False positives abound in trans-eQTL discovery. The authors of @ajhgnews.bsky.social's latest article develop a method to identify the mapping artifacts that produce spurious results: https://www.cell.com/ajhg/abstract/S0002-9297(26)00270-3 #ASHG @gokcumenlab.bsky.social #HumanGenetics

Typeset version of new paper out in @genomebiolevol.bsky.social. Link: academic.oup.com/gbe/article/... We identified segmental duplications in genomes from 117 vertebrate species (thanks to @vertebrategenomes.bsky.social ). We describe the properties and evolution of segmental duplications.

Genomes From 117 Vertebrate Species Reveal Rapidly Evolving Segmental-Duplication Landscapes

Abstract. Segmental duplications are major drivers of evolutionary innovation; yet, their dynamics across vertebrates remain poorly understood. Here, we id

academic.oup.com

@alberaqil.bsky.social et al. identify segmental duplications from genomes of 117 vertebrates, finding that the genomic architecture underlying segmental duplications is highly dynamic, uniquely shaping each lineage's potential to adapt 🔗 doi.org/10.1093/gbe/evag043 #societyjournal #evolution

Genomes From 117 Vertebrate Species Reveal Rapidly Evolving Segmental-Duplication Landscapes

Abstract. Segmental duplications are major drivers of evolutionary innovation; yet, their dynamics across vertebrates remain poorly understood. Here, we id

doi.org

New paper with @rajivmccoy.bsky.social @ajhgnews.bsky.social. Bottom line: Polymorphic gene duplications absent in the reference genome can produce spurious trans-eQTLs, and we propose a method to identify these false positives. authors.elsevier.com/c/1nWChgeXHnOF

🧬 New from Aqil et al! 📄 Mismapping of sequencing reads from polymorphic duplications generates spurious trans-eQTLs

Mismapping of sequencing reads from polymorphic duplications generates spurious trans-eQTLs

Polymorphic gene duplications absent from the reference genome can generate spurious trans-eQTLs. Specifically, variants tagging the polymorphic duplicate may masquerade as trans-eQTLs regulating the ...

cell.com

Only 3 days left to submit an abstract for the Great Lakes Annual Meeting of Evolutionary Genomics! The abstract submission deadline is July 24; registration will remain open until August 10. GLAM will be held on August 15, at the University at Buffalo. The participation is capped at 100 people.

GLAM-Evogen 2026 Registration and Abstract Submission Portal

GLAM-Evogen will be held on August 15, 2026 at University at Buffalo, NY. We aim to bring together faculty and trainees from a range of backgrounds with a particular focus on work at the interface bet...

forms.gle

Come to my talk today at 2:30 PM in the Expression/Transcriptomics session #Evol2026 I’ll talk about how gene duplication and regulatory architecture drive the evolution of new traits in salivary glands, and hopefully convince you that this is a cool system for studying the evol of gene expression!

We are excited to announce that the 2026 Great Lakes Annual Meeting of Evolutionary Genomics (GLAM-EvoGen) will take place on Saturday, August 15, 2026 at the University at Buffalo. More information is available on our website: gokcumenlab.org/glam2026/ @gokcumenlab.bsky.social

T2T assemblies for nearly all major Y chromosome haplogroups courtesy of a collab between @humanpangenome.bsky.social and HGSVC! What was once the hardest human chromosome to finish can now be routinely assembled thanks to ONT + Verkko www.biorxiv.org/content/10.6...

Our paper on recurrent independent duplications in the primate amylase locus is now out in Cell Reports! Huge thanks to @petarpajic, @spit-lab.bsky.social and @gokcumenlab.bsky.social for their support. More about the work in the thread below from when we first shared the preprint last August.

Convergent evolution through independent rearrangements in the primate amylase locus

Structurally complex loci can repeatedly generate similar traits; Karageorgiou et al. established primate amylase locus as a structural variation hotspot, potentially seeded by transposable elements. ...

cell.com

1/ New paper out in Nature Communications! We studied the salivary amylase gene, AMY1, in Indigenous Andean populations and found evidence that high AMY1 copy number rapidly increased in frequency, likely through recent positive selection. doi.org/10.1038/s414...

Rapid adaptive increase of amylase gene copy number in Indigenous Andeans - Nature Communications

The salivary amylase gene exhibits copy-number variation linked to dietary shifts. Here, the authors describe an adaptive expansion of the amylase gene in Indigenous Andean populations coinciding with...

doi.org

The special issue Functional and Adaptive Effects of Genomic Structural Variation is now out in Heredity. Many thanks to all contributors for their submissions, to the editorial team at @heredityjournal.bsky.social and to @ellenleffler.bsky.social, @mydennis.bsky.social & @gokcumenlab.bsky.social!

Special Issue: Functional and Adaptive Effects of Genomic Structural Variation

See more information on the new Heredity special issue on functional and adaptive effects of genomic structural variation.

nature.com

Nice surprise this morning! A Dispatch on our paper on paralog interference now out in Current Biology! By Krishna Swamy and Jun-Yi Leu. www.cell.com/current-biol...

Evolution: Paralog interference stabilizes gene duplicates

Gene duplicates are traditionally viewed as evolutionarily unstable, as one copy can freely accumulate deleterious mutations and be lost. A new study reveals that paralog interference exposes certain ...

cell.com

Gene Expansion and Regulatory Rewiring Shape Sex-Biased Evolution of the Mouse Submandibular Gland Secretome https://www.biorxiv.org/content/10.64898/2026.03.18.712472v1

Gene Expansion and Regulatory Rewiring Shape Sex-Biased Evolution of the Mouse Submandibular Gland Secretome https://www.biorxiv.org/content/10.64898/2026.03.18.712472v1

Pajic & @gokcumenlab.bsky.social synthesize the evolution of VNTRs in mammals, including mutational mechanisms and selective forces driving their evolution, and propose a theoretical framework for their persistence through evolutionary tradeoffs. 🔗 doi.org/10.1093/gbe/evaf250 #genome #evolution

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

Abstract. Understanding genomic function has historically relied on sequence conservation across evolutionary time. However, advances in genomics have reve

doi.org

New review from @gokcumenlab.bsky.social led by Petar Pajic on VNTRs. If you’re interested in VNTRs, this is a very nice synthesis. academic.oup.com/gbe/article/...

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

Abstract. Understanding genomic function has historically relied on sequence conservation across evolutionary time. However, advances in genomics have reve

academic.oup.com

academic.oup.com/gbe/article/... 🦷🦷 #TEETH 🥛🥛 #MILK 💧💧 #SALIVA❗️

Our preprint, "Read mismapping from segmental duplications drives spurious trans associations," is out! We argue that both RNA and DNA read mismapping can lead to false signals in QTLs, Hi-C, GWAS, and gene co-expression. And there is a way to identify them! Link: www.biorxiv.org/content/10.1...

Read mismapping from segmental duplications drives spurious trans associations

Heritable variation in gene regulation shapes both disease risk and evolution. Trans -acting quantitative trait loci ( trans -QTLs) are the primary source of this variation within species, yet they re...

biorxiv.org

What have 🦷🦷 #TEETH 🦷🦷, 🥛 #MILK 🥛, and💧💧 #SALIVA 💧💧to do with each other? Ask PetarPajic, Luane Landau, and Omer Gokcumen @gokcumenlab.bsky.social ❗️ academic.oup.com/gbe/article-...

Saliva Protein Genes in Humans were Shaped During Primate Evolution

Abstract. Genes within the secretory calcium-binding phosphoprotein locus diversified along with the formation of a calcified skeleton in vertebrates, the

academic.oup.com

Pajic, @gokcumenlab.bsky.social @spit-lab.bsky.social et al. explored the evolution of saliva-related SCPP genes, observing extensive diversification of SCPP genes within mammals, driven by gene duplications and losses. 🔗 doi.org/10.1093/gbe/evaf165 #genome #evolution #primates

New paper with @spit-lab.bsky.social @genomebiolevol.bsky.social - Bottom-line: genes that encode secreted saliva genes evolve pretty fast and gene duplications/deletions are mostly the culprit. academic.oup.com/gbe/advance-...

✨ 1 of the proudest achievements of the lab. the sex- and diet-dependent effects of an ancient deletion (>Neanderthal–human divergence) in the 3rd conserved exon of GHR (GHRd3). growth, resistance to hunger, and metabolism. www.science.org/doi/10.1126/... #BioRenderForGrants #ScienceAdvances

Such a great talk this morning on primate amylase evolution by @evobioclio.bsky.social #ESEB2025

Postdoctoral Research Associate sought for lipid biology and evolutionary genomics project. Ideal candidates in cell biology or bioinformatics; must be eager to learn interdisciplinary skills. Contact Dr. Ekin Atilla-Gokcumen: ekinatil@buffalo.edu. More info: https://atillalab.org/ #postdoc

Our latest preprint explores the evolution of the primate amylase locus, uncovering structural innovations, regulatory shifts and molecular convergence. www.biorxiv.org/content/10.1...

Convergent evolution through independent rearrangements in the primate amylase locus

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 ...

biorxiv.org

Very nice comparative study led @evobioclio.bsky.social from @gokcumenlab.bsky.social, using the the primate amylase locus to reveal how structural and regulatory modularity in complex genomic regions drives evolutionary innovation and molecular convergence 🧪🧬 www.biorxiv.org/content/10.1...

Convergent evolution through independent rearrangements in the primate amylase locus

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 ...

biorxiv.org

❗️❗️❗️👄👄 #MOUTH 👄👄 🦷🦷 #TEETH 🦷🦷 💧💧 #SALIVA 💧💧🦠🦠 #MICROBIOME🦠🦠 🍭🍭 #glycotime 🍭🍭 ❗️❗️❗️ ❗️We are hiring❗️Check out this full-time tenure track academic faculty position in the #UBSDM's Department of Oral Biology. ms.spr.ly/6045sKrT9

Assistant Professor/Associate Professor, Oral Biology

The University at Buffalo School of Dental Medicine (SDM) invites applications from qualified early- to mid-career oral health scientists and/or clinician-scientists for a full-time tenure track acade...

ubjobs.buffalo.edu

Check out our latest work co-led by @dcsoto.bsky.social and @jmuribescr.bsky.social identifying hundreds of human duplicated gene families using the new T2T-CHM13 assembly, with a focus on those potentially contributing to brain evolution 🧪: authors.elsevier.com/a/1lTQtL7PXu...

Outreach volunteers sought! @imprintedgene.bsky.social and I will host “Breaking Bread: Exploring the Evolution of Amylase in humans” at Festa Major de Gràcia, Barcelona (16 Aug, 19:00). We need 1-2 volunteers (ES/EN) for visitor guidance and on-site translation. Please DM or email me if interested.