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.

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

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!

Excited to talk about balancing selection, hybridization, and independent evolution at the #SMBE2025 hybridization & introgression symposium! Symposium 14: Day 3, Room 2 @ 11:30am Beijing Time

🚨Preprint🚨

Sex chromosome identification & genome curation from a single individual with SCINKD
www.biorxiv.org/content/10.1...

Incredible work led by @drpintothe2nd.bsky.social in collaboration w/ @drsimonegable.bsky.social @stuartvnielsen.bsky.social @tonygamble.bsky.social SE Keating & CH Smith

Please share with early career researchers interested in pursuing a PhD! Our goal is to make the application process more transparent with info sessions and 1:1 mentorship.

📣📣📣 So pleased to see @vdbijl.bsky.social's stunning analysis of the inheritance and genetics of guppy color diversity out today @natecoevo.nature.com! Deep learning reveals the complex genetic architecture of male guppy colouration. www.nature.com/articles/s41...

1/9 Excited to share the preprint for the second half of my PhD with @mollyschumer.bsky.social: Connecting human environmental impacts to hybridization in swordtail fish through genomics, GIS, water chemistry, and histology. Thread below!

#SciSky

www.biorxiv.org/content/10.1...

We’ve had success with this hybrid approach, but preliminarily >40x ONT UL alone also seems to get us near T2T. Genome is 720mb. Didn’t collect HiC for this individual and scaffolded to an existing reference

Black are gaps (contig breaks) and red are telomeres!

Already seeing big improvements by combining PacBio and ONT Ultralong reads!

Awesome new paper by @lucalivraghi.bsky.social et al.
doi.org/10.1016/j.cu...
in @currentbiology.bsky.social
on the evo-devo of a butterfly color variation

enjoy the show!

A project five years in the making, we've now published complete "T2T" genomes for six additional ape species! It turns out that finishing (and analyzing) six genomes is slightly more work than one... doi.org/10.1038/s415...

Call for Papers! Special Issue: Functional and Adaptive Effects of Genomic Structural Variation in @heredityjournal.bsky.social

📅 Submission Deadline Extended: 1st April 2025
Guest Editors: @ellenleffler.bsky.social, @mydennis.bsky.social, Omer Gokcumen, and myself
www.nature.com/collections/...

New NIH funded research from our group now out. We are interested in development and evolution of cell types and adult phenotypes. In this paper, postdoc Dylan Huang and collaborators asked how a pigmentary ornament of bright white cells develops on the fin of zebrafish. www.pnas.org/doi/10.1073/...

Finally ready to see the world! Theories of balancing selection - past, present and future: www.biorxiv.org/content/10.1... A true collaborative effort that brought together theoreticians and empiricists, models, data, and fresh perspectives on how balancing selection can shape genetic variation.

Rising temperatures are not slowing #mosquitoes down... A new study coauthored by Stanford's Lisa Couper and @stanfordwoods.bsky.social Erin Mordecai finds that mosquitoes -- and the diseases they carry -- can adapt to hotter temperatures. Read the study: bit.ly/3PqTNw8

Congrats to @jeffgroh.bsky.social et al on publication of "Ancient structural variants control sex-specific flowering time morphs in walnuts and hickories"

www.science.org/doi/10.1126/...

Moved here recently and figured I should shamelessly promote our recent paper for my very first post.