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Speciation Genomics in an Obligate Fig Pollination Mutualism

Primary Supervisor: Dr Simon T Segar, Crop & Environmental Sciences

Secondary supervisor: Ed Harris

PhD project title: Speciation Genomics in an Obligate Fig Pollination Mutualism

University of Registration: Harper Adams University

Biodiversity is not evenly distributed, with tropical rainforests (particularly those along mountains) contributing well over half of the known vascular plant species to the global total. These irreplaceable crucibles of genetic and functional diversity are under direct and extreme threat, yet we have very little understanding of the eco-evolutionary processes that fuel them. Seeking a ‘unified theory of speciation’ outlining the rules of population diversification is a core goal of fundamental ecological research. A highly comparative approach is clearly required, moving beyond model systems to more representative and complex interactions.

Both abiotic and biotic selective pressures have been shown to be important drivers of ecological speciation (e.g. speciation in sympatry or parapatry rather than allopatry). For example, local populations can adapt to clines in pollution gradients or host plant chemistry. It is well established that speciation can occur in the face of geneflow, and that reproductive isolation can be maintained by lineage specific ‘barrier loci’. We understand much less about the demography of reciprocal speciation, how do organisms codiversify and what are the molecular signatures of reciprocal biotic selection?

The first objective of this project will be to document the demography of speciation for both partners in a co-evolved obligate pollination mutualism (e.g. when did species split and is there ongoing gene flow?). Our study system is the fig-fig wasp mutualism, a highly diverse radiation of tropical plants in the family Moraceae pollinated by ‘species specific’ chalcid wasps. A huge advantage of this system is that the fitness of each partner is directly linked, and relatively easy to measure: a small number of specific wasps pollinate each fig and these can be reared from discrete and enclosed units (the fig ‘fruits’). Ongoing study of figs and their pollinators along the slopes of Mt Wilhelm in Papua New Guinea is shedding light on how figs and wasps may have co-diverged (Souto-Vilaros et al., 2019). The proposed project will build on previous characterisations of population genetic structure that suggests a decoupling of speciation dynamics between mutualists driven by asymmetrical rates of speciation, wasps likely speciate much faster than figs. Our results suggest a ‘split and sort’ process of speciation (Cook and Segar, 2010) whereby incipient fig species are pollinated by multiple wasps species across a parapatric range before eventual sorting and reproductive barriers restore a one-to-one partner specificity. Subsequent work will test hypotheses relating to genic speciation in each partner, can we find highly divergent regions of the genome that may maintain reproductive isolation in the face of gene flow? Are these regions associated with key traits responsible for host choice in pollinators or volatile cues produced by hosts (Segar et al., 2019), for example?

We will utilise current and newly developed genomic resources to address these questions: including three draft (Chromium 10X) fig genomes, one wasp genome and tens of thousands of SNPs derived from nextRAD sequencing (Souto-Vilaros et al., 2019). Published annotated genomes for both figs and wasps will be used reference sources. In addition we will collaborate with other teams working on fig and wasp genomics to compliment these data with long read PacBio sequencing and transcriptomes. Depending on the interests of the student there are opportunities to conduct field work in Papua New Guinea (in collaboration with the Binatang Research Centre) and analyse chemical traits in collaboration with the University of Turku. Applicants should have a broad interest in ecology and evolution as well as some experience with (or willingness to learn) modern methods in bioinformatics.

A more holistic understanding of how lineages diversify will help us to test the generality of proposed mechanisms for speciation, and the processes underlying the generation and maintenance of global biodiversity itself. This work focuses on one of the most fundamental ‘rules of life’: how do new species form?

The project fits within an ongoing research programme that integrates molecular ecology, morphometrics, behaviour and chemical ecology to address patterns of speciation. The proposed Ph.D studentship will help us to focus on the underlying molecular determination of these traits in unprecedented detail.

Lab techniques include:

  • DNA/RNA extraction and qPCR.
  • Use of HPLC-MS or GC-MS if students develop an interest in chemical ecology.
  • Microscopy and morphometrics.

Field work:

  • Organisation and implementation of field collection expeditions in remote locations.
  • Design and implementation of host preference trials and rearing of insect herbivores.

Analytical techniques:

  • Assembly and annotation (gene prediction and homology) of plant and insect genomes (including Supernova, Augustus software).
  • Use of population genomics tools to map SNP loci (e.g. Bowtie and Samtools).

The Jean Jackson Entomology Building at Harper Adams University is equipped with state of the art entomological equipment and managed by the PI, while the Molecular Diagnostics Laboratory managed by Professor Simon Edwards provides all necessary equipment for DNA extraction, qPCR and gel electrophoresis. Technical support is available at both facilities.

The supervisor has strong connections with a number of international laboratories (e.g. the Czech Academy of Science, the University of Turku and East China Normal University) where facilities can be made available on a collaborative (costs only) basis.

Other (E.g. a requirement for field work, night shift requirement etc).

Field work in Papua New Guinea is physically demanding and involves long hours in challenging conditions. During periods of field-work working hours will be irregular.

Contact: Dr Simon T Segar, Harper Adams University