Just posted: a group paper describing major updates to my software pixy, for population genetic summary statistics. www.biorxiv.org/content/10.6... New since 2021: arbitrary ploidy, multiallelic sites, missingness-aware Watterson's θ and Tajima's D, Hudson's FST, multicore execution!

Happy to share the final version of our study on the evolution of chromatin states across eukaryotes, out today in @natgenet.nature.com Led by @crisnava.bsky.social and @seanamontgomery.bsky.social www.nature.com/articles/s41... Some highlights below

Diversity and evolution of chromatin regulatory states across eukaryotes - Nature Genetics

This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...

nature.com

Why is the X chromosome rich in L1 mobile elements? @science.org X-chromosome inactivation draws L1 mutagenesis to the human X chromosome | Science www.science.org/doi/10.1126/...

X-chromosome inactivation draws L1 mutagenesis to the human X chromosome

X-chromosome inactivation (XCI) enables gene dosage compensation in XX eutherians. Long interspersed element-1 (LINE-1 or L1) retrotransposons are unusually abundant on the human X chromosome and are ...

science.org

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

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

📢 Genome Informatics 2026 (Hinxton UK + virtual, 2–4 Dec) is coming! Some confirmed speakers now listed: coursesandconferences.wellcomeconnectingscience.org/event/genome... Early-bird registration & bursary deadlines: 7 Sept. Abstract deadline: 5 Oct. Please submit your work & join us!

Beyond providing insight into the centromere paradox, this work demonstrates that complete chromosome reconstruction is now possible from wild-caught flies, opening new opportunities for population, functional, and quantitative genomics in Drosophila. Preprint here: www.biorxiv.org/content/10.6...

A conserved architectural domain shapes centromere evolution in Drosophila

Centromeres ensure faithful chromosome segregation despite being embedded within rapidly evolving repetitive DNA, a contradiction known as the centromere paradox. While centromere identity is defined ...

biorxiv.org

CRISPR-mediated centromere fission generates neochromosomes with distorted meiotic inheritance in Arabidopsis biorxiv.org/content/10.6... new preprint from us - includes changing the Arabidopsis karyotype from 5 -> 6 chromosomes using Cas9 & outcomes of 5/6 chromosome hybrid meiosis

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

How do transposons jump when they’re released from host control? I babysat two chromosomes for 2 years, making sure they are ok without most piRNAs. Here’s what we found & excited to share my 1st postdoc paper: “piRNA loss unleashes episodic transposition bursts” www.biorxiv.org/content/10.6...

piRNA loss unleashes episodic transposition bursts

In Metazoa, transposon expression is suppressed by the piRNA pathway, and disruption of this pathway leads to rampant transposon expression. However, it remains unclear whether increased transposon ex...

biorxiv.org

bioRxivpreprint@biorxivpreprint.bsky.social · last mo.

Replication fork directionality reveals how structural variants arise under replication stress https://www.biorxiv.org/content/10.64898/2026.06.29.735381v1

Super excited to share new work with my advisor @nanditagarud.bsky.social! We re-examine the rapidity of adaptation in the human gut microbiome and begin to characterize the adaptive architecture of selective sweeps spreading across human guts. www.biorxiv.org/content/10... 1/n:

Complex adaptive architectures constrain the pace of adaptations sweeping across human gut microbiomes

Recent work has shown that commensal gut bacteria can evolve rapidly within hosts on short timescales of days to months, fueled by the enormous mutational input generated daily in the microbiome. Yet ...

biorxiv.org

Starting as I mean to go on at #SMBE2026: DROSOPHILA!!!!

Congratulations to Prof Richard Durbin, winner of the 2026 Genetics Society Medal! His pioneering work in computational genomics has transformed how we analyse and understand genome sequences.

Our previously preprinted study "Influence of cis-regulatory elements on expression divergence in human segmental duplications" is now published in @genomeresearch.bsky.social! Please check it out: genome.cshlp.org/content/earl...

Megan Dennis@mydennis.bsky.social · 10mo ago

Happy to share work spearheaded by former grad student Colin Shew testing shared duplicated cis regulatory elements (CREs) using an MPRA. While we find some high effect CREs, collectively paralog differences represent modest effects accounting for observed gene expression divergence.

Our late Neandertal paper is officially out! 💀❤️🧬 www.nature.com/articles/s41... It was years in the making, a tremendous feat spearheaded by our PhD student Alba Bossoms Mesa and co-led by @janetk.bsky.social and @benmpeter.bsky.social

Excited to share our new preprint, "Inference of elevated mutation rates and variant effects using 700k exomes"! - www.biorxiv.org/content/10.6... Using gnomAD v4, we estimate per-variant missense selection coefficients, and find loss-of-function (LoF) mutations with enhanced mutation rates.

Inference of elevated mutation rates and variant effects using 700k exomes

Genomic sequencing is now widely accessible for genetic diagnostics and is emerging as a component of newborn screening. This technological development generates the need to characterize incoming muta...

biorxiv.org

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!

Excited to see @jonj-udd.bsky.social's fantastic work out @genetics-gsa.bsky.social. Selection in _heterozygotes_ is the primary force shaping allele frequencies of loss-of-function mutations in humans, even in genes only associated with purely recessive diseases. 🧪🧬 doi.org/10.1093/gene...

Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes

Abstract. The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model pred

doi.org

A few snippets from "Talk Nerdy to Me" last night! Thank you to everyone who showed up, asked questions and supported our speakers!

Charikleia Karageorgiou (Clio)@evobioclio.bsky.social · 2mo ago

Are you in Buffalo and interested in science outreach? Join us for the next Talk Nerdy to Me on June 18th! Please RSVP here: forms.gle/f1nidZLh76qy... If you're a postdoc in Buffalo and would like to present at a future Talk Nerdy to Me event, send me a DM and I'll share the speaker interest form!

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

Joint dog and wolf genealogies reveal the evolution of the canine genome https://www.biorxiv.org/content/10.64898/2026.06.18.729863v1

Transposable elements underlie chromosomal fusions and fissions in a highly species-rich group of butterflies https://www.biorxiv.org/content/10.64898/2026.06.15.732387v1

Great resource for comparative genomics: A Curated Genome-Scale Nucleotide Diversity Panel of Non-Human Primates 🧪🧬 www.biorxiv.org/content/10.6...

A Curated Genome-Scale Nucleotide Diversity Panel of Non-Human Primates

Background: Primates constitute one of the most phylogenetically and ecologically diverse Eutherian mammalian orders, with a central role in advancing our knowledge of human evolution, speciation proc...

biorxiv.org

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

1/n Check out our new paper, spearheaded by @fborne.bsky.social, just out in PLoS Genetics doi.org/10.1371/jour....

Epistasis among clustered lineage-specific amino acid substitutions in the Drosophila Trio protein

Author summary Proteins fold into three-dimensional structures that are essential for their function. Because these structures depend on interactions among amino acids, the fitness effect of a mutatio...

doi.org

Very excited to finally have this out in the world! The first paper from my PhD (and my first first-author publication) makes the case for a new entrant to the world of long-lived animal models: Heliconius butterflies. Out now in @natcomms.nature.com www.nature.com/articles/s41... (1/10)

Evolution of increased longevity and slowed ageing in a genus of tropical butterfly - Nature Communications

Studying long-lived species across the animal kingdom could provide insights into healthy ageing in humans. This study reveals long lifespans and slowed ageing in Heliconius butterflies, identifying t...

nature.com

How did complex cells emerge? In this groundbreaking paper, @tonigabaldon.bsky.social & co show that eukaryotes arose through multiple waves of ancient genetic exchange involving diverse bacteria (& giant viruses!) revealing a far more complex origin than we imagined. www.nature.com/articles/s41...

Very excited to share our new review on the complexity of SMA genetics, now online @cp-trendsgenetics.bsky.social! General interest in complex genetics? Want to know more about long-read sequencing? Segmental duplications? ✅✅✅ Have a look! www.cell.com/trends/genet...

The SMN locus in the T2T era: Structure, gene conversion, and clinical implications

Long-read sequencing, paralog-aware variant calling, and telomere-to-telomere (T2T) human genome assemblies now enable the resolution of copy-, haplotype-, and nucleotide-level complexities in segment...

cell.com