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The epigenetic basis of early-life effects in a wild bird exposed to urban environmental stress

Periodic Reporting for period 1 - URBANEPIGENETICS (The epigenetic basis of early-life effects in a wild bird exposed to urban environmental stress)

Reporting period: 2015-04-01 to 2017-03-31

Urban areas are the most rapidly expanding form of land cover across the globe and more than half of the world’s population live in urban centres. This has significant implications for standards of living, human health and the environment. Just as the development of urban areas presents both opportunities and challenges for people, urbanisation offers advantages and disadvantages for wildlife. Some animals actively avoid towns and cities, while others manage to co-exist alongside humans. Birds are a typical feature of urban wildlife. Towns and cities can potentially benefit birds by offering a milder climate and an abundance of food. However, just as there can be adverse effects for human health, there may also be negative effects for birds, associated with exposure to air pollutants, artificial light and noise in urban areas.

There is increasing evidence that exposure to “stressors”, such as air pollutants, causes changes in the structure of DNA. Specifically, stress-exposure can change the number and location of methyl groups that are attached to DNA, which can subsequently affect gene expression. In other words, environmental conditions can determine which genes are switched on or off and the level at which they are expressed. Patterns of gene expression subsequently influence the establishment of characteristics or traits, for example body size and immune responses. Thus, DNA methylation may mechanistically link environmental conditions and observable characteristics of an individual.

In particular, the environment experienced during early life is known to be very important, in both humans and animals, for determining fixed life-long characteristics relating to, for example, body size, personality and health. Changes in DNA methylation are proposed to be the mechanistic link between the early-life conditions and determining later-life health and survival. Through this study, we seek to better understand how urban-dwelling birds are affected – both positively and negatively – by exposure to urban “stressors”. Understanding how and why exposure to stressors in towns and cities may affect health and survival of birds is important for progression of our knowledge of animal biology, implementation of effective conservation measures, and improving our own health and wellbeing.
"Firstly, we set out to describe the natural variation in patterns of gene expression between urban- and rural-dwelling birds. State-of-the-art technology, known as RNA-sequencing, was employed for characterising all the RNA molecules extracted from a biological sample. Along with DNA and proteins, RNA is one of the major biological macromolecules that is essential for life. With the help of state-of-the-art bioinformatic tools, we revealed all of the genes that were actively being expressed in tissues. We found large differences in the levels at which genes were expressed between urban- and rural-dwelling birds. Urban birds exhibited higher expression of genes linked to immune and inflammatory responses and detoxification mechanisms. This supports the expectation that urban environments present birds with a range of stressors, arising from for example air pollution and different pathogens to which they would be exposed in natural environments. The result is the stimulation of biological stress responses to counter these stressors. While these stress responses have evolved to enable animals to cope with stressors, there are likely to be negative effects if urban birds have to constantly run immune and detoxification systems at high levels. This study was published in March 2017 in a peer-reviewed journal, Scientific Reports (https://www.nature.com/articles/srep44180). The results have also been disseminated widely through numerous presentations at international conferences, in Swedish national media and via social media. By application of another state-of-the-art technique, known as Reduced Representation Bisulphite Sequencing, quantitative data on DNA methylation patterns in urban and rural birds have been obtained. This technique has been rarely applied to ""non-model"" organisms, presenting a challenge - since there is little knowledge and experience to draw on - but also great potential for advancing our scientific understanding of how the environment affects gene expression. Analysis of the data is ongoing, and it is hoped that exciting novel results will be disseminated in 2018.

Oxidative stress is defined as an imbalance of damage-inducing pro-oxidants and the antioxidant defences that can counteract or detoxify these reactive molecules and repair damage. By increasing the oxygen concentration in the atmosphere, our objective was to induce oxidative stress during development in the eggs of a wild bird. While this method has been used to successfully induce oxidative stress in fish and insects, there is no published literature concerning the application to birds. Preliminary analysis of seven different biomarkers has revealed that the experimental manipulation did not induce significant oxidative stress in developing embryos and had no effect on telomere length – a marker of genomic stability and linked to senescence. However, depletion of antioxidants that the mother deposits in the yolk suggests that the yolk buffers the embryo against damage. The study offers a valuable contribution to our understanding of the causes and consequences of oxidative stress during development.
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Along with climate change, urbanisation has been identified as one of the most pressing issues currently faced by biodiversity worldwide. For this reason, the project was timely to address core questions concerning how wild animals respond and deal with the “stressors” faced in our towns and cities. The project has made (and will continue to make) valuable contributions to furthering our understanding of the potential resilience of wildlife to intensifying urban development. This helps to build on a sound scientific knowledge base, on which policy-makers and city-planners can make informed decisions. Through the project's various channels of regular communications with local municipalities, stakeholders and the general public, the project has been educating citizens and decision-makers about urban wildlife, and about the potential opportunities and challenges that wild animals face in our towns and cities.

Through the use of state-of-the-art technologies and representing one of a relatively few number of studies applying such techniques to “non-model” organisms, the project has made valuable and novel contributions to the field. The knowledge gained will help to inform future projects and improve available tools and methodologies. The project has resulted in the generation of hugely valuable information for researchers – communicated via invited talks, conference presentations and peer-reviewed publications - and for the laboratories that provide the state-of-the-art services – via extensive discussions during project planning and execution. Labs can use this knowledge to better inform current and future customers about the potential applications and challenges of methods, and to improve methodologies.

Biological sequence data generated by the project has been deposited in an open database, creating opportunities for use by others and thus increasing the impact and potential value of the study. Further data will be deposited upon the publication of results in peer-reviewed journals.
The great tit: a key species for studying effects of urbanisation across Europe (Johan Nilsson)