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Convergent evolution through independent rearrangements in the primate amylase locus [Baboon]

ABSTRACT: Structurally complex regions of the genome are increasingly recognized as engines of evolutionary convergence due to their propensity to generate recurrent gene duplications that give rise to similar gene expression patterns and traits across lineages. However the mutational mechanisms driving these duplications and the regulatory changes enabling novel expression patterns remain poorly understood. The primate amylase locus, marked by independent gene duplications, provides an ideal model to investigate these dynamics. Leveraging high-quality genome assemblies from 53 primates and multi-tissue transcriptomes from Old World monkeys, we reconstructed the evolutionary history of the recurrent gene duplications across the primate phylogeny. Our data suggest that lineage-specific LTR retrotransposon insertions are associated with initial structural instability, while subsequent duplications are primarily driven by non-allelic homologous recombination. Recurrent independent duplications in rhesus macaques, olive baboons, and great apes gave rise to distinct amylase gene copies with convergent expression in the pancreas and salivary glands. We found that these independent gene duplications are accompanied by episodic diversifying selection on lineage-specific copies, likely driving the emergence of functional divergence. Our comparative analyses in primates indicate that the gene ancestral to great ape AMY1 and AMY2A was expressed in both salivary glands and pancreas in the Catarrhini ancestor. The great ape–specific duplication of this ancestral gene likely facilitated subfunctionalization into salivary gland- and pancreas-specific expression, respectively. Comparative analysis of primate amylase promoter regions reveals regulatory rewiring, driven by motif turnover mediated by structural rearrangements, and partially explaining evolutionary shifts in expression. Together, our findings highlight how structural and regulatory modularity in complex genomic regions drives evolutionary innovation and molecular convergence, and we provide a genomic framework for dissecting these processes across diverse lineages.

ORGANISM(S): Papio anubis

PROVIDER: GSE305241 | GEO | 2025/08/27

REPOSITORIES: GEO

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Project description:Structurally complex regions of the genome are increasingly recognized as engines of evolutionary convergence due to their propensity to generate recurrent gene duplications that give rise to similar gene expression patterns and traits across lineages. However the mutational mechanisms driving these duplications and the regulatory changes enabling novel expression patterns remain poorly understood. The primate amylase locus, marked by independent gene duplications, provides an ideal model to investigate these dynamics. Leveraging high-quality genome assemblies from 53 primates and multi-tissue transcriptomes from Old World monkeys, we reconstructed the evolutionary history of the recurrent gene duplications across the primate phylogeny. Our data suggest that lineage-specific LTR retrotransposon insertions are associated with initial structural instability, while subsequent duplications are primarily driven by non-allelic homologous recombination. Recurrent independent duplications in rhesus macaques, olive baboons, and great apes gave rise to distinct amylase gene copies with convergent expression in the pancreas and salivary glands. We found that these independent gene duplications are accompanied by episodic diversifying selection on lineage-specific copies, likely driving the emergence of functional divergence. Our comparative analyses in primates indicate that the gene ancestral to great ape AMY1 and AMY2A was expressed in both salivary glands and pancreas in the Catarrhini ancestor. The great ape–specific duplication of this ancestral gene likely facilitated subfunctionalization into salivary gland- and pancreas-specific expression, respectively. Comparative analysis of primate amylase promoter regions reveals regulatory rewiring, driven by motif turnover mediated by structural rearrangements, and partially explaining evolutionary shifts in expression. Together, our findings highlight how structural and regulatory modularity in complex genomic regions drives evolutionary innovation and molecular convergence, and we provide a genomic framework for dissecting these processes across diverse lineages.

Project description:Small apes (family Hylobatidae), encompassing gibbons and siamangs, occupy a pivotal evolutionary position within the hominoid lineage, bridging the gap between great apes and catarrhine monkeys. Although they possess distinctive genomic and phenotypic features—such as rapid chromosomal rearrangements and adaptations for brachiation—functional genomic studies on small apes have been hindered by the limited availability of biological samples and developmental models. Here, we address this gap by successfully reprogramming primary skin fibroblasts from three small ape species: lar gibbons (Hylobates lar), Abbott’s gray gibbons (Hylobates abbotti), and siamangs (Symphalangus syndactylus). Using Sendai virus-based stealth RNA vectors, we generated 31 reprogrammed cell lines, five of which were developed into transgene-free induced pluripotent stem cells (iPSCs). These iPSCs displayed canonical features of primed pluripotency, both morphologically and molecularly, consistent with other primate iPSCs. Directed differentiation experiments confirmed the capacity of small ape iPSCs to generate cells representing all three germ layers. Particularly, the successful differentiation into limb bud mesoderm cells underscores their utility in investigating the molecular and developmental mechanisms unique to small ape forelimb evolution. Transcriptomic profiling of small ape iPSCs revealed significant upregulation of pluripotency-associated genes, alongside elevated expression of transposable elements. Remarkably, LAVA retrotransposons—a class of elements specific to small apes—exhibited particularly high expression levels in these cells. Comparative transcriptomic analyses with iPSCs from humans, great apes, and macaques identified evolutionary trends and clade-specific gene expression signatures. These signatures highlighted processes linked to genomic stability and cell death, providing insights into small ape-specific adaptations. This study positions small ape iPSCs as a transformative tool for advancing functional genomics and evolutionary developmental biology. By facilitating detailed investigations into hominoid genome evolution and phenotypic diversification, this system bridges critical gaps in comparative research, enabling deeper exploration of the genetic and cellular underpinnings of small ape-specific traits.

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Convergent evolution through independent rearrangements in the primate amylase locus [Baboon]

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