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Pollinator Genomics

Principal Supervisor: Dr Robert Hammond, Department of Genetics and Genome Biology

Co-supervisor: Dr Eamonn Mallon

PhD project title: Pollinator Genomics

University of Registration: University of Leicester

Project outline:

Eighty four percent of the crops cultivated in Europe and 70% of crops worldwide are dependent on pollination by insects, particularly the Hymenoptera – the bees, ants and wasps. This ecosystem service is essential for human health and wellbeing and contributes hundreds of billions of pounds to the world economy [1].

Both solitary and eusocial Hymenoptera are, like many species, under increasing pressure of anthropogenic change with the result their populations are decreasing in size and becoming fragmented [2]. Importantly, understudied aspects of the genetics and life-history of Hymenoptera make these changes potentially much more damaging [3].

1) Sex determination. In many species sex is determined by a single genetic locus, the complimentary sex determination locus (CSD). Normally heterozygotes develop as females while hemizygotes (haploid) develop as males, but unwanted homozygotes can and do develop as males (so called diploid males). Diploid males can have a huge impact on population fitness as they can be unviable, infertile or fertile (but lead to triploid and infertile offspring) and can increase extinction threat above that of inbreeding in diplodiploids by an order of magnitude [4].

2) Haplodiploidy. Because of male haploidy natural selection is predicted to be more efficacious in haplodiploids than in diplodiploids. The result is that mildly deleterious variation that might be important for future adaptation to changing environments is more efficiently removed by negative selection.

3) Eusociality. The effective population size (Ne) of eusocial species is much smaller than census population size because most individuals in eusocial species are non-reproducing workers. Species that are commonly observed in nature may in fact be losing genetic variation on account of the small number of reproductive individuals that contribute genetically.

These three elements are understudied. For example, the molecular genetic basis of the CSD locus is only known in the honey bee genus Apis [5], although evidence points potentially to a degree of conservation of mechanism [6], and only recently have there been attempts to investigate the effects of selection in haploplodiploids on a genomic scale [7], and the influence of low Ne caused by eusociality on genetic variation [8].

The development of high-throughput DNA sequencing technologies and reducing costs of using such techniques means that it is now possible to investigate these issues on a genomic scale.

The aim of this PhD is to investigate the population genomic effects of selection in haplodiploid pollinator species such as bumble bees of the genus Bombus. The work will use high throughput next generation sequencing to survey genetic variation across the genome and to compare signatures of selection in response to differential gene expression and recombination. The project will use already developed information on differential gene expression in bees in collaboration between the two supervisors [9].


  1. Gallai N., Salles J.M., Settele J., Vaissière B.E. 2009 Economic valuation of the vulnerability of world agriculture confronted with pollinator decline. Ecological Economics 68(3), 810-821. (doi:10.1016/j.ecolecon.2008.06.014).
  2. Potts S.G., Biesmeijer J.C., Kremen C., Neumann P., Schweiger O., Kunin W.E. 2010 Global pollinator declines: trends, impacts and drivers. Trends Ecol Evol 25(6), 345-353. (doi:10.1016/j.tree.2010.01.007).
  3. Chapman R.E., Bourke A.F.G. 2001 The influence of sociality on the conservation biology of social insects. Ecol Lett 4(6), 650-662. (doi:10.1046/j.1461-0248.2001.00253.x).
  4. Zayed A., Packer L. 2005 Complementary sex determination substantially increases extinction proneness of haplodiploid populations. Proc Natl Acad Sci U S A 102(30), 10742-10746. (doi:10.1073/pnas.0502271102).
  5. Beye M., Hasselmann M., Fondrk M.K., Page R.E., Omholt S.W. 2003 The gene csd is the primary signal for sexual development in the honeybee and encodes an SR-type protein. Cell 114(4), 419-429. (doi:10.1016/s0092-8674(03)00606-8).
  6. Miyakawa M.O., Mikheyev A.S. 2015 QTL Mapping of Sex Determination Loci Supports an Ancient Pathway in Ants and Honey Bees. PLOS Genetics 11(11), e1005656. (doi:10.1371/journal.pgen.1005656).
  7. Harrison M.C., Mallon E.B., Hammond R.L. In review Purged haploids - sheltered diploids: ploidy infuences selection efficacy in a haplodiploid bee.
  8. Romiguier J., Lourenco J., Gayral P., Faivre N., Weinert L.A., Ravel S., Ballenghien M., Cahais V., Bernard A., Loire E., et al. 2014 Population genomics of eusocial insects: the costs of a vertebrate-like effective population size. Journal of Evolutionary Biology 27(3), 593-603. (doi:10.1111/jeb.12331).
  9. Harrison M.C., Hammond R.L., Mallon E.B. 2015 Reproductive workers show queenlike gene expression in an intermediately eusocial insect, the buff-tailed bumble bee Bombus terrestris. Molecular Ecology 24(12), 3043-3063. (doi:10.1111/mec.13215).

BBSRC Strategic Research Priority: Food Security

Techniques that will be undertaken during the project:

  • High throughput massively parallel genome sequencing.
  • Bioinformatics (Linux environment, shell scripting, Python programming, use of R for statistics).
  • Quantitative analysis of genetic variation.
Contact: Dr Robert Hammond, University of Leicester