Understanding the resilience of wild birds to climate change: seasonal genomics of the annual migratory breeding cycle

The potentially devastating effects of climate change have recently been officially recognized and a global emergency declared. To understand how environmental change is impacting on biological systems, we have a unique opportunity to study, in both migratory and resident sub-species of bird, the molecular pathways that regulate annual reproductive cycles, behaviour and potential to survive. We have at our disposal, a very unique set of samples collected from a variety of arctic and North American bird species, representing different tissues at different stages of the breeding cycle, under exposure to different environmental conditions.
Two closely related subspecies of white-crowned sparrow in North America, the Gambel's (GWCS) and the Nuttall's (NWCS), represent very recent and rapid subspecies divergence. This presents an excellent opportunity to study the recent evolution of seasonal behaviour by comparing the long-distance migrant, GWCS, with the year-long resident of California, NWCS. The white-crowned sparrow had a common ancestor with the Rufous-collared sparrow (RCS) during the Pleistocene era. RCS resides in the very distinct environment of South America and provides a powerful model for understanding the evolutionary adaptation of the seasonal behaviour of these wild-birds to historic and recent climate change. One population of Z. capensis has become non-seasonal allowing further "natural experimental" comparisons of gene networks involved in seasonality and vulnerable, or robust, they will be in the face of climate change.
We propose to examine which genes show expression changes in a variety of tissues that are known as important regulators and targets of seasonal hormones. We know there are strong sex differences in gene expression and hormone levels, so we will use both males and females from each sub-species. We will compare NWCS with GWCS during different stages and behaviours during the year (during winter, arrival in Arctic, egg-laying, and pre-basic moult). For the selected genes, that we identify as critical, will use antibody staining to create 3D images for their protein localisation in the hypothalamus and pituitary. We will also follow up the significant genes, tissues and stages in the ancestral RCS to determine the evolutionary history of these regulators of annual behaviour.
High-quality annotated genomes will be developed for these three species to understand their genetic differences and in order for accurate analysis of gene expression to be undertaken. This will also allow other researchers to conduct similar genome-wide studies in these species and empower further international research into the impact of climate on our wild-birds.
We will thus be able to better understand seasonal periodicity and the recent evolutionary history of the sex-specific molecular processes that enable our wild birds to adapt their behaviour to a changing climate. Understanding these key processes and evolutionary history will help us better understand and predict the impact of the current climate emergency on our wild birds. Results from this study will be of consequence not just to science but will help inform at the very heart of the policy changes that will need to be made in our rapidly changing society.
Understanding the ability of wild birds to adapt the basic biology of species (via changes in gene expression, behaviour, reproductive potential, environmental adaptability etc.) to a changing climate will allow us to better understand the impact of global environmental change and begin to develop strategies to mitigate these potentially devastating effects that will have consequences for all life on earth.

We will investigate whether evolutionary radiation of Zonotrichia subspecies, with distinct annual timing and migratory life-cycles, could be predictive of the genomic robustness of these pathways to the current climate emergency. We will exploit a large archive of frozen tissues held at Roslin, which was collected across the annual cycle in sparrows. To facilitate high-throughput and comparative genomics and phylogenetic analysis we will assemble high-quality contiguous and annotated references for the genomes of Z. leucophrys and Z. capensis. To this end we will leverage Dovetail Hi-C and PacBio long-read assemblies, together with high quality IsoSeq full-length gene transcripts using the novel PacBio Sequel II platform. Using RNASeq and enzymatic Methy-Seq and we will measure genomic changes in the transcriptional and epigenetic regulation of seasonal timing and examine how these have evolved in response to the recent evolutionary radiation of Zonotrichia leucophrys subspecies (resident Z.l. nuttalii and migratory Z.l. gambelii). These assays will target hypothalamic, pituitary, gonad, liver and adrenal tissues from both sexes to measure annual changes across the major hormonal signalling axes. Key pathway changes will be identified with pathway enrichment, network visualisation and multi-omic integration. Mutli-omics data will be integrated using a joint latent variable approach to rank features important for key events in seasonal timing. These key feature and pathway changes will be followed up with 3D confocal immunohistochemistry, qRT-PCR, in situ hybridization and methyl-PCR. We will also investigate changes in the ancestral Zonotrichia capensis (resident Z.c. chilensis, migrant Z.c. australis, and the non-seasonal resident of Atacama Desert Z.c. peruviensis). This will address the validity of the evolutionary flexibility hypothesis which is directly pertinent to their ability to adapt to climate change under relatively short timescales.

Immediate beneficiaries:
Scientists whose research is in the field of climate modelling, evolutionary genetics, seasonal biology, avian biology, molecular ecology and the emerging field of migratory genomics. Our findings, published in high impact journals will provide further advances in avian seasonal biology. Three new high quality avian genomes will provide a resource for further genomics projects on these species and will contribute to the effort of the B10K consortium, of which the co-I is part (https://b10k.genomics.cn/). The analysis pipelines we develop for high throughput genomics (disseminated in high impact publications, project workshop/seminars and public repositories) will provide a resource that will improve access to genomics analysis for the research community.

Life-long learning of skills and training:
PhD, MSc and undergraduate students by active participation in research, bioinformatics and lab skills, and engagement with the field of avian seasonal biology. They represent the next generation of researchers in avian seasonal biology.

PDRA in developing their career to independence through skill development in public engagement, paper and grant writing.

PDRA and participants of the project workshop/seminars will obtain experience and skills in high throughput bioinformatics and genomics for seasonal biology. This will increase expertise and capacity within the field.

The public will benefit from access (through press releases and social media) to knowledge about how wild bird migration is regulated and a better understanding of how climate change could affect the seasonal breeding cycles of our wild birds.

Students and teachers will benefit from our classroom resources (via Easter Bush Science Outreach Centre) for learning about the breeding biology of birds and the effects of climate change on our wild birds.

Conserving biodiversity for future generations:
Migrating bird populations will benefit from an increased understanding and awareness concerning how best to mitigate the detrimental effects of human activity on their natural breeding cycles.

High impact publications that improve the field's understanding of how genetically robust our migratory birds are to climate change has the potential to directly impact policy development in areas related to biodiversity and climate change (high impact publication, press releases, social media, liaison with Scottish Parliament). The project's engagement with the public (press releases, social media, teaching resources) has the potential to further inform and positively impact public-opinion and further influence policy outcomes that could directly affect the strategies for conserving our wild birds for future generations.

Industrial Stakeholders:
Companies that work in Environmental Impact Assessment will benefit from the research findings in high impact papers from the project, which will help inform how impacts on the seasonal biology of wild birds are assessed.

There are also implications for the poultry industry as we identify the genetics underlying resilience in avian species.