Yuki Haba
@yukihaba.bsky.social
Evolution, genomics, neuroethology - from mosquitoes to mole-rats | Leon Levy Scholar at Columbia Zuckerman Institute / Abdus-Saboor lab | PhD at Princeton McBride lab | Tokyo native, 麻布高/東大 alum 🇯🇵 yukihaba.github.io
New preprint! www.biorxiv.org/content/10.6... Nearly a decade after starting the project, the first major results from our comparative connectomics work is online! Comparing the head direction circuits of the central complex in bees, ants and flies, recapitulating >300million years of evolution.
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:
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
Susumu Tonegawa, Nobel Prize in Medicine 1987: How I define creativity... RIP www.youtube.com/watch?v=fnzN...
Susumu Tonegawa, Nobel Prize in Medicine 1987: How I define creativity...
YouTube video by Nobel Prize
youtube.com
We are heartbroken to have lost our founder, who provided so much inspiration, but we are all honored to carry on the science he loved so much. picower.mit.edu/news/picower... #neuroscience #biology
Picower Professor Susumu Tonegawa, renowned molecular biologist and Nobel laureate, dies at 86
Tonegawa made landmark discoveries about how the immune system generates antibody diversity and how the brain forms memories.
picower.mit.edu
Incredible and exciting work!! Mole rats never cease to amaze...
Mohammed Khallaf@khallaf.bsky.social · 3w agoOur new paper is out in @nature.com! We uncovered how a naked mole-rat queen 👑 controls an entire colony: a natural contraceptive scent that suppresses reproduction in other females! A remarkable mammalian parallel to bees and ants! 🐝🐜 @garyrlewin.bsky.social youtu.be/enfv3zJrWKM?...
For me this paper is a career highlight..truly astonishing biology! www.nature.com/articles/s41...
A queen odour mediates reproductive suppression in a eusocial mammal - Nature
Naked mole-rat (Heterocephalus glaber) queens produce isopropyl myristate, a low-volatility ester that high-ranking animals detect and avoid, which alters prolactin and progesterone in other females t...
nature.com
Our new paper is out in @nature.com! We uncovered how a naked mole-rat queen 👑 controls an entire colony: a natural contraceptive scent that suppresses reproduction in other females! A remarkable mammalian parallel to bees and ants! 🐝🐜 @garyrlewin.bsky.social youtu.be/enfv3zJrWKM?...
Naked mole-rats are ruled by a queen: this chemical puts her in power
YouTube video by nature video
youtu.be
I am excited to tell you about our new study led by Tyler Audet and in collaboration with Stefan Lüpold's group. Below you see two species. On the right is Drosophila melanogaster. On the left, Drosophila prolongata. Notice the highly exaggerated legs of the males in D.p! doi.org/10.1093/evol...
New paper from the lab on the molecular regulation of parenting in ants. Spearheaded by postdocs Alex Paul and @tomaskay.bsky.social
Tomas Kay@tomaskay.bsky.social · 4w agoIn an article published today, we show that ancient feeding-related neuropeptides have been repurposed to control brood care in clonal raider ants. Photo: Bart Zijlstra, UNIL /1
🧪 Physiology is a hidden dimension of diversity in the radiation of woodland salamanders | PNAS www.pnas.org/doi/10.1073/...
Physiology is a hidden dimension of diversity in the radiation of woodland salamanders | PNAS
Morphological evolution can be explosive, producing visually spectacular adaptive radiations like Caribbean anoles, Malagasy vangas, and African Ri...
pnas.org
Rapid urban evolution of the dengue mosquito in West African cities Shift in genome and behavior of the mosquitoes towards greater specialization on humans, over just five years. Such cool work, congrats Noah Rose et al! www.biorxiv.org/content/10.6...
Rapid urban evolution of the dengue mosquito in West African cities
Aedes aegypti is an exceptionally effective global vector of human disease because of its strong specialization on human hosts and habitats. However, in its native range in Africa, many populations ne...
biorxiv.org
So excited to announce that I will be starting the Chen Lab at EMBL Rome in September 2026 🎉 ! The Chen Lab will investigate the genetics + evolution of innate behavior w/ high-throughput sequencing + computational methods across diverse rodent species. Stay tuned for upcoming opportunities...
New preprint from the last portion of my PhD! Despite low masked load, we found evidence for strong inbreeding depression in Devils Hole pupfish. The reason? A recessive lethal haplotype that causes a heart defect among developing embryos. www.biorxiv.org/content/10.6...
Long-term small effective population size, inbreeding, and a recessive lethal haplotype drive premature death in the endangered Devils Hole pupfish (Cyprinodon diabolis)
As anthropogenic habitat fragmentation and population decline accelerate globally, growing numbers of species face compounding demographic and genetic threats to long-term survival. Many populations a...
biorxiv.org
I’m honored to receive this year’s Hamilton Award at Evolution! It was such a privilege to be surrounded by so many outstanding scientists doing such incredible work!
Society for the Study of Evolution@sse-evolution.bsky.social · 2mo agoCongratulations to this year’s Hamilton Award winner, Princeton Vaughn! @princetonvaughn.bsky.social www.evolutionsociety.org/index.php?mo...
Do you know an outstanding aquarist? We're hiring a Senior Aquarist to help run our cephalopod facility at Columbia University. Our team maintains a colony of 250+ cuttlefish, develops new husbandry techniques (inc transgenics) & studies cuttlefish camouflage and social behavior. 1/3 [Pls repost!]
Andy Kern, who doesn't (really) have an account here, would like to share his group's new tool for speeding up pop gen summary stat calculations using GPUs. Check it out here: www.biorxiv.org/content/10.6... And see his thread over at the other place: x.com/pastramimach...
biorxiv.org
Spontaneous problem-solving in bumble bees. Amazing work by the bees who were put in these puzzling situations by @akshayebhambore.bsky.social in the lab of @olliloukola.bsky.social www.science.org/doi/10.1126/...
Hello #world, meet 1,000× Expansion Microscopy. A small gel would grow to the size of an Olympic swimming pool, while amino-acid-scale distances become visible with ordinary light microscopy. Led by Helena Hu from @eboyden3.bsky.social's lab, in collab with us. Story: www.biorxiv.org/content/10.6...
Very happy to announce a big new paper from the lab, led by grad students @smishra677.bsky.social and Laia Pomar-Pallarès (in collaboration with @roblanfear.bsky.social). We introduce a new way to study introgression, with accompanying software (DAFT) 1/n 🧵 www.biorxiv.org/content/10.6...
biorxiv.org
Researchers have identified superparamagnetic macrophages in the livers of rock pigeons to be crucial for magnetic sensing. The finding uncovers an unexpected role for immune cells in sensory perception and may fundamentally change our understanding of animal navigation. https://scim.ag/4nTQ3nq
So fun hosting visitors from Alison Barker's lab at MPI-Brain in the Abdus-Saboor Lab at the Columbia Zuckerman Institute! A great exchange of data and new ideas on the behavior and neuroscience of naked mole-rats. cc Alena Lemazina
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 agoJoin 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.
I am delighted to share new work with Simon Myers (www.biorxiv.org/content/10.6...), on how genetic variants that influence binding patterns of PRDM9 and slow down the repair of meiotic double-strand breaks impact mammalian spermatogenesis and fertility. 1/n
biorxiv.org
I’m happy to share a protocol we’ve been working on for building modular, synchronized multimodal data acquisition systems for systems neuroscience behavior rigs. @mbd1mbd1.bsky.social @arkarupbanerjee.bsky.social dx.doi.org/10.17504/pro...
A modular toolkit for synchronized multimodal data acquisition in systems neuroscience
A modular toolkit for synchronized multimodal data acquisition in systems neuroscience. Animal behavio. Read full protocol, steps, and materials on protocols.io
dx.doi.org
Our implantable living materials work is officially out @science.org! We confined therapeutic bacteria in stiff and tough hydrogels for deployment in vivo. Check out the paper shorturl.at/qT6db and perspective shorturl.at/3ntm9 here
Tetsuhiro Harimoto@tetsuharimoto.bsky.social · 10mo agoMy postdoc work is now on bioRxiv! We combined engineered bacteria and hydrogels to create implantable living materials that safely confine bacteria while letting them sense disease and release drugs from within. 🔗 www.biorxiv.org/content/10.1...
Happy to highlight new findings by Vanesa Getseva and Lin Poyraz about the sources of variation in germline mutation rates among humans: www.biorxiv.org/content/10.6... Joint work with Anastasia Stolyarova and @ipsitaagarwal.bsky.social. 1/n
A sibling study of variation in parental mutation rates
People are born with variable numbers of de novo germline mutations (DNMs), depending primarily on the ages of their parents. To explore additional causes, we developed an approach to call DNMs from nucleotide differences between siblings in genomic regions inherited identical by descent from both parents. Applying it to whole genome sequences from 28,985 sibling pairs of diverse genetic ancestries present in the UK Biobank and All of Us datasets, as well as 2,330 trios, we identified >800K autosomal DNMs and characterized mutation phenotypes in 27,645 sets of parents. We found subtle shifts in the mutation spectrum but no differences in total DNM rates among genetic ancestry groups, or between smokers and non-smokers. Testing for associations between parental mutation phenotypes and their burden of loss-of-function and deleterious missense variants in a set of 180 DNA repair and maintenance genes, we discovered that disruptions in REV1 and LIG1 increase germline mutation rates, and thus that rare mutator alleles segregate in population cohorts. ### Competing Interest Statement The authors have declared no competing interest. NIH, R35 GM083098
biorxiv.org
