The Great Tit HapMap Project

Most people interested in science are aware that the last decade has witnessed dramatic advances in genomics tools and techniques.
Excitingly, these new technologies are not limited to humans or classical model organisms like fruitflies and yeasts, but can now be applied to organisms which have long interested ecologists but which, until now, lacked genetics tools. We have taken advantage of the opportunities afforded by so-called next generation sequencing to develop genomics resources for the great tit.

Great tits (Parus major) are one of the most widely studied invertebrates because they are common and readily breed in artifical nest boxes. As a result a number of long term studies of great tit populations have been conducted across Europe, some of which have been ongoing for more than 50 years and include data on tens of thousands of individual birds.
These long-term datasets are rich resources for studying important ecological questions such as: How organisms adapt to climate change, How organisms allocate resources to breeding and other activities, How species evolve in the face of natural selection.

Using funds won from the European Research Council (ERC) and the Netherlands government, we have begun to map genes responsible for variation in life history and morphological traits in two of the most intensively studied populations - at Wytham Woods in the UK and de Hoge Veluwe in The Netherlands. By working as a UK-Dutch collaboration we have pooled genomics resources and developed a tool called a SNP chip which allows us to type more than 9000 genetic markers in each of our study populations. We have now typed more than 2000 Dutch birds and 2700 UK birds with this chip. In this proposal, we request funds to type a further 16 great tit populations (50 birds per population). Why do we want to do this? The main reason is that by typing the same genetic markers in lots of different populations we can characterise genetic variation across the entire species range in order to learn more about the species evolutionary history. Projects of this nature are sometimes called HapMap Projects because they involve the mapping of markers linked along a chromosome (HAPlotypes). The best known HapMap project has been conducted in humans and has led to great insight into how our species colonised the world after migrating from Africa, how different populations are related to each other, and how genes have enabled us to adapt to e.g. different environmental conditions, novel challenges such as emerging diseases, changes in diet etc. By carrying out a Great Tit HapMap Project we can address similar questions in this widely studied ecological model organism. This also means we can extend the findings from the Wytham and de Hoge Veluwe populations to ask fundamental questions about evolutionary genetics. For example: Do the same genes explain adaptation in different populations? Do beneficial genes that arise in one population rapidly spread to other populations? Do the genes that explain variation within a population also explain differences between populations? Does migration between populations play a major role in maintaining genetic diversity? Does this gene flow help or hinder local adaptation?

There is perhaps no other vertebrate for which multiple long-term ecological datasets and such extensive genomics resources are available. Therefore, the great tit is an ideal organism in which to perform the first 'natural population' HapMap Project.

Our project addresses fundamental questions in evolutionary genetics; as such it is largely blue-skies research and will advance understanding of the genetic architecture of quantitative genetic variation. Apart from standard activities (attending conferences, publishing our research, and presenting scientific seminars) we intend to engage in the following impact activities:

We will explain our science to the public via the media, public science events including literary/book festivals and through UCAS visit days. We showcase research in the Molecular Ecology lab to over 1000 visitors to the department every year, showing them how genomics tools and techniques can be used to address ecological questions. Biology students should also be beneficiaries of the research. Previous research from the team has featured in biology textbooks and we will promote the inclusion of this research in future editions.

Wider commercialisation of a SNP chip.
The SNP chip we have developed will be tested in multiple populations. Having evaluated its applicability to their own populations, researchers leading other great tit long-term projects will be able to purchase chips via the provider Illumina, a global company with a UK headquarters.

Our research team will continue to ensure that we promote our NERC-funded science with support from the University's Press Office.