Genomic Signatures Of Adaptation In Eukaryotic Systems

Abstract

Phenotypic variation between species or between individuals of a single species is encoded in their genomes, reflecting their specific evolutionary path. By comparing genomes and functional molecular data from several species and/or multiple individuals from a single species we can investigate the molecular signatures that underlie phenotypic diversity. The emergence and improvement of RNA and DNA sequencing and genome wide data analysis methods have facilitated the study of the molecular processes that shape phenotypic traits in an ever-expanding set of species beyond traditional model organisms. Taking advantage of these technologies and accumulating data, here I explore the molecular basis of two important phenotype traits, brain cell morphology and sexual selection in mammals and local adaptation in a plant species for which molecular underpinnings remain poorly understood. First, using a comparative genomics approach on 19 mammalian species for which brain cell composition data and fully sequenced genomes are available, I determined the relationship between variation in brain cellular composition of the brain and variations in gene family size (GFS). The results revealed significant associations between changes in gene family size and different cell composition parameters. Gene families associated neuron number, neuron density, glia to neuron ratio and encephalization were enriched various developmental related functions in the brain and generally including cell projection and neuron development whereas families associated with glia to neuron ratio were enriched in translation and cell migration. Immune system functions were also enriched among encephalization and neuron number associated gene families. These results are not explained by phylogenetic relatedness or associations among the different variables studied. Secondly, using a similar approach, I investigated the link between GFS changes and sexual size dimorphism (SSD) in mammals to elucidate the molecular signatures of differing degrees of sexual selection. From the 44 mammalian species assessed, it was observed that 729 gene families are significantly correlated with changes in GFS and SSD. Families expanding in line with increases in size dimorphism were found to be enriched in regulation of cell adhesion and stimulatory C type lectin receptor signalling pathway. Interestingly, gene families associated with reduced size dimorphism were found to be enriched in various aspects of brain development. These results could suggest that monogamous lineages experience higher selection on brain complexity to deal with the more elaborate social structures. Associations were not accounted for phylogenetic relatedness or by co-varying overall body mass. Finally, I examined transcriptome profiles of 19 samples of the searocket Cakile maritima (family Brassicaceae), stemming from five different locations. Using a phylogenetically corrected comparative approach it was shown that changes in gene expression are associated with various aspects of bioclimatic variation. These associated genes were significantly enriched in various functional categories related to the response mechanisms of plants to stress, e.g. regulation of endopeptidase activity, sugars metabolic processes, cell redox homeostasis, regulation of gene expression and DNA duplex unwinding. Crucially, these results are not explained by non-heritable phenotypic plasticity as transcriptome profiles were obtained from plants grown in controlled conditions from collected seeds. These results contribute to the understanding of the genetic mechanisms of adaptation to changing environments in plants. Overall, the findings presented in this thesis provide novel insights into the molecular background of complex phenotypes in eukaryotes using genomic and transcriptome data bioinformatics analyses. Importantly, the results presented here could not be inferred from single species analyses in model organisms as the phenotypes of interest. Large brains, high and low sexual selection and local adaptation to arid environments are not found in mammalian rodent models or the model plant Arabidopsis thaliana.

Date of Award	24 Jun 2020
Original language	English
Awarding Institution	University of Bath
Supervisor	Araxi Urrutia (Supervisor) & Nicholas Priest (Supervisor)