New genes for new biology in animal evolution

Thesis

Gene novelty is one of the mechanisms by which phenotypic novelty may arise and has contributed to the animal diversity observed today. This thesis aims to advance our understanding of evolutionary innovation arising from gene novelty through the integration of multiple levels of analysis, incorporating genomic novelty, expression and morphological function.

Chapter 2 explores and discusses the rationale for the development of a pipeline to identify new genes, and how this requires modification when working with nodes spanning different evolutionary timescales. Chapter 3 demonstrates that gene duplication and divergence are the primary drivers of novel gene emergence and describes two examples of extensive duplication within Lepidoptera, one of which was identified as a putative HGT named ‘Propellin’. Chapter 4 integrates these molecular insights with phenotypic evolution, exploring how changes in gene expression may contribute to the morphological reduction of T1 legs in Nymphalid butterflies, and how this may have resulted in the evolution of a chemosensory function in these appendages. Chapter 5 extends this perspective across Bilateria, specifically investigating novel genes which demonstrate tissue-specific enrichment in gut, nerve cord / nervous system and muscle tissue.

Together, this research highlights the coordination between gene sequence innovation, regulatory dynamics and morphological diversification, offering a comprehensive view of how genomic and developmental processes may contribute to evolutionary novelty. Through the combination of these multi-level analyses, this research offers both conceptual and methodological advances, establishing a model for studying the molecular mechanisms underlying trait evolution across diverse animal lineages, in the context of novel gene evolution.

Authors: Hoile, AE

• DOI: 10.5287/ora-wr1ve4rx2
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: phylogenetics; gene duplication; evolution; bioinformatics; genetics; development; lepidoptera; bilateria; horizontal gene transfer (HGT); gene novelty; Darwin tree of life project (DToL); orthofinder; phenotype
• Subjects: Development; Bioinformatics; Evolution (Biology); Genetics