Li Zhao

De novo genes arise from previously non-coding sequences. This evolutionary path — when randomly expressed sequences become folded and active proteins — challenges our understanding of genetic innovation. New Review by @bornberglab.bsky.social and @lacholt.bsky.social out now!

For me, this is a neat example of evolution's flexibility: similar ecological traits can evolve through distinct genetic mechanisms yet converge on the same physiology, even in closely related species.

We recreated this CO₂ sensitivity in D. melanogaster by generating transgenic lines that swap regulatory or protein-coding sequences from D. suzukii and D. subpulchrella and found that enhancers and proteins in each species play different roles in this convergent trait.

Interestingly, D. suzukii and D. subpulchrella showed stronger firing, but behaviorally, they showed indifference to CO2, suggesting another layer of central brain innovation.

What’s wild: D. suzukii and its sister species show an early burst of neural firing when they smell CO₂, a timing feature missing in D. melanogaster. Same cue, different neural code.

Molecular evolution of CO2-sensing ab1C neurons underlies divergent sensory responses in the Drosophila suzukii species group Author summary Animals rely on their senses to locate food sources and identify suitable reproductive sites in their environment. Closely related species can evolve strikingly different preferences as...

Very excited to share the work by Alice Gadau. We found that D. suzukii (the invasive pest that loves ripe fruit) doesn’t hate CO₂, while classic lab flies avoid it. That tiny sensory shift helps explain a big ecological transition.
journals.plos.org/plosgenetics...

Registration for the 2026 NY Area Population Genetics meeting is now open, at events.simonsfoundation.org/e0mEoL?rt=8k.... Registration is free but required; if you are submitting an abstract, note that the deadline is *January 30th*.

Dear Mark, Only three days left to nominate for the Larry Sandler Award! The award recognizes excellent recent graduates who have completed a PhD in Drosophila research. The awardee will receive a fantastic opportunity to present the Larry Sandler Memorial Lecture at the 67th Annual Drosophila Research Conference in Chicago, IL! The deadline to nominate is Monday, December 15, 2025. Nominate Here For more information visit the website.

Fly Friends: The Larry Sandler Award recognizes the PhD student with the most amazing these using Drosophila as a model. Just three days left to nominate someone. For more info on the process and the link to nominations, see:
genetics-gsa.org/drosophila-2...

Please help spread the words @cedricfeschotte.bsky.social @anthonygeneva.bsky.social @danielbolnick.bsky.social @levine-lab.bsky.social @itaiyanai.bsky.social @lucksmith.bsky.social

Our NY area population genetics meeting is back and "upgraded", as Simons Foundation @simonsfoundation.org generously agreed to host. Please save the date: March 9, 2026. Look forward to seeing many of you from NY and beyond.

Wow. You truly transformed the house into a great one. How did you mange to have a garden and make sure deers don't eat everything?

A. James Hudspeth, neuroscientist who unlocked secrets of hearing, has died - News A. James Hudspeth, a Rockefeller neuroscientist who discovered how sound waves are converted into electrical signals in the ear's cochlea, died Saturday at his home in Manhattan. A pioneering scientist and dedicated mentor, he was the university's F.M. ...

We are deeply saddened to share that our friend and colleague Jim Hudspeth passed away on Saturday. We will remember and continue to be inspired by Jim’s integrity, his humility, and his unwavering commitment to discovery.

I am delighted to be starting as an assistant professor in the Department of Molecular Genetics & Microbiology at the University of Florida in January 2026. The lab is broadly interested in the functional, developmental, and evolutionary genetics of cell types and organs across flies and beyond 🪰🧬

as one would wonder if it's the tMAC effect or Achi/Vis effect. For the transgenic+RNAseq analysis we see 5 genes (aly, come, tomb, p55 and wuc) showed positive exp. correlations with vis expression, whereas topi and mip40 did not. The 5 genes may play a partial role although we are not sure yet.

Thanks for the kind words, Jongmin. This work was the work I briefly mentioned in the Q&A (but not the talk) related to your question in my seminar visit at Cornell last fall. We checked the tMAC complex and the pattern observed by large-scale computation is specific to Achi/Vis... ( next thread)

Thank you for your kind words. Look forward to seeing more of your work in this subfield too.

How new genes get switched on - News Scientists discovered an identical neural circuit that operates differently in male and female mice.

Here is the Rockefeller press release: www.rockefeller.edu/news/38025-h.... Thank you for promoting our science.

Gene regulatory networks and essential transcription factors for de novo-originated genes Nature Ecology & Evolution - A combination of computational methods applied to single-cell RNA sequencing data and genetic experiments shows that a small number of transcription factors are...

Our latest paper is out: rdcu.be/ev6Ym — one of my favorite projects. It began about 8 years ago when Nobel laureate Torsten Wiesel asked me: what transcription factors regulate new genes? I had no idea then. Now we have some answers.

Topsicle: a method for estimating telomere length from whole genome long-read sequencing data Telomeres protect chromosome ends and its length varies significantly between organisms. Because telomere length variation is associated with various biomedical and eco-evolutionary phenotypes, many b...

I'm very excited to share a new method my grad student @linhngk.bsky.social and I have developed. Here's Topsicle a new computational method for analyzing long read sequencing data and estimate telomere length. Please see our preprint or this thread for detail!
www.biorxiv.org/content/10.1...

How new genes get switched on - News Scientists discovered an identical neural circuit that operates differently in male and female mice.

Rockefeller's @lizhao.bsky.social has spent nearly a decade cataloguing evolutionarily young genes. Now, complementary studies in @pnas.org and @natecoevo.nature.com are the first to demonstrate how these new genes are regulated and expressed.

If you are an SMBE member and received the election email (it may have gone to your junk folder), I would be honored if you would consider voting for me for councilor. You may also choose to vote for other scientists, and I encourage you to participate in the election. Thank you!

I hope to take a PhD student in the coming application cycle. Please reach out if you are interested in joining our lab in EEB at Yale, especially if interested in working on the natural history/ phylogenetics/ morphology/ population biology/ development/ genomics of siphonophores. dunnlab.org

Postdoc job opportunity! We're looking for ECR in evolutionary genomics to study the relation between intra-specific gene expression variability, polymorphism, and macro-evolutionary rates. We have the data in 3 fishes & amphioxus, just waiting for your expertise and enthusiasm!
tinyurl.com/3aewk286

Duke to Award Three Honorary Degrees at 2025 Commencement Ceremony | Duke Today

Congratulations to Feng Zhang (Vallee Scholar 2013) (Broad Inst, MIT, HHMI Investigator) who received an honorary doctorate from Duke University on Sunday!

today.duke.edu/2025/04/duke...

A Synergistic, Cultivator Model of De Novo Gene Origination Abstract. The origin and fixation of evolutionarily young genes is a fundamental question in evolutionary biology. However, understanding the origins of ne

4) he provided evidence supporting the cultivator model of de novo gene origination, a model he proposed to explore the link between novel genes/lncRNAs and nearby functionally important genes academic.oup.com/gbe/article/...

2) he used single cell cluster and RNA FISH to confirm that many important "maker genes" show rapid changes of gene expression among specie, 3) he also find some interesting patterns of transcriptional busting size/frequency in spermatogenesis,

Comparative single-cell analysis of transcriptional bursting reveals the role of genome organization in de novo transcript origination | PNAS Spermatogenesis is a key developmental process underlying the origination of newly evolved genes. However, rapid cell type–specific transcriptomic ...

I’m very glad to share our recent publication
@pnas.org
, led by UnJin Lee from our lab at
@rockefelleruniv.bsky.social
: pnas.org/doi/10.1073/.... In this work, he 1) developed a method to efficiently compare single-cell RNA-seq data from rapidly evolving tissues across multiple species, and

We are witnessing the destruction of science in America | Paul Darren Bieniasz If we stay on this administration’s course, future life-saving medicines may never be invented

We are witnessing the destruction of science in America | Paul Darren Bieniasz

I lost my job at the National Science Foundation yesterday, along with 167 of my colleagues, including some dear friends. This was the best job I've ever had, and I thought it would be my last. The PI community has been sympathetic and supportive, without exception. I will miss working for you.

We're excited to announce the 2025 Larry Sandler Award recipient, @peiwei-chen.bsky.social 🎉

This award recognizes students completing a PhD in Drosophila research. Dr. Chen will present the Larry Sandler Memorial Lecture on evolutionary innovation in genome defense at #Dros25 in March.

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