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NSF Research News features Aqil and Gokcumen's study of genetic variation in balancing selection

Genetic study of modern humans, Neanderthals and Denisovans points to the importance of balancing selection in evolution

Published March 21, 2023

The NSF News features a story about the research of Alber Aqil, PhD candidate,  and Professor Omer Gokcumen. Their study investigates a key question in biology: why genomic variation persists in a population for extended periods. According to Rebecca Ferrell, NSF Biological Anthropology program director, "the project demonstrates the value of an expanding genomic toolkit for studying human evolution, revealing new details about the complex variation and relationships among hominins." Visit NSF News.

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Faculty Profile

  • Omer Gokcumen

    PhD

    Omer Gokcumen.

    Omer Gokcumen

    PhD

    Omer Gokcumen

    PhD

    Professor
    Distinguished Postdoc Mentor Award, 2019
    Department of Biological Sciences
    College of Arts and Sciences

    Research Interests

    Human and primate evolution, ancient humans (including Neanderthals and Denisovans), anthropological genomics

    Education

    • PhD, University of Pennsylvania
    • Postdoctoral Research, Harvard Medical School

    Research Statement

    Omer Gokcumen is an expert in evolutionary anthropology — the study of how humans evolved and how they differ from non-human primates such as gorillas and chimpanzees. His work is tied to human evolution, including evolutionary adaptation and the evolutionary processes that lead to genetic disease.

    Gokcumen’s research examines the role that genomic variants, especially deletions and duplications, play in human disease and biology. His laboratory investigates the evolutionary history of genetic variations tied to interesting traits and diseases in modern and ancient human populations.

    Selected Publications

    • Veilleux, C.C., Garrett, E.C., Pajic, P.*, Saitou, M.*, Ochieng, J., Dagsaan, L.D., Dominy, N.J., Perry, G.H., Gokcumen, O.*,  Melin, A.D. (2023). Veillex Human subsistence and signatures of selection on chemosensory genes. Communications Biology. 6: 683. [co-Corresponding Author].
    • Lu, D., Parisi, L.R., Gokcumen, O.*, Attila-Gokcumen, E.A. SREBP activation contributes to fatty acid accumulations in necroptosis. (2023). RSC Chem Biol. 4: 310–322.
    • Aqil, A*, Gill, S., Gokcumen, O.*, Malhi, R.S., Reese, E.A., Smith J.L., Heaton, T.T., Lindqvist, C. A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska (2023). iScience. 26, 106581
    • Sun, Y.H., Cui, H., Song, Chi., Shen, J.T., Zhuo, X., Wang, R.H., Yu, X., Ndamba, R., Mu, Q., Gu, H., Wang, D., Murthy, G.G., Li, P., Liang, F., Liu, L., Tao, Q., Wang, Y., Orlowski, S., Xu, Q., Zhou, H., Jagne, J., Gokcumen, O.*, Anthony, N., Zhao, X., Li, X.Z.. Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity. (2023). Nature Communications. 14:812. 
    • Dos Santos, A.L.C.*, Sullasi, H.S.L., Gokcumen, O.*, Lindo, J., DeGiorgio, M. Spatiotemporal fluctuations of population structure in the Americas revealed by a meta-analysis of the first decade of archaeogenomes (2022). American Journal of Biological Anthropology. 180: 703-714.
    • A Aqil, L Speidel, P Pavlidis, O Gokcumen (2023) Balancing selection on genomic deletion polymorphisms in human. Elife. 12, e79111.
    • Nikkanen, J., Leong, W.A., Krause, W.C., Dermadi, D., Maschek, J.A., Van Ry, T., Cox, J.E., Weiss, E.J., Gokcumen, O.*, Chawla, A., Ingraham, H.A. (2022). Trade-Offs Between Hepatic Host Defense and Metabolic Programs Underlie Sex-Biased Diseases. Science. 378: 290-295.
    • Dos Santos, A.L.C., Owings, A., Sullasi, H.S.L., Gokcumen, O.*, DeGiorgio, M., Lindo, J. Genomic evidence of ancient migrations along South America's Atlantic coast. (2022). Proceedings of the Royal Society B. 289: 20221078.
    • Pajic, P.*, Shen, S., Qu, J., May, A.J., Knox, S., Ruhl, S., Gokcumen, O.* (2022) A mechanism of gene evolution generating mucin function. Science Advances. 8: 34. [Corresponding author].
    • Saitou, M.*, Masuda, N., Gokcumen, O.* (2022). Similarity-based analysis of allele frequency distribution among multiple populations identifies adaptive genomic structural variants. Molecular Biology and Evolution. 39: msab313. [Corresponding Author]. 
    • Saitou, M.*, Resendez, S.*, Pradhan, A.J., Wu, F., Lie, N.C., Hall, N.J., Zhu, Q.,  Reinholdt, L. Satta, Y., Speidel, L., Nakagome, S., Hanchard, N. A., Churchill, G., Lee, C., Atilla-Gokcumen,  G. E., Mu, X., Gokcumen, O.* (2021). Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor. Sci Adv. 7, eabi4476. [Corresponding Author].
    • Starr, I.*, Seiffert-Sinha, K, Sinha, A.A., Gokcumen, O.* (2021). Evolutionary Context of Psoriatic Immune Skin Response. Evolution, Medicine and Public Health. 9: 474-486 [Corresponding Author].  
    • Pliss, A., Kuzmin, A.N., Lita, A., Kumar, R., Celiku, O., Atilla-Gokcumen G.E., Gokcumen, O.*, Chandra, D., Larion, M., Prasad, P.N. (2021). Single Organelle Optical Omics Platform for Cell Science and Biomarker Discovery. Analytical Chemistry. 93:8281.
    • Pradhani et al. (2021). Protein acylation by saturated very long chain fatty acids and endocytosis are involved in necroptosis. Cell Chemical Biology. (In Press)
    • Xu, D., Gokcumen, O*., Khurana, E. (2020). Loss-of-function tolerance of enhancers in the human genome. PLoS Genetics. 6:e1008663.
    • Eaaswarkhanth, E., dos Santos, A.L.*, Gokcumen, O.*, Al-Mulla, F., Thanaraj, T.A. (2020). Genome-Wide Selection Scan in an Arabian Peninsula Population Identifies a TNKS Haplotype Linked to Metabolic Traits and Hypertension. Genome Biology and Evolution, 12:  77–87 [Highlighted in Human Genetics].
    • Gokcumen, O. (2020) Archaic hominin introgression into modern human genomes. Yearbook of Physical Anthropology. 171: 60.
    • Saitou, M.* & Gokcumen, O. (2020). An Evolutionary Perspective on the Impact of Genomic Copy Number Variation on Human Health. Journal of Molecular Evolution. 88: 104.
    • Thamadilok, S., Choi, K.-S., Ruhl, L., Schulte, F., Kazim, A. L., Hardt, M., Gokcumen, O*., Ruhl, S. (2020).Human and Non-Human Primate Lineage-Specific Footprints in the Salivary Proteome. Molecular Biology and Evolution. 37:39-405.
    • O Gokcumen, M Frachetti. The Impact of Ancient Genome Studies in Archaeology.  Annual Review of Anthropology. (2020) 49:277–98
    • Saitou, M*., Gaylord, E., Xu, D.,Neznanova, L., Nathan, S., Grawe, A., Chang, J., Ryan, William., Ruhl, S., Knox, S.M., and Gokcumen, O*.  (2020). Functional Specialization of Human Salivary Glands and Origins of Proteins Intrinsic to Human Saliva. Cell Reports. 33, 108402. [Corresponding Author].
    • Ozgur Taskent, Yen Lung Lin, Ioannis Patramanis, Pavlos Pavlidis and Omer Gokcumen, 2020. Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage. https://doi.org/10.1534/genetics.120.303167
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    • Pradhani et al. (2021). Protein acylation by saturated very long chain fatty acids and endocytosis are involved in necroptosis. Cell Chemical Biology. (In Press)
    • Xu, D., Gokcumen, O*., Khurana, E. (2020). Loss-of-function tolerance of enhancers in the human genome. PLoS Genetics. 6:e1008663.
    • Eaaswarkhanth, E., dos Santos, A.L.*, Gokcumen, O.*, Al-Mulla, F., Thanaraj, T.A. (2020). Genome-Wide Selection Scan in an Arabian Peninsula Population Identifies a TNKS Haplotype Linked to Metabolic Traits and Hypertension. Genome Biology and Evolution, 12:  77–87 [Highlighted in Human Genetics].
    • Gokcumen, O. (2020) Archaic hominin introgression into modern human genomes. Yearbook of Physical Anthropology. 171: 60.
    • Saitou, M.* & Gokcumen, O. (2020). An Evolutionary Perspective on the Impact of Genomic Copy Number Variation on Human Health. Journal of Molecular Evolution. 88: 104.
    • Thamadilok, S., Choi, K.-S., Ruhl, L., Schulte, F., Kazim, A. L., Hardt, M., Gokcumen, O*., Ruhl, S. (2020).Human and Non-Human Primate Lineage-Specific Footprints in the Salivary Proteome. Molecular Biology and Evolution. 37:39-405.
    • O Gokcumen, M Frachetti. The Impact of Ancient Genome Studies in Archaeology.  Annual Review of Anthropology. (2020) 49:277–98
    • Saitou, M*., Gaylord, E., Xu, D.,Neznanova, L., Nathan, S., Grawe, A., Chang, J., Ryan, William., Ruhl, S., Knox, S.M., and Gokcumen, O*.  (2020). Functional Specialization of Human Salivary Glands and Origins of Proteins Intrinsic to Human Saliva. Cell Reports. 33, 108402. [Corresponding Author].
    • Ozgur Taskent, Yen Lung Lin, Ioannis Patramanis, Pavlos Pavlidis and Omer Gokcumen, 2020. Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage. https://doi.org/10.1534/genetics.120.303167
    • Saito, M., Gokcumen, O. (2019). Resolving the insertion sites of polymorphic duplications reveals a HERC2 haplotype under selection. Genome Biology and Evolution. evz107  [Corresponding Author].
    • Pajic, P., Pavlidis, P., Dean, K., Neznanova, L., Daugherity, E., Romano R-A., Garneau, D., Globig, A., Ruhl, S., Gokcumen, O. (2019). Independent amylase gene copy number bursts correlate with dietary preferences in mammals. eLife. 8:e44628 [Corresponding Author].
    • Chow J, Starr I*, Jamalzadeh S, Muniz O, Kumar A, Gokcumen, O.*, Ferkey DM, Cullen PJ. 2019. Filamentation Regulatory Pathways Control Adhesion-Dependent Surface Responses in Yeast. Genetics [Internet]:genetics.302004.2019. Available from: http://dx.doi.org/10.1534/genetics.119.302004
    • Lin, Y.-L.*, & Gokcumen, O.* (2019). Fine-Scale Characterization of Genomic Structural Variation in the Human Genome Reveals Adaptive and Biomedically Relevant Hotspots. Genome Biology and Evolution, 11(4), 1136–1151.  [Corresponding Author].Lin, Y-L., Gokcumen, O. (2018). Fine-scale characterization of genomic structural variation in the human genome reveals adaptive and biomedically relevant hotspots. BioRxiv [preprint]. April 4, 2018. Available here.
    • Pajic, P., Pavlidis, P., Dean, K., Neznanova, L., Daugherity, E., Romano R-A., Garneau, D., Globig, A., Ruhl, S., Gokcumen, O. (2018). Amylase copy number analysis in several mammalian lineages reveals convergent adaptive bursts shaped by diet. BioRxiv [preprint]. June 5, 2018. Available here.
    • Saito, M.*, Satta, Y., Gokcumen, O.* (2018). Complex haplotypes of GSTM1 gene deletions harbor signatures of a selective sweep in East Asian populations. G3. 8:2953.
    • Saito, M*. Lizardo, D., Taskent, R. O.*, Millner, A., Gokcumen, O., Atilla-Gokcumen, G. (2018). An evolutionary transcriptomics approach links CD36 to membrane remodeling in replicative senescence. Mol Omics 14, 237 (a journal of Royal Society of Chemistry). [Cover article, co-Corresponding Author]. 
    • Saito, M.*, Satta, Y., Gokcumen, O.*, Ishida, T. (2018). Complex evolution of the GSTM gene family involves sharing of GSTM1 deletion polymorphism in humans and chimpanzees. BMC Genomics. 19:293. [co-Corresponding Author, IF:4.3]. 
    • Quillen, E., Norton, H., Parra, E., Lona-Durazo, F., Ang, K., I, Florin M., Pearson, L., Shriver, M., Lasisi, T., Gokcumen, O., Starr, I*., Lin, YL*., Martin, A., Jablonski, N. (2018). Shades of complexity: New perspectives on the evolution and genetic architecture of human skin. Yearbook of Physical Anthropology. (Early View).
    • Gokcumen, O. (2018). The Year in Genetics Anthropology: New Lands, New Technologies, New Questions. American Anthropologist. 120:266. [Also highlighted in the special virtual issue: “Genetics, Biology, and Race: Understanding Human Difference”].
    • Resendez, S.D.*, Bradley, J.*, Xu, D.*, Gokcumen, O.* (2018). Structural variants in ancient genomes. In: Rajora and Lindqvist, eds. Paleogenomics. Springer Population Genomics Series.
    • Schmidt, C. and Gokcumen, O.* (In press). Primate Genomics and Phylogenetics. In: O’Rourke, eds. A Companion to Anthropological Genetics. Wiley Press
    • Taskent et al. (2017). Variation and functional impact of Neanderthal ancestry in Western Asia.  Genome Biology and Evolution.  evx216. For press release.
    • Xu et al. (2017). VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences. BMC Bioinformatics. 18:426.
    • Xu et al. (2017). Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variation. Mol Biol Evol. Press release from UB Press Office. A write-up in the Guardian is here. For further media coverage, please see its Altmetric page.
    • Taskent and Gokcumen (2017). The multiple histories of Western Asia: Perspectives from ancient, and modern genomes. PrePrint (before proofs). Hum. Bio.
    • Lizardo et al. (2017). Regulation of lipids is central to replicative senescence.  Molecular BioSystems. 13, 498-509 – This study was also recognized by the Royal Society of Chemistry as an article of particular interest.
    • Pajic et al. (2016). The psoriasis-associated deletion of late cornified envelope genes LCE3B and LCE3C has been maintained under balancing selection since Human Denisovan divergence. BMC Evolutionary Biology. 16,265.
    • Muthukrishnan et al. (2016). Atopic Dermatitis Susceptibility Variants In Filaggrin Hitchhike Hornerin Selective Sweep. Genome Biology and Evolution. 8, 3240 – For media coverage, please see its Altmetric page.
    • Xu et al. Recent Evolution of the salivary mucin MUC7. (2016). Scientific Reports. 6, 31791. Press release from UB Press Office. For further media coverage, please see its Altmetric page.
    • Lin et al. (2015). The evolution and functional impact of human deletion variants shared with archaic hominin genomes. Mol Biol Evol. Early Access. [Corresponding Author]. – Press release from UB Press Office. For further media coverage, please see its Altmetric page.  Here is also Omer’s Talk on this paper at EMPH @Tempe 2015.
    • Muthukrishan et al. (2014). Geographic Distribution And Adaptive Significance Of Genomic Structural Variants: An Anthropological Genetics Perspective. Hum Bio. 86(4):260-275. 2014. [Cover Article].