• Research

Population Genomics of Pollinating Insects

Using bumblebee genomics to better understand current threats to UK pollinator populations

Project summary.

Led by: Wilfried Haerty

Start date: 2019

End date: Ongonig

Funding: BBSRC

Pollinator species are in decline all over Europe. Bees, in particular, are under severe threat from both habitat loss and harmful pesticides. Of 270 bee species in the UK, 35 are under threat, while we’ve lost 13 species already in the past few decades.

That decline poses a severe problem for biodiversity and agriculture. Bees, hoverflies and other insects fertilise a vast amount of crops and wildflowers, both of which become less productive with a decline in pollinating insects. If we are to continue to feed ourselves, and enjoy a biodiverse planet for generations to come, we must better understand and protect pollinators.

Earlham Institute has already begun to sequence the genomes of important bee species. This project - in collaboration with researchers at Natural History Museum (NHM), Imperial College London, the University of East Anglia (UEA), the University of Plymouth (UoP), and the Bumblebee Conservation Trust (BBCT) - is capturing a snapshot of bee populations in the UK, assessing the structure and health of these populations at the genetic level.

The Evolutionary Genomics Group at EI is working on species that are currently flourishing in the UK, with the aim of generating similar datasets for species in decline. This important comparative approach has the power to identify genetic changes that could be associated with population health in our native bee populations. 


There are several aspects to the project, including the sequencing of several new bee genomes, the analysis and comparison of bee genomes, and understanding both the ecological and scientific impact of those genomes.

Sequencing of new bee genomes, including:

  • Conservation priority species: The Moss Carder Bee (Bombus muscorum) sequenced by a hybrid approach of long and short read data. In collaboration with the NHM; The large Yellow Bumble Bee (Bombus distinguendus). In collaboration with BBCT 
  • Successful species: The Vestal Cuckoo bee (Bombus vestalis). Contributing genome assembly and analysis to a project led by UEA

Large scale monitoring of bees

With access to thousands of bee samples past and present, in collaboration with the Natural History Museum we can analyse them to inform conservation strategies. We can identify risk factors, for example:

  • How populations with low genetic diversity are affected by inbreeding depression
  • Genetic markers that signify a particular susceptibility to parasites
  • Historical bottlenecks due to agricultural intensification
  • Species prone to habitat fragmentation, for example those with low pollen dispersal ability

Ecological impacts.

With collaborators at UEA and the University of Plymouth, we are looking to understand the spread and success of bee species that have colonised the UK in the last two decades.

Fundamental research into bees, including haplodiploidy

How male bees develop from unfertilised eggs, meaning that they possess only one set of chromosomes. Using parallel computing techniques, we can compare population data to study gene selection in such a scenario.


Natural History Museum

The University of East Anglia

The University of Plymouth

Bumblebee Conservation Trust

The Darwin Tree of Life Consortium

Impact statement.

Pollinators are under threat, and we need to understand better ways to protect them.

Thanks to modern genomic methods, we are able to sequence and analyse the genomes of thousands of individuals to get a better understanding of how their populations vary across the UK, and through time. By studying species that are flourishing in the current environment, we will learn about the pressures shaping their populations and how they interact with our agricultural system.

Through studying bee species that are in decline, we will provide primary conservation resources. We will deliver insight into these threatened species at a resolution never possible before, enabling prioritisation of key population centers and potential routes to genetic rescue.