Using genomes to dissect the speciation process - a comparative approach

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Although speciation is one of the most fundamental biological processes, we still know surprisingly little about it. For example, it is not know whether species splits are generally abrupt, which would be expected if speciation mostly occurs as a result of populations becoming separated in different places, or whether speciation generally involves a protracted period of hybridisation which eventually ceases. It is also unclear what type of selection matters most for making species reproductively isolated: species may become isolated from each other simply by adapting to different environments or, alternatively, as a result of selection on traits that only benefit one sex. For example, in many insects, males increase the number of offspring by producing very many or very large sperm, while females have evolved mechanisms to kill, store and select sperm. This sexual antagonism leads to a reciprocal armsrace and rapid evolution of reproductive traits which in itself may be strong enough to drive speciation.Because the genome of an individual is made up of contributions from an enormous number of ancestors, even a small sample of genomes contains a lot of information about the population of ancestors and about when and how fast this ancestral population split into distinct species. Since speciation is a slow process, the only chance to understand how species typically arise in nature is by extracting this genomic information about past speciation events. For example, recent comparisons of individual human genomes have shown that our own genomes are a result of past hybridisation between modern humans and more archaic forms such as Neandertals. The main aim of my project is to use genomic data to estimate speciation histories and find out what factors drive speciation in nature. Comparing speciation histories across many different insect species and between different parts of the genome, will allow me answer fundamental questions about how new species are born. This work comes in two parts. Firstly, I will develop new statistical methods to reconstruct past speciation events from genome data. To make such inferences realistic, many biological processes that effect patterns of diversity in the genome must be incorporated into a mathematical model: During reproduction, genetic material is combined from different parents and passed on to successive generations by chance. While the splitting of populations leads to separated gene pools, individuals from different populations may migrate and hybridise, causing genes to "flow" between diverging species. In particular, I will focus on reconstructing the duration and direction of such gene flow after divergence which gives a measure of how fast speciation has happened. Secondly, I will use these methods to ask how the process of speciation has played out in 40 species of wasps, flies, beetles and butterflies many of which are common in UK. I will sequence multiple individual genomes in 20 pairs of closely related species and compare speciation parameters between species pairs with more and less intensive sexual antagonism, as indicated by their mating behaviour. This will reveal whether sexual antagonism speeds up speciation. A second comparison will explore the link between speciation and ecological specialisation by testing whether species that specialise on a small number of hosts generally evolve from generalists or vice versa. Finally, I will compare the speed at which sex chromosomes and autosomes become distinct during speciation to test whether genes important in speciation accumulate more rapidly on sex chromosomes.This work will build a statistical framework for us to use genome sequences as a window into the past and to understand the role of selection, geography and hybridisation in speciation - an important step towards solving Darwin's mystery of mysteries of how species come about.