Ancestral splice variation is a key substrate for rapid diversification in African cichlids

Area of Science:

• Evolutionary biology
• Genomics
• Molecular biology

Background:

• Adaptive radiation is a key driver of biodiversity.
• Morphological diversification in radiations is linked to genetic variation and admixture.
• The role of gene regulation in translating genetic variation into phenotypes is poorly understood.

Purpose of the Study:

• To investigate the role of alternative splicing (AS) and gene expression (GE) in cichlid adaptive radiations.
• To understand how genetic variation is rapidly translated into novel phenotypes.
• To explore the evolutionary dynamics of AS in generating biodiversity.

Main Methods:

• Analysis of 200 transcriptomes from three African cichlid adaptive radiations.
• Comparative analysis of alternative splicing (AS) and gene expression (GE) evolution.
• Phylogenetic analysis to trace the origins and frequency changes of alternative isoforms.

Main Results:

• Alternative splicing (AS) evolved faster than gene expression (GE) in cichlid radiations.
• Ancestral alternative isoforms, initially at low frequency, increased during adaptive radiation.
• Novel isoforms of craniofacial genes evolved rapidly, contributing to trophic adaptations.
• Rapid AS turnover suggests relaxed and directional selection dynamics.

Conclusions:

• Alternative splicing plays a pivotal role in generating novel trophic adaptations and biodiversity in cichlid radiations.
• The interplay between splicing and selection facilitates protein-coding diversity and evolutionary innovation.
• Rapid evolution of AS enables ecological diversification on short timescales.