Avocados come in 2 varieties - A-types start each day female and switch to male midday. B-types do the reverse. In work just published from the last chapter of my PhD, we show this system evolved 40+million yrs ago and is regulated by alleles of 1 transcription factor www.pnas.org/doi/10.1073/...

Balanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado | PNAS

In avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...

pnas.org

1/ The world's songbirds sing in just 8 basic sounds. And where a bird lives decides which ones it uses. My first PhD paper is out now in @science.org (www.science.org/doi/10.1126/science.aee6239) Here is what we found:

Very excited to share our new manuscript by Arif Maulana @arf-mln.bsky.social on 338 beetle genomes. It shows how beetle genomes have evolved and how this compares to fly and Lepidoptera genome evolution. It was a great pleasure to collaborate with @kamilsjaron.bsky.social and his team on this.

KamilSJaron.bsky.social@kamilsjaron.bsky.social · 2w ago

New preprint: 338 coleopteran genomes reveal exceptional rearrangement variation compared to other insect orders. Big congrats to @arf-mln.bsky.social, for getting this giant piece together. Big collaboration of @joanameier.bsky.social's and my groups. 🧵👇 doi.org/10.64898/202...

🎨 job alert 🐠 Come join us! We have two positions open! These are part of our @erc.europa.eu funded project on the mechanisms underpinning convergence of colour patterns in cichlid fishes! Closing date: 16th August. Postdoc: www.cam.ac.uk/jobs/researc... Technician: www.cam.ac.uk/jobs/researc...

Callipterus Cichlid Collecting Shell

ALT: Callipterus Cichlid Collecting Shell

static.klipy.com

The evolution of structural variation across 500 million years of vertebrate evolution https://www.biorxiv.org/content/10.64898/2026.06.26.733778v1

Big thanks to @tododge.bsky.social and @mollyschumer.bsky.social for their invaluable mentorship!! I’ll also be presenting a poster on this work at PEQG this Thursday (8:30-10pm, PgmNr 284T)

Tris Dodge@tododge.bsky.social · 2mo ago

Excited to share new work on two sex-linked pigment traits in Xiphophorus! This project was led by undergrad @lagiven.bsky.social, who’s worked with me for the last 3(!) years. www.biorxiv.org/content/10.6...

Exciting new work from the lab led by @lagiven.bsky.social & co-advised by @tododge.bsky.social mapping pigmentation variation in the swordtail X. nezahualcoyotl! Spotting variation is linked to xmrk but embedded in complex genomic regions that Tris & Lyle tackled with UL nanopore: shorturl.at/Ljw1z

Two melanic pigment patterns are associated with a sex chromosome-linked oncogene in the mountain swordtail Xiphophorus nezahualcoyotl

Sex-linked traits are widespread, but their genetic architecture has been challenging to characterize, due in part to the repetitive and structurally complex nature of sex chromosomes. In swordtails a...

shorturl.at

Excited to share new work on two sex-linked pigment traits in Xiphophorus! This project was led by undergrad @lagiven.bsky.social, who’s worked with me for the last 3(!) years. www.biorxiv.org/content/10.6...

Two melanic pigment patterns are associated with a sex chromosome-linked oncogene in the mountain swordtail Xiphophorus nezahualcoyotl

Sex-linked traits are widespread, but their genetic architecture has been challenging to characterize, due in part to the repetitive and structurally complex nature of sex chromosomes. In swordtails a...

biorxiv.org

We are excited to share our pan-pangenome paper! This is a long time coming work of my postdoc with the incredible @psudmant.bsky.social, and a stellar group of people! I hope you enjoy reading it! And I am excited to talk more more about it this week at #PEQG26!! www.biorxiv.org/content/10.6...

A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos

Complete, haplotype-resolved genome assemblies have provided unprecedented insight into the evolution of structurally complex, rapidly evolving regions of human genomes; however, population-scale pang...

biorxiv.org

We are often asked whether pangenomes are worth the hassle. The files can be large and methods to explore them are much more challenging than linear references. Earlier this week, we preprinted a clear example of how and why pan-genome graphs are so important for trait discovery.

bioRxiv Genomics@biorxiv-genomic.bsky.social · 3mo ago

Dissecting the regulatory and genomic drivers of the dichogamy determining G-locus in pecan https://www.biorxiv.org/content/10.64898/2026.05.14.725045v1

Thrilled to present my dissertation research at the Hamilton Symposium! We used approaches including GWAS, long-read sequencing, phylogenetic methods, and behavior experiments to uncover the genetic basis and evolutionary history of a shared polymorphism. Can’t wait to share what we’ve learned!

Society for the Study of Evolution@sse-evolution.bsky.social · 3mo ago

Join us at virtual #Evol2026 this Friday to hear from the finalists for the SSE Hamilton Award for Outstanding Student Presentation! This symposium is in 3 sessions starting at 11 am Eastern.

Thrilled that our new review article on animal hybridization is now up on EcoEvoRxiv! 🎉 Working on this review with @mollyschumer.bsky.social was a blast, and it was such a wonderful opportunity to catch up on all the amazing work in animal hybridization over the last few years!

Molly Schumer@mollyschumer.bsky.social · 3mo ago

Excited to share this new pre-print from the fantastic @kelsiehunnicutt.bsky.social! Kelsie put together a thoughtful and thorough review on hybridization in animal evolution: ecoevorxiv.org/repository/v.... She tracks notable shifts in perspectives on the study of hybridization through time.

Ver excited to share my just-published Darwin Review with @lh3lh3.bsky.social on population-scale long-read sequencing! royalsocietypublishing.org/rspb/article...

Population-scale long-read DNA sequencing: peering under the hood of the new evolutionary genomics

Abstract. Population-scale long-read DNA sequencing (PLRS) is rapidly reshaping our understanding of genomic variation in humans and non-model species. In

royalsocietypublishing.org

Happy to announce the alpha release of the SCINKD3! SCINKD3 is an extension of SCINKD streamlines the use of WGS data from multiple individuals to identify sex chromosomes. In testing, its shown to be robust in many cases with as few as 4 individuals. github.com/DrPintoThe2n...

GitHub - DrPintoThe2nd/SCINKD3: development repo of SCINKD (v3)

development repo of SCINKD (v3). Contribute to DrPintoThe2nd/SCINKD3 development by creating an account on GitHub.

github.com

Long reads carry multiple small vars and SVs and their phasing. LongcallD is the only caller that tightly integrates germline/mosaic small/structural vars/MEIs and their phasing in a single C program. One command line to get competitive small variant calls and better SVs. Led by Yan Gao.

bioRxiv Genomics@biorxiv-genomic.bsky.social · 5mo ago

LongcallD: joint calling and phasing of small, structural and mosaic variants from long reads https://www.biorxiv.org/content/10.64898/2026.03.20.713111v1

Excited so share our newest study using a single-library HiFi-CiFi approach to generate chromosome-scale diploid assemblies of two vole genomes, identifying putative drivers of divergent pair-bonding behavior, namely a prairie-vole-specific duplication of Avpr1a gene, led by @mabuelanin.bsky.social

bioRxiv Genomics@biorxiv-genomic.bsky.social · 5mo ago

Single-library chromosome-scale diploid assemblies of vole genomes resolve a species-specific duplication implicated in pair bonding https://www.biorxiv.org/content/10.64898/2026.03.13.711624v1

Proud that this work is now published! We hope it helps orient future #Nanopore long-read sequencing studies hunting for structural variants Also really happy to share eight new high-coverage (>100x) long-read read pools and assemblies with the #Drosophila community! doi.org/10.1093/g3jo...

Manual validation finds ultra-long-read sequencing best enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin with nanopore

Abstract. The increasing accessibility of long-read sequencing and the rapid development of automated variant callers are promoting the generation of popul

doi.org

James Hemker@jahemker.bsky.social · last yr.

Excited to share the first manuscript from my PhD in which we leveraged ultra-long Nanopore sequencing, D. melanogaster inbred lines, and a ton of manual validation to investigate the effects of long-read length on population-level structural variant (SV) calling accuracy! doi.org/10.1101/2025...

I am hiring a staff bioinformatician for my new lab at the University of Utah! Please consider applying if you are on the hunt: employment.utah.edu/salt-lake-ci...

Excited to join PAG this year! Tomorrow (01/11) I will be sharing my work on black-footed cat genomics! Stop by the "Wildlife Genomics" session @ 8:55 am in Pacific F-G to learn about Africa's smallest cat

I'll be presenting my work tomorrow morning at #PAG33! Stop by Pacific C (Comparative Genomics - Animals) @9:16am to learn about structural variation of swordtail Y-chromosomes and alternative reproductive tactics.

Excited to present at #PAG33 on the dynamic evolution of a balanced polymorphism. We've uncovered unexpected patterns using long-read sequencing and other fun methods. Talk: Saturday @8:40am in Pacific C (Comparative Genomics - Animals) Poster: Monday @10-11:30am in Golden State Ballroom (P216)

Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...

Modestly, we decided to review a century's worth of theories of balancing selection :) onlinelibrary.wiley.com/doi/10.1111/...

A century of theories of balancing selection

Traits that affect organismal fitness are often highly genetically variable. This genetic variation is vital for populations to adapt to their environments, but it is also surprising given that natur...

onlinelibrary.wiley.com

Beautiful work by @nadiahaghani.bsky.social and @mollyschumer.bsky.social on perhaps the most charismatic coloration trait in swordtails and platys!

Molly Schumer@mollyschumer.bsky.social · 9mo ago

I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A

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.

bioRxiv Genomics@biorxiv-genomic.bsky.social · 10mo ago

Influence of cis-regulatory elements on regulatory divergence in human segmental duplications https://www.biorxiv.org/content/10.1101/2025.10.03.680410v1

Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin

First pop gen paper from our lab! We find repeated evolutionary turn over of sex chromosomes in darters contributes to reproductive isolation. Turnover may be an escape hatch to resolve mitonuclear conflict & neo sex chromosomes evolved via a rare recessive mutation. www.biorxiv.org/content/10.1...

The Sudmant lab at UC Berkeley is seeking a postdoc to work on a fully funded NIH project to understand differences in DNA repair and somatic mutation across the primate tree of life. Please spread widely to those who may be interested aprecruit.berkeley.edu/JPF05052

Postdoctoral Scholar – Genomics, Aging, Somatic Mutation, Structural Variation, Evolution , Cancer – Integrative Biology

University of California, Berkeley is hiring. Apply now!

aprecruit.berkeley.edu

If you're attending #SMBE2025 check out graduate student @tododge.bsky.social 's talk at 11:30 am tomorrow (8:30 pacific time tonight if you're watching remotely). It's a wild ride with lots of complex structural variation, balancing selection, and introgression!