by DNA metabarcoding

1. Pollination by insects is a key ecosystem service, and important to wider ecosystem function. Most species-level pollination networks studied have a generalised structure, with plants having several potential pollinators, and pollinators in turn visiting a number of different plant species. This is in apparent contrast to a plant?s need for efficient conspecific pollen transfer. 2. The aim of this study was to investigate the structure of pollen transport networks at three levels of biological hierarchy: community, species, and individual. We did this using hoverflies in the genus Eristalis, a key group of non-Hymenopteran pollinators. 3. We constructed pollen transport networks using DNA metabarcoding to identify pollen. We captured hoverflies in conservation grasslands in west Wales, UK, removed external pollen loads, sequenced the pollen DNA on the Illumina MiSeq platform using the standard plant barcode rbcL, and matched sequences using a pre-existing plant DNA barcode reference library. 4. We found that Eristalis hoverflies transport pollen from 65 plant taxa, more than previously appreciated. Networks were generalised at the site and species level, suggesting some degree of functional redundancy, and were more generalised in late summer compared to early summer. In contrast, pollen transport at the individual level showed some degree of specialisation. Hoverflies defined as ?single-plant visitors? varied from 40% of those captured in early summer to 24% in late summer. Individual hoverflies became more generalised in late summer, possibly in response to an increase in floral resources. Rubus fruticosus agg. and Succisa pratensis were key plant species for hoverflies at our sites 5. Our results contribute to resolving the apparent paradox of how generalised pollinator networks can provide efficient pollination to plant species. Generalised hoverfly pollen transport networks may result from a varied range of short-term specialised feeding bouts by individual insects. The generalisation and functional redundancy of Eristalis pollen transport networks may increase the stability of the pollination service they deliver.publishersversionPeer reviewe

Floral resource partitioning by individuals within generalised hoverfly pollination networks revealed by DNA metabarcoding

Pollination is a key ecosystem service for agriculture and wider ecosystem function. However, most pollination studies focus on Hymenoptera, with hoverflies (Syrphidae) frequently treated as a single functional group. We tested this assumption by investigating pollen carried by eleven species of hoverfly in five genera, Cheilosia, Eristalis, Rhingia, Sericomyia and Volucella, using DNA metabarcoding. Hoverflies carried pollen from 59 plant taxa, suggesting they visit a wider number of plant species than previously appreciated. Most pollen recorded came from plant taxa frequently found at our study sites, predominantly Apiaceae, Cardueae, Calluna vulgaris, Rubus fruticosus agg., and Succisa pratensis, with hoverflies transporting pollen from 40% of entomophilous plant species present. Overall pollen transport network structures were generalised, similar to other pollination networks elsewhere. All hoverfly species were also generalised with few exclusive plant/hoverfly interactions. However, using the Jaccard Index, we found significant differences in the relative composition of pollen loads between hoverfly genera, except for Volucella, demonstrating some degree of functional complementarity. Eristalis and Sericomyia species had significant differences in relative pollen load composition compared to congeners. Our results demonstrate the range of pollens transported by hoverflies and the potential pollination function undertaken within this ecologically and morphologically diverse guild

Data from: Experimental species removals impact the architecture of pollination networks

Mutualistic networks are key for the creation and maintenance of biodiversity, yet are threatened by global environmental change. Most simulation models assume that network structure remains static after species losses, despite theoretical and empirical reasons to expect dynamic responses. We assessed the effects of experimental single bumblebee species removals on the structure of entire flower visitation networks. We hypothesized that network structure would change following processes linking interspecific competition with dietary niche breadth. We found that single pollinator species losses impact pollination network structure: resource complementarity decreased, while resource overlap increased. Despite marginally increased connectance, fewer plant species were visited after species removals. These changes may have negative functional impacts, as complementarity is important for maintaining biodiversity–ecological functioning relationships and visitation of rare plant species is critical for maintaining diverse plant communities

Data from: Statistically testing the role of individual learning and decision-making in trapline foraging

Trapline foraging, a behavior consisting of repeated visitation to spatially fixed resources in a predictable sequence, has been observed over diverse taxa and is important ecologically for efficient resource gathering. Despite this, few null models exist to test the significance of suspected traplines, particularly for studies interested in the role of individual decision-making in the formation of traplines versus the role of resource layouts and random movement patterns. Here we present a spatially explicit, individual-based null model, which may be used to test whether resource layout and realistic forager movement may account for sequence repeats in suspected traplines. In our model, we generate resource visitation sequences by modeling a forager without spatial memory using a random walk to discover and visit spatially-fixed resources. We quantify traplining using Determinism, a metric derived from recurrence quantification analysis. Using both simulated and empirical bee foraging data, we compared our model with two existing null models—a completely random model and a sample randomization model. The former creates null sequences by randomly selecting available resources, while the latter randomizes the order of visits in observed sequences. We found that our model has a higher propensity of being (correctly) rejected than a sample randomization model for trapliners, and a lower propensity of being (incorrectly) rejected for non-trapliners compared to a completely random model. The use of a spatially explicit individual-based null model to test the statistical significance of patterns in empirical data is a novel approach that may be useful for other spatial and individual-based processes

raw network data, Brosi et al. Biology Letters

pollination network data, with site, experimental state (control or manipulation), and plant and pollinator species. The README file has the identities of the manipulated (removed) bumble bee species for each site

Reduced density and visually complex apiaries reduce parasite load and promote honey production and overwintering survival in honey bees.

Managed honey bee (Apis mellifera) colonies are kept at much greater densities than naturally occurring feral or wild colonies, which may have detrimental effects on colony health and survival, disease spread, and drifting behavior (bee movement between natal and non-natal colonies). We assessed the effects of a straightforward apiary management intervention (altering the density and visual appearance of colonies) on colony health. Specifically, we established three "high density / high drift" ("HD") and three "low density / low drift" ("LD") apiary configurations, each consisting of eight bee colonies. Hives in the HD apiary configuration were of the same color and placed 1m apart in a single linear array, while hives in the LD apiary configuration were placed 10m apart at different heights, facing outwards in a circle, and made visually distinctive with colors and symbols to reduce accidental drift between colonies. We investigated disease transmission and dynamics between the apiary configurations by clearing all colonies of the parasitic mite Varroa destructor, and subsequently inoculating two randomly-chosen colonies per apiary with controlled mite doses. We monitored the colonies for two years and found that the LD apiary configuration had significantly greater honey production and reduced overwinter mortality. Inoculation and apiary management intervention interacted to affect brood mite levels, with the highest levels in the inoculated colonies in the HD configuration. Finally, foragers were more than three times more likely to drift in the HD apiary configurations. Our results suggest that a relatively straightforward management change-placing colonies in low-density visually complex circles rather than high-density visually similar linear arrays-can provide meaningful benefits to the health and productivity of managed honey bee colonies