NSF Research News

Genetics publishes paper by Taskent and Gokcumen on Haplotypic Variation & Deletion Polymorphisms

Genetics, published by the Genetics Society of America, contains a paper co-authored by UB alum Ozgur Taskent, a recent PhD graduate, and Omer Gokcumen,Associate Professor, Department of Biological Sciences. The work presents a comprehensive analysis of the unusually divergent haplotypes in the Eurasian genomes and showed that they can be traced back to multiple introgression events. Funded by the U.S. National Science Foundation, the research reinforces the concept that Neanderthal DNA has been woven into the modern human genome on multiple occasions as our ancestors met Neanderthals time and again in different parts of the world. Read the news article by Charlotte Hsu.

In 2019, Ozgur Taskent successfully defended his PhD thesis, "A Genetic Record of Admixture Between Humans and Ancient Hominins”, with Dr. Gokcumen serving as his advisor. 

GENETICS is a scholarly society that seeks to deepen our understanding of the living world by advancing our understanding of genetics. Since 1916, GENETICS has published original research presenting novel findings bearing on genetics and genomics. The journal publishes empirical studies of organisms ranging from microbes to humans, as well as theoretical work.

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Ozgur Taskent, PhD.

Ozgur Taskent, PhD

Omer Gokumen.

Omer Gokcumen, PhD

Research News

Modern humans, Neanderthals share a tangled genetic history, study affirms

DNA strand.

Results of a new story reinforce the concept that Neanderthal DNA has been woven into the modern human genome on multiple occasions as our ancestors met Neanderthals time and again in different parts of the world.

By CHARLOTTE HSU

Published April 3, 2020

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headshot of Omer Gokcumen.
“It’s not a single introgression of genetic material from Neanderthals. It’s just this spider web of interactions that happen over and over again, where different ancient hominins are interacting with each other, and our paper is adding to this picture. ”
Omer Gokcumen, associate professor
Department of Biological Sciences

In recent years, scientists have uncovered evidence that modern humans and Neanderthals share a tangled past. In the course of human history, these two species of hominins interbred not just once, but at multiple times, the thinking goes.

A new study supports this notion, finding that people in Eurasia today have genetic material linked to Neanderthals from the Altai mountains in modern-day Siberia. This is noteworthy because past research has shown that Neanderthals connected to a different, distant location — the Vindija Cave in modern-day Croatia — have also contributed DNA to modern-day Eurasian populations.

The results reinforce the concept that Neanderthal DNA has been woven into the modern human genome on multiple occasions as our ancestors met Neanderthals time and again in different parts of the world.

The study was published on March 31 in the journal Genetics.

“It’s not a single introgression of genetic material from Neanderthals,” says lead researcher Omer Gokcumen, a UB biologist. “It’s just this spider web of interactions that happen over and over again, where different ancient hominins are interacting with each other, and our paper is adding to this picture. This project will now add to an emerging chorus — we’ve been looking into this phenomenon for a couple of years, and there are a couple of papers that came out recently that deal with similar concepts.

“The picture in my mind now is we have all these archaic hominin populations in Europe, in Asia, in Siberia, in Africa,” Gokcumen says. “For one reason or another, the ancestors of modern humans in Africa start expanding in population, and as they expand their range, they meet with these other hominins and absorb their DNA, if you will. We probably met different Neanderthal populations at different times in our expansion into other parts of the globe.”

Gokcumen, associate professor of biological sciences, College of Arts and Sciences, led the study with first author Recep Ozgur Taskent, a recent UB PhD graduate in the department. Co-authors include UB PhD graduate Yen Lung Lin, now a postdoctoral scholar at the University of Chicago, and Ioannis Patramanis and Pavlos Pavlidis of the Foundation for Research and Technology in Greece.

The research was funded by the U.S. National Science Foundation.

To complete the project, scientists analyzed the DNA of hundreds of people of Eurasian ancestry. The goal was to hunt for fragments of genetic material that may have been inherited from Neanderthals.

This research found that the Eurasian populations studied could trace some genetic material back to two different Neanderthal lineages: one represented by a Neanderthal whose remains were discovered in the Vindija cave in Croatia, and another represented by a Neanderthal whose remains were discovered in the Altai mountains in Russia.

Scientists also discovered that the modern-day populations they studied also share genetic deletions — areas of DNA that are missing — with both the Vindija and Altai Neanderthal lineages.

The DNA of the Vindija and Altai Neanderthals, along with the modern human populations studied, were previously sequenced by different research teams.

“It seems like the story of human evolution is not so much like a tree with branches that just grow in different directions. It turns out that the branches have all these connections between them,” Gokcumen says. “We are figuring out these connections, which is really exciting. The story is not as neat as it was before. Every single ancient genome that is sequenced seems to create a completely new perspective in our understanding of human evolution, and every new genome that’s sequenced in the future may completely change the story again.”

Faculty Profile

Omer Gokcumen

PhD

Omer Gokcumen.

Omer Gokcumen

PhD

Omer Gokcumen

PhD

Professor
Meyerson Award for Undergraduate Mentoring, 2025
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
  • 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.* 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].
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