Parallel evolution of gene expression between trophic specialists despite divergent genotypes and morphologies

Area of Science:

• Evolutionary Biology
• Genomics
• Ecology

Background:

• Convergent evolution of gene expression often drives niche specialization.
• Parallel gene expression changes can also facilitate divergent specialization.
• Understanding these patterns is key to deciphering adaptive radiation.

Purpose of the Study:

• Investigate gene expression divergence and genetic variation in three sympatric pupfish species.
• Examine the relationship between gene expression and genetic differentiation during niche specialization.
• Clarify the role of parallel gene expression in divergent ecological speciation.

Main Methods:

• Compared gene expression using total mRNA from three pupfish species at two developmental stages.
• Analyzed whole-genome genetic variation across 42 resequenced genomes.
• Assessed gene expression patterns in relation to genetic differentiation between generalist and specialist populations.

Main Results:

• Eighty percent of differentially expressed genes between snail-eaters and generalists showed parallel regulation in scale-eaters.
• No shared fixed genetic variants were found underlying these parallel expression changes.
• Genes with parallel expression evolution were enriched in metabolic processes; divergent expression genes related to cranial development and pigment biosynthesis.

Conclusions:

• Divergent niche specialists can exhibit convergent adaptation to higher trophic levels via shared genetic pathways.
• Parallel evolution in gene expression can accompany divergent ecological speciation.
• This study reveals a counterintuitive mechanism in adaptive radiation.