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All phenotypic adaptations are encoded in the genome, although untangling the relationships between specific phenotypes and genomic changes is complicated by the fact that at the molecular level, most changes are associated not with selection but neutral processes. Distinguishing between the two is necessary for reliable interpretation of any potential signature of selection. In this respect, this thesis addresses three aspects of genome evolution: biasing factors for the interpretation of protein evolutionary rates, the adaptive significance of presence/absence variation (PAV) in the model plant A. thaliana and the evolution of alternative splicing alongside increasing organism complexity. A comparative genomics approach is used throughout, taking advantage of the increasing availability of high-throughput sequencing data. We show that (i) lineage-specific substitutions and the differential conservation of the edges of exons influence interpretations of protein evolutionary rate, (ii) that PAV in A. thaliana can be explained without invoking adaption, despite enrichments for PAV events in genes considered as positively selected, and (iii) that alternative splicing is amongst the strongest predictors of organism complexity, consistent with an adaptive role of transcript diversification in determining a genome’s functional information capacity. Taken together, we find that the signatures and targets of adaptation can either be masked by, or re-interpreted in the context of, non-adaptive processes and that with the increasing availability of high-throughput data, such considerations are of increasing relevance.

This thesis traces the development of the concept of freedom through three generations of the Modern Arab Renaissance (Nahda). The first chapter challenges the claim that the concept of freedom, in the sense of a political right, was absent from Arab thought prior to the French occupation of Egypt (1798-1801). ‘Abd al-Rahman al-Jabarti’s (1754-1825/6) chronicle of the occupation reveals that he possessed the concept of freedom despite the lack of an Arabic word to identify it. Therefore, when Rifa’a Rafi’ al-Tahtawi (1801-73) translated the French term liberté into Arabic, through a semantic expansion of the word hurriyah, he was naming rather than introducing the concept. The second chapter turns to Syria and examines how Butrus al-Bustani’s (1819-83) advocacy of the freedom of conscience (hurriyat al-damir) as an individual right reflects the influence of his American missionary mentors. However, while the missionaries used this concept to defend their narrow sectarian interests, Bustani believed that the freedom of all citizens must be protected equally by a secular government. The third chapter follows two Syrian friends, Muhammad Rashid Rida (1865-1935) and Farah Antun (1874-1922), who migrated to Egypt where their differing visions of reform brought them into conflict on the pages of their respective literary journals. While Antun argued that secularism provides the best guarantee of freedom, Rida contended that true freedom is only found in Islam. Despite this divide, they shared the same fundamental understanding of the value and meaning of freedom. This chapter shows that the concept of freedom is compatible with differing political ideologies while maintaining its core semantic field. Although there were some changes in how Arab intellectuals conceived of freedom during the nineteenth century, this study demonstrates that there was considerable continuity.