Bee sensitivity to a century of agricultural land-use change.

Lead Research Organisation: Natural History Museum
Department Name: Earth Sciences

Abstract

The world's natural resources have been placed under significant pressure over the past century, due to the exponential growth rate of the global human population. This has resulted in a significant increase in agricultural land-use and subsequent loss of 'natural habitats', a pattern associated with high losses in biodiversity. Declines of insect pollinators, such as bumblebees, are of particular concern as their role in maintaining floral health and diversity is vital, and as agricultural crop pollinators they possess large economic benefits. Understanding threats to these populations is therefore of high priority.

Here we take the approach that to understand future threats and solutions we must understand the past, and that to accurately predict future patterns and risks to species, we must gain a better understanding of what is causing those changes. Unfortunately, archival data on insect pollinator abundance rarely goes back more than a couple of decades, and most have been collected in a haphazard way. To fill this knowledge gap we will take a novel approach in which, using a combination of DNA sequencing, morphological and phenological (life-history data looking at seasonal activity) measures, along with experimental test of pesticide resistance, we will test whether populations experiencing different agricultural land use change intensity show signatures of population declines and adaptation to these new agricultural environments (i.e. support for a causal relationship).

Here, we will study a large collection of historical bumblebee specimens from six leading natural history museums across the UK. The morphological and genomic data represented in these specimens holds the key to determining how variation in population size, body shape and genetic diversity have changed over the last century.
Recent advances in the recovery and analysis of ancient DNA, and developments in the resolution of CT scanning, will enable us to gain unprecedented and novel insights. By working with historical samples from locations that have undergone different amounts of agricultural land use change (for example differences between the east and west of UK) we can specifically test whether temporal changes occur, rather than relying on end point data.
It is widely considered that bumblebees are threatened by two of the major factors associated with agricultural intensification: the loss of flowers leading to reduced nutritional resource, and increased exposure to pesticides. However, to our knowledge the interactive effects of these have not been experimentally tested. This project will also conduct a controlled laboratory experiment to understand how changes to nutritional availability and pesticide exposure impact on colony growth and the production of new queens and males.

Planned Impact

The proposed project will provide results of interest not only to academics, but to a wide range of beneficiaries including: (i) policy makers (ii) agriculturists (iii) commercial parties relating to the chemical/pesticide industries (iv) conservationists and wildlife trusts (v) museums and (vi) the general public.

Bee pollination provides a service that has an economic value of >£300 million in the UK alone (>$150bn p.a. globally) thus identifying the factors causing bee declines is of fundamental importance. In relation to (i) policy makers, the project will provide data that can aid pesticide regulatory authorities by informing on how bees are coping in a pesticide exposure landscape. The data produced could also contribute to evidence considered by the EFSA on the risks of pesticide exposure to beneficial arthropods (primarily bees). The neonicotinoid pesticide under investigation in our proposed demographic pinch point experiment is currently under restrictions for use on flowering crops, therefore our findings may help to inform decisions on future applications. We believe that research in this field has the potential to change policy especially if we consider that previous work by Gill was used to debate and influence the EU moratorium, and has been presented at Parliament.

Land managers, farmers and beekeepers (ii) have a vested interest in the success of insect pollinators. Our proposed research could inform these parties regarding warning signs of future population crashes and future trends. It will also assist them to identify best agricultural practices and to develop mitigation strategies to benefit pollinators regarding pesticide application procedures. Moreover, by identifying specific detoxification genes this will be of broad use to (iii) ecotoxicologists and the chemical companies themselves (such as Syngenta).

Understanding the threats to insect pollinators, such as bees, is on the priority list of the International Platform of Biodiversity and Ecosystem Services (IPBES). Our findings can help to predict future trends of insect pollinators and other beneficial organisms that may inadvertently be affected by agricultural land use change and agricultural practices. It will also provide conservation groups (iv) with data on the regional population and community status of bees.
In relation to museums (v), our project would bring together curators and collections across the UK to address a grand challenge and reinforce a UK entomological collection network. The multiple museum collections involved will benefit from the genetic data, 3D reconstructions and morphological measurements that we will obtain, and intend to link (likely via QR codes), to each specimen. We envisage that these will be displayed for the visiting public (vi) in each of the respective museums. As has been evident over recent years, there is large appeal of bees to the general public, for instance the press interest surrounding the decline of bees and its impact on food security. We therefore hope that by understanding the past to predict the future this proposed research can assist with mitigating the threats to insect pollinators for conservation, future food security and general human welfare.
 
Title First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing 
Description Insect declines are a global issue with significant ecological and economic ramifications. Yet we have a poor understanding of the genomic impact these losses can have. Genome-wide data from historical specimens has the potential to provide baselines of population genetic measures to study population change, with natural history collections representing large repositories of such specimens. However, an initial challenge in conducting historical DNA data analyses, is to understand how molecular preservation varies between specimens. Here, we highlight how Next Generation Sequencing methods developed for studying archaeological samples can be applied to determine DNA preservation from only a single leg taken from entomological museum specimens, some of which are more than a century old. An analysis of genome-wide data from a set of 113 red-tailed bumblebee (Bombus lapidarius) specimens, from five British museum collections, was used to quantify DNA preservation over time. Additionally, to improve our analysis and further enable future research we generated a novel assembly of the red-tailed bumblebee genome. Our approach shows that museum entomological specimens are comprised of short DNA fragments with mean lengths below 100 base pairs (BP), suggesting a rapid and large-scale post-mortem reduction in DNA fragment size. After this initial decline, however, we find a relatively consistent rate of DNA decay in our dataset, and estimate a mean reduction in fragment length of 1.9bp per decade. The proportion of quality filtered reads mapping our assembled reference genome was around 50 %, and decreased by 1.1 % per decade. We demonstrate that historical insects have significant potential to act as sources of DNA to create valuable genetic baselines. The relatively consistent rate of DNA degradation, both across collections and through time, mean that population level analyses - for example for conservation or evolutionary studies - are entirely feasible, as long as the degraded nature of DNA is accounted for. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
URL http://datadryad.org/stash/dataset/doi:10.5061/dryad.5mkkwh787
 
Description British Ecological Society Annual General Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at the BES 2022 Annual General Meeting demonstrating the potential of museum specimens for conservation projects. The session was a key theme session at the meeting. The meeting is an international meeting of over 1,000 delegates.
Year(s) Of Engagement Activity 2022
 
Description Poster at Irish Ecology and Evolution Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presented a poster on our paper in Methods in Ecology and Evolution on utilising DNA from museum insect collections.
Year(s) Of Engagement Activity 2023
 
Description Session on Collections Genomics at the British Ecological Society meeting. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Session on Collections Genomics at the British Ecological Society meeting, which generated discussion during and after the session.
Year(s) Of Engagement Activity 2022
 
Description Talk To RMS for Girls - For Science Week 2020 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact ~50 Students and Parents (Age range 5-18) attended for a talk on Natural Diversity which was part of an evening event for Science Week 2020 "Our Diverse Planet". Themes discussed included how museum collections can help our understanding of our planets natural diversity.
Year(s) Of Engagement Activity 2020
 
Description Talk at British Ecology Theme Day on Leveraging natural history collections to study global change 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk on utilising museum insect specimens for conservation studies
Year(s) Of Engagement Activity 2023
 
Description Talk at Conservation Genomics at the Population Level in Cambridge 2022. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact A talk at Conservation Genomics at the Population Level in Cambridge 2022 generated interest from participants, including questions after the talk and discussion with other participants.
Year(s) Of Engagement Activity 2022
 
Description Talk at Darwin Tree of Life Scientific Showcase 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Demonstration of the power of reference genomes in regards to museum genomic work for conservation to an audience of academics and potential funders including industry and government organisations.
Year(s) Of Engagement Activity 2022
 
Description Talk at Irish Pollinator Network Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact A meeting of academics interested in pollinator research in Ireland. Demonstrating the use of museum specimens for conservation of pollinators.
Year(s) Of Engagement Activity 2023
 
Description Talk in ancient DNA session, Plant and Animal Genomes meeting 2023 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact c80 scientists were in the ancient DNA session at the Plant and Animal Genomes meeting, and several approached me afterward for discussion about the project.
Year(s) Of Engagement Activity 2023
 
Description Talk to Women's Institute group (Horsell, Surrey) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact The purpose of this 45 minute talk was to introduce and engage the audience in the concept of genetics, the ancient DNA field and the research project. The broad audience consisted of approximately 20 older women. This prompted questions and discussion afterwards. Several of the audience made similar remarks regarding a lack of understanding of genetics prior to the talk, but post talk they felt they had a basic grasp of genetics and our project.
Year(s) Of Engagement Activity 2019