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The genomics of haplo-diploid pollinators

Principal Supervisor: Dr Rob Hammond, Department of Genetics

Co-supervisor: Dr Eamonn Mallon, Department of Genetics and Genome Biology

PhD project title: The genomics of haplo-diploid pollinators

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].

This PhD will add considerably to our understanding of Haplodiploidy. Hymenoptera are haplodiploid, with males being normally haploid (but see below for exceptions) and females being diploid. These differences in ploidy predict that natural selection is more effective in haplodiploids than in diplodiploids. Furthermore, there should be a difference in the action of selection between those genes that are expressed only in haploid state (those genes expressed in both males and females) and those only expressed in diploid state (those only expressed in females) because recessive mutation will be not be masked by alternative alleles in the former but not in the latter. The predicted result is that mildly deleterious variation that might be important for future adaptation to changing environments is more efficiently removed by negative selection in haplodiploids, while adaptive but recessive variation is more likely fixed by positive selection. However, these predictions have been rarely tested empirically.

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. However, by inbreeding or reduced genetic variation, caused by declining populations, leads to individuals homozygous at CSD which can, and do, develop as diploid males. Diploid males can have an enormous impact on population fitness as they can be unviable, infertile, or fertile but lead to triploid and infertile offspring. Importantly, diploid male production has been shown theoretically to increase extinction threat above that of inbreeding in diplo-diploids by an order of magnitude [4].

These two elements of hymenopteran genetics 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].

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 and complimentary sex determination in haplodiploid pollinator species such as bumble bees of the genus Bombus, and selected, important, solitary bee pollinators. The research will use high throughput next generation sequencing to measure differential gene expression and to survey genetic variation across the genome. These data will be used to compare signatures of selection in response to differential gene expression and recombination. The project will be aided by already developed information on differential gene expression in bees in collaboration between the two supervisors [8].

References:

  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. 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 Straregic 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 Rob Hammond, University of Leicester