Primate Amylase

Convergent evolution through independent rearrangements in the primate amylase locus

Representative publications on this topic include:

  1. Karageorgiou, C., Ruhl, S., & Gokcumen, O. (2025). Convergent evolution through independent rearrangements in the primate amylase locus. bioRxiv, 2025-08.

Our latest preprint explores the evolution of the primate amylase locus, uncovering structural innovations, regulatory shifts and molecular convergence. We find repeated gains and losses of amylase copies, arising independently, revealing it as a structural hotspot in primate genomes.

From a single ancestral AMY2B gene, a γ‐actin insertion and duplication in Catarrhini created AMY1′. In great apes, AMY1′ acquired an ERV insertion and underwent further duplications, giving rise to AMY1 (salivary) and AMY2A (pancreatic) specialization.

In rhesus macaques and olive baboons, NAHR produced lineage‐specific amylase duplicates (AMYm, AMYp1, AMYp2) within the last ~5 Myr, showing structural innovation has occurred multiple times in this locus.

LTR retrotransposons are enriched at the amylase locus and correlate with copy number gains. Other TE types are depleted. LTRs may prime the locus for structural instability and recurrent duplications.

In baboons, the novel AMYp2 gene shows strong positive selection, while the ancestral AMY2B carries a premature stop codon, hinting at functional compensation. Multiple paralogs contribute to salivary amylase in Old World monkeys.

Ancestral AMY1′ was expressed in both pancreas and salivary glands. In great apes, duplication led to AMY1 (salivary) and AMY2A (pancreatic). In macaques and baboons, AMY1′ still shows dual expression, with a tendency toward higher salivary expression.

Regulatory motifs alone don’t explain tissue specificity. FOXC1 sites appear in most paralogs. Patterns likely reflect combinatorial motif turnover plus cis-regulatory context (promoters/enhancers), chromatin accessibility and locus architecture altered by duplications.

Our findings show that structural changes, TE insertions, and regulatory shifts in the primate amylase locus have repeatedly altered its structure and function, underscoring its role as a recurrent site of evolutionary change. If you ask me, the real mystery is still this: why this locus?