The genomic and transcriptomic architecture of niche breadth, adaptation, and speciation

Ecological divergence between populations and even speciation can occur over rapid timescales.

Whether specific genomic or transcriptomic architectures underly these processes, remains a persistent gap in evolutionary biology. Evidence suggests that structural variants (SVs), like inversions, have an immense impact on evolution.

Repetitive content, specifically transposable elements (TEs), also represent a previously underappreciated yet pervasive axis of genomic variation.

Importantly, both TEs and SVs have the potential to impact transcriptional variation, leading to novel or divergent phenotypes.

However, the mechanisms by which genomic architecture influences gene expression and alternative splicing are not well known.My project explores the role of SVs and TEs in niche breadth, adaptive divergence, and speciation using peacock flies.

I have documented features making these flies an ideal system to test the transcriptional role of SVs and TEs, including a genome expansion driven by TEs, a large inversion differentiating evolved specialists, and expression differences among specialized flies.

I will uncover the transcriptomic mechanisms by which SVs and TEs generate plastic or divergent phenotypes and affect fitness.

Unraveling these mechanisms will enhance our understanding of the genomic basis of adaptive evolution and speciation and will improve our ability to predict how organisms respond to environmental change based on their genomic and transcriptomic architecture.