Petar Pajic

Publications

All publications

Petar Pajic Petar Pajic · Genome Biology and Evolution · Jan 1, 2026
Journal

Evolutionary Balancing of Genetic Consequence and Innovation in Mammals Through Variable Number Tandem Repeats

Understanding genomic function has historically relied on sequence conservation across evolutionary time. However, functional innovations often arise from rapidly evolving, nonconserved elements. Variable number tandem repeats (VNTRs) act as engines of both functional innovation and phenotypic consequence, influencing gene regulation, protein structure, and phenotypic diversity. This review synthesizes emerging insights into the functional and evolutionary impact of VNTRs in mammals, outlining the mutational mechanisms driving their evolution, the selective forces maintaining structural heterogeneity, and a theoretical framework for their persistence through evolutionary tradeoffs.

Evolutionary Balancing of Genetic Consequence and Innovation in Mammals Through Variable Number Tandem Repeats
Petar Pajic Petar Pajic · Genome Biology and Evolution · Aug 22, 2025
Journal

Saliva Protein Genes in Humans Were Shaped During Primate Evolution

The secretory calcium-binding phosphoprotein (SCPP) gene family, which includes genes expressed abundantly in human saliva, evolved alongside major evolutionary milestones in vertebrates. We explored the evolution of saliva-related SCPP genes using genomic and transcriptomic resources, finding previously undocumented convergent gene duplications in primate genomes. These saliva-related genes show signatures of positive selection while neighboring genes remain conserved, suggesting dietary and pathogenic pressures drove adaptive diversification of saliva composition in primates, including humans.

Petar Pajic Petar Pajic · Nucleic Acids Research, Vol. 53 · Mar 24, 2025
Journal

Tuning the Tropism and Infectivity of SARS-CoV-2 Virus-Like Particles for mRNA Delivery

SARS-CoV-2 virus-like particles (VLPs) are ~100-nm bioinspired mimetics of the authentic virus, engineered here as a platform for mRNA delivery. A three-plasmid VLP system displayed ~7-fold higher viral entry efficiency than four-plasmid co-transfection, transducing over 90% of human ACE2-expressing cells. Viral tropism could be reprogrammed by swapping glycoproteins from other viral strains, and VLPs carried up to four transgenes, including functional Cas9 mRNA for genome editing, with successful delivery to mouse lungs.

Petar Pajic Petar Pajic · Science · Oct 24, 2024
Journal

Reconstruction of the Human Amylase Locus Reveals Ancient Duplications Seeding Modern-Day Variation

Human adaptation to a wide range of diets is a hallmark of our species, sometimes even reflected in our genomic diversity. The amylase gene encodes an enzyme that digests starch, a complex carbohydrate found in many modern human diets. Genomic studies have found substantial variation in the number of amylase gene copies, believed to be an adaptive response to dietary changes among human populations after the advent of agriculture. We reconstruct the locus's evolutionary history, tracing duplications that predate agriculture and seeded modern structural variation.

Reconstruction of the Human Amylase Locus Reveals Ancient Duplications Seeding Modern-Day Variation
Petar Pajic Petar Pajic · bioRxiv · Nov 28, 2023
Preprint

Ancient AMY1 Gene Duplications Primed the Amylase Locus for Adaptive Evolution Upon the Onset of Agriculture

Starch digestion is a cornerstone of human nutrition, and the amylase enzyme plays a key role in starch metabolism. The copy number of the human amylase gene (AMY1) has been associated with metabolic diseases and adaptation to agricultural diets. We show that amylase gene duplications originated over 700,000 years ago, predating the human-Neanderthal divergence, and likely primed the locus for rapid dietary adaptation during the agricultural transition through nonallelic homologous recombination.

Petar Pajic Petar Pajic · Communications Biology · Jul 3, 2023
Journal

Human Subsistence and Signatures of Selection on Chemosensory Genes

Chemosensation (olfaction, taste) is essential for detecting and assessing foods, such that dietary shifts elicit evolutionary changes in vertebrate chemosensory genes. We explore the effects of subsistence behaviors on olfactory and taste receptor genes among rainforest foragers and neighboring agriculturalists in Africa and Southeast Asia, analyzing 378 functional OR and 26 functional TASR genes across 133 individuals. We find no evidence of relaxed selection in agricultural populations but identify subsistence-related signatures of local adaptation within each geographic region.

Petar Pajic Petar Pajic · Science Advances · Aug 26, 2022
Journal

A Mechanism of Gene Evolution Generating Mucin Function

How novel gene functions evolve is a fundamental question in biology. Mucin proteins, a functionally but not evolutionarily defined group of proteins, allow the study of convergent evolution of gene function. By analyzing the genomic variation of mucins across a wide range of mammalian genomes, we propose that exonic repeats and their copy number variation contribute substantially to the de novo evolution of new gene functions, identifying 15 undescribed instances of evolutionary convergence in mucin origin.

Petar Pajic Petar Pajic · Journal of Virology · Apr 16, 2020
Journal

Modified Sialic Acids on Mucus and Erythrocytes Inhibit Influenza A Virus Hemagglutinin and Neuraminidase Functions

Sialic acids (Sia) are the primary receptors for influenza viruses and are widely displayed on cell surfaces and in secreted mucus. Modifications of Sia in mucus may have potent effects on the functions of influenza A virus (IAV) hemagglutinin and neuraminidase, affecting both pathogens and the normal flora of different mucosal sites.

Petar Pajic Petar Pajic · eLife · May 14, 2019
Journal

Independent Amylase Gene Copy Number Bursts Correlate with Dietary Preferences in Mammals

The amylase gene (AMY), which codes for a starch-digesting enzyme, underwent several gene copy number gains in humans, dogs, and mice, possibly along with increased starch consumption during the evolution of these species. We present comprehensive evidence for AMY copy number expansions that independently occurred in several mammalian species which consume starch-rich diets, and provide correlative evidence that AMY duplications may be an essential first step for amylase to gain expression in saliva.

Petar Pajic Petar Pajic · BMC Ecology and Evolution · Dec 5, 2016
Journal

The Psoriasis-Associated Deletion of Late Cornified Envelope Genes LCE3B and LCE3C Has Been Maintained Under Balancing Selection Since Human-Denisovan Divergence

A common, 32kb deletion of LCE3B and LCE3C genes is strongly associated with psoriasis and is ancient, predating Human-Denisovan divergence. We show that the haplotype harboring the deletion retains high allele frequency among extant and ancient human populations, harbors unusually high nucleotide variation, and has an unusually long coalescence time, consistent with the LCE3BC deletion having evolved under balancing selection — possibly a tradeoff between autoimmunity and pathogen exposure.