The genomics of adaptation to climate in European great tit (Parus major) populations

Understanding the genomics of adaptation to past climate changes is important to consider in evolutionary ecology. Using the great tit (Parus major), as a model species, I sought to gain insight into the processes of adaptation, both within and between populations, in a wild system. I performed two different types of tests to detect regions under positive selection. In Chapter 2, I performed a multiple-population genome-environment association (GEA) analysis broadly spanning the species range. I identified 36 candidate genes associated with adaptation to climate. The data suggested that climate adaptation appears to be polygenic and genetically complex, involving many different genes and biological process pathways. In Chapter 3, I performed extended haplotype homozygosity testing to detect regions under selective sweeps. I identified 17 potential climate adaptation regions, that had long haplotypes consistent with positive selection in single or geographically close populations. I found little evidence of signatures of parallel evolution in different populations.

I then further investigated the temporal trends of the 11 sweep regions associated with climate adaptation in the UK populations, using whole-genome sequenced museum specimens (Chapter 4). Three candidate climate adaptation SNPs showed significant allele frequency changes over the last century. The closest genes to these three potential climate adaptation regions were identified as the best supported candidate genes. Evidence supporting them included stringent tests to detect selection from genomic data and an unusually strong temporal trend in the UK.

The GEA analysis in chapter 2 suggests that substantial climate-associated genetic variation remains in the pan-European populations, which is likely to be important for adaptation in response to future predicted climate changes. Models of future climate changes particularly relevant to wild great tit populations include more frequent and intense heat waves predicted in the Mediterranean region, which could cause population crashes due to heat stress, especially in the nestling stage where parental care is required.