Yuki Haba
@yukihaba.bsky.social
Studying why and how behavior evolves, from mosquitoes to mole-rats | Postdoc/Leon Levy Scholar @Columbia working with Ishmail Abdus-Saboor | PhD @Princeton with Lindy McBride | 麻布/東大 alum 🇯🇵 | yukihaba.github.io
Pinned
Yuki Haba
@yukihaba.bsky.social
· Oct 25
Ancient origin of an urban underground mosquito
Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. In this work, we investigate a widely cited example of urban adaptation, Culex pipie...
www.science.org
How does life evolve to adapt to modern cities?
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Reposted by Yuki Haba
Did you know there are 2 types of avocado varieties? A-types switch from female to male, B-types male to female, within a single day. This reciprocal sex alternation promotes cross-pollination and has a simple genetic basis. Read more in this recent preprint from the final chapter of my PhD thesis 🥑
Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado
In avocado and certain wild relatives in Lauraceae, pollination occurs via a synchronized rhythm of floral sex timing between two hermaphroditic flowering types. A-type plants present female-phase flo...
www.biorxiv.org
December 29, 2025 at 7:13 PM
Did you know there are 2 types of avocado varieties? A-types switch from female to male, B-types male to female, within a single day. This reciprocal sex alternation promotes cross-pollination and has a simple genetic basis. Read more in this recent preprint from the final chapter of my PhD thesis 🥑
Reposted by Yuki Haba
All right it’s time for the annual “please tell us about one (or a few if you are ambitious) paper from 2025 that really impressed you and why we should all read it“! Go! If you tell us how it changed your view of the world and what makes it so powerful and consequential It would be excellent.
December 21, 2025 at 3:10 AM
All right it’s time for the annual “please tell us about one (or a few if you are ambitious) paper from 2025 that really impressed you and why we should all read it“! Go! If you tell us how it changed your view of the world and what makes it so powerful and consequential It would be excellent.
Reposted by Yuki Haba
Wendy Valencia-Montoya and team uncover thermal infrared as one of the most ancient pollination signals uniting plants and animals. From the field to single proteins.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
December 11, 2025 at 9:09 PM
Wendy Valencia-Montoya and team uncover thermal infrared as one of the most ancient pollination signals uniting plants and animals. From the field to single proteins.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Yuki Haba
The final version of the clonal raider ant reference brain is now out OA in @currentbiology.bsky.social:
🐜 🧠 🐜 🧠 🐜 🧠 🐜 🧠 🐜 🧠 🐜
www.sciencedirect.com/science/arti...
🐜 🧠 🐜 🧠 🐜 🧠 🐜 🧠 🐜 🧠 🐜
www.sciencedirect.com/science/arti...
December 5, 2025 at 4:30 PM
The final version of the clonal raider ant reference brain is now out OA in @currentbiology.bsky.social:
🐜 🧠 🐜 🧠 🐜 🧠 🐜 🧠 🐜 🧠 🐜
www.sciencedirect.com/science/arti...
🐜 🧠 🐜 🧠 🐜 🧠 🐜 🧠 🐜 🧠 🐜
www.sciencedirect.com/science/arti...
Reposted by Yuki Haba
I have a new preprint demonstrating a genome-architecture-aware approach to inferring species trees and introgression landscapes from a small number of genomes. If you are interested in phylogenomics, birds, or hybridization, this is for you! www.biorxiv.org/content/10.1...
December 1, 2025 at 7:35 PM
I have a new preprint demonstrating a genome-architecture-aware approach to inferring species trees and introgression landscapes from a small number of genomes. If you are interested in phylogenomics, birds, or hybridization, this is for you! www.biorxiv.org/content/10.1...
Reposted by Yuki Haba
This has been an intense, crazy week. My plasmid competition paper is finally out and we have a new preprint on Bioarxiv! Plus I'm leaving the US after 10 years here. See you soon America! Hello Zurich!!!
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 21, 2025 at 8:26 PM
This has been an intense, crazy week. My plasmid competition paper is finally out and we have a new preprint on Bioarxiv! Plus I'm leaving the US after 10 years here. See you soon America! Hello Zurich!!!
Reposted by Yuki Haba
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Yuki Haba
Two weeks ago now @jennytung.bsky.social and I published a new review in Current Opinion in Genetics and Development, entitled “Evolutionary genetics meets ecological immunology: insights into the evolution of immune systems.” www.sciencedirect.com/science/arti...
A thread below...
A thread below...
Evolutionary genetics meets ecological immunology: insights into the evolution of immune systems
Immune genes show remarkably consistent evidence of selection, modification, and diversification across the tree of life. Parasites are a key force in…
www.sciencedirect.com
November 17, 2025 at 10:28 AM
Two weeks ago now @jennytung.bsky.social and I published a new review in Current Opinion in Genetics and Development, entitled “Evolutionary genetics meets ecological immunology: insights into the evolution of immune systems.” www.sciencedirect.com/science/arti...
A thread below...
A thread below...
Reposted by Yuki Haba
After analyzing the DNA sequences from 357 modern and 22 historic specimens, new research led by @yukihaba.bsky.social and @lindymcbr.bsky.social at @science.org uncovers the true, ancient origin of the "London Underground mosquito."
Ancient origin of an urban underground mosquito
Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. In this work, we investigate a widely cited example of urban adaptation, Culex pipie...
bit.ly
November 20, 2025 at 2:23 PM
After analyzing the DNA sequences from 357 modern and 22 historic specimens, new research led by @yukihaba.bsky.social and @lindymcbr.bsky.social at @science.org uncovers the true, ancient origin of the "London Underground mosquito."
Reposted by Yuki Haba
Our preprint is out! www.biorxiv.org/content/10.1...
Peter Skovorodnikov and I are excited to present FERAL: a new video-understanding toolkit that maps raw video directly to behavior, no pose estimation required.
It works across species, from lab to field, and even in collective systems. (🧵1/n)
Peter Skovorodnikov and I are excited to present FERAL: a new video-understanding toolkit that maps raw video directly to behavior, no pose estimation required.
It works across species, from lab to field, and even in collective systems. (🧵1/n)
FERAL: A Video-Understanding System for Direct Video-to-Behavior Mapping
Animal behavior unfolds continuously in time, yet quantitative analyses often require segmenting it into discrete, interpretable states. Although manual annotation can achieve this, it remains slow, s...
www.biorxiv.org
November 19, 2025 at 6:30 PM
Our preprint is out! www.biorxiv.org/content/10.1...
Peter Skovorodnikov and I are excited to present FERAL: a new video-understanding toolkit that maps raw video directly to behavior, no pose estimation required.
It works across species, from lab to field, and even in collective systems. (🧵1/n)
Peter Skovorodnikov and I are excited to present FERAL: a new video-understanding toolkit that maps raw video directly to behavior, no pose estimation required.
It works across species, from lab to field, and even in collective systems. (🧵1/n)
Reposted by Yuki Haba
As a longtime fan of cool papers in @currentbiology.bsky.social, I am really thrilled to see this out!
This study sets the stage for understanding the origins of novel (vocal) behaviors.
Big shout out to the main architects of this work @xmikezheng20.bsky.social and @cliffscience.bsky.social
This study sets the stage for understanding the origins of novel (vocal) behaviors.
Big shout out to the main architects of this work @xmikezheng20.bsky.social and @cliffscience.bsky.social
Great @currentbiology.bsky.social study by @xmikezheng20.bsky.social @cliffscience.bsky.social @arkarupbanerjee.bsky.social 🧪🧠🐭🎶
Vocal repertoire expansion in singing mice by co-opting a conserved midbrain circuit node
www.cell.com/current-biol...
Vocal repertoire expansion in singing mice by co-opting a conserved midbrain circuit node
www.cell.com/current-biol...
Vocal repertoire expansion in singing mice by co-opting a conserved midbrain circuit node
Zheng and Harpole et al. show that singing mice produce two major vocal modes: ancestral
USVs and novel songs that follow a linearly decelerating rhythm. Although acoustically
distinct, songs and USVs...
www.cell.com
November 19, 2025 at 6:42 PM
As a longtime fan of cool papers in @currentbiology.bsky.social, I am really thrilled to see this out!
This study sets the stage for understanding the origins of novel (vocal) behaviors.
Big shout out to the main architects of this work @xmikezheng20.bsky.social and @cliffscience.bsky.social
This study sets the stage for understanding the origins of novel (vocal) behaviors.
Big shout out to the main architects of this work @xmikezheng20.bsky.social and @cliffscience.bsky.social
Reposted by Yuki Haba
Le moustique du métro londonien est-il "né" dans le métro ? Une nouvelle étude parue dans Science révèle que cet insecte s'est adapté à l'humain et aux espaces confinés au Moyen Orient il y a plusieurs millénaires avant de coloniser les souterrains européens.
Expikations 🦟⬇️
Expikations 🦟⬇️
Le moustique du métro londonien n'a pas évolué dans les souterrains
Le moustique du métro londonien est-il "né" dans le métro ? Une nouvelle étude parue dans Science révèle que cet insecte nommé Culex pipiens molestus s'est adapté à l'humain et aux espaces confinés au...
www.radiofrance.fr
November 17, 2025 at 6:45 AM
Le moustique du métro londonien est-il "né" dans le métro ? Une nouvelle étude parue dans Science révèle que cet insecte s'est adapté à l'humain et aux espaces confinés au Moyen Orient il y a plusieurs millénaires avant de coloniser les souterrains européens.
Expikations 🦟⬇️
Expikations 🦟⬇️
Reposted by Yuki Haba
Come do a joint postdoc with me and @tinakim-neuro.bsky.social, splitting your time between Princeton and Columbia. Come design new activity-dependent labeling enzymes and transcriptional reporters optimized for application in the peripheral nervous system.
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
Postdoctoral Scientist- Kim and Abdus-Saboor Lab
Primary Work Address: Dept of Molecular Biology, Princeton, NJ, 08544 Current HHMI Employees, click here to apply via your Workday account. The Kim Lab at Princeton University and Abdus-Saboor Lab at ...
hhmi.wd1.myworkdayjobs.com
November 17, 2025 at 5:34 PM
Come do a joint postdoc with me and @tinakim-neuro.bsky.social, splitting your time between Princeton and Columbia. Come design new activity-dependent labeling enzymes and transcriptional reporters optimized for application in the peripheral nervous system.
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
Reposted by Yuki Haba
SAVE THE DATE: the yearly NY Population Genetics meeting will be back on March 9 2026, generously hosted by the
@simonsfoundation.org. Details to follow. Please RT.
@simonsfoundation.org. Details to follow. Please RT.
November 14, 2025 at 5:05 PM
SAVE THE DATE: the yearly NY Population Genetics meeting will be back on March 9 2026, generously hosted by the
@simonsfoundation.org. Details to follow. Please RT.
@simonsfoundation.org. Details to follow. Please RT.
Reposted by Yuki Haba
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
Insertion of an invading retrovirus regulates a novel color trait in swordtail fish
For over a century, evolutionary biologists have been motivated to understand the mechanisms through which organisms adapt to their environments. Coloration and pigmentation are remarkably variable wi...
shorturl.at
November 12, 2025 at 8:34 PM
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
Reposted by Yuki Haba
An empirical approach to evaluating the prevalence of long-lived balancing selection in humans--and important limitations. Work by @hannahmm.bsky.social
November 11, 2025 at 7:14 PM
An empirical approach to evaluating the prevalence of long-lived balancing selection in humans--and important limitations. Work by @hannahmm.bsky.social
Reposted by Yuki Haba
How is functional variation at large-effect loci maintained in natural populations, even as environments change? In a paper led by @mkarag.bsky.social, we tracked known pesticide resistant alleles in outdoor 𝘋. 𝘮𝘦𝘭𝘢𝘯𝘰𝘨𝘢𝘴𝘵𝘦𝘳 cages & inferred selection and dominance from temporal sequencing data.
November 6, 2025 at 9:51 PM
How is functional variation at large-effect loci maintained in natural populations, even as environments change? In a paper led by @mkarag.bsky.social, we tracked known pesticide resistant alleles in outdoor 𝘋. 𝘮𝘦𝘭𝘢𝘯𝘰𝘨𝘢𝘴𝘵𝘦𝘳 cages & inferred selection and dominance from temporal sequencing data.
Reposted by Yuki Haba
Parental care, and more complex cooperative systems of care, have independently evolved in hundreds of animal lineages. In an article published today, we explore how these behaviors evolve 𝘢𝘵 𝘢 𝘮𝘰𝘭𝘦𝘤𝘶𝘭𝘢𝘳 𝘭𝘦𝘷𝘦𝘭l shorturl.at/g5OPw /1
Convergent evolution of a conserved molecular network underlies parenting and sociality - Nature Reviews Genetics
Kay et al. review evidence that parental care, and more complex social behaviour based on parental care, evolved in multiple species through the repeated co-option of members of a pleiotropic molecula...
shorturl.at
November 4, 2025 at 3:57 PM
Parental care, and more complex cooperative systems of care, have independently evolved in hundreds of animal lineages. In an article published today, we explore how these behaviors evolve 𝘢𝘵 𝘢 𝘮𝘰𝘭𝘦𝘤𝘶𝘭𝘢𝘳 𝘭𝘦𝘷𝘦𝘭l shorturl.at/g5OPw /1
Reposted by Yuki Haba
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Thank you so much Ryan!! From the Cpip samples from Iowa to our discussion at Kolymbari, your contributions have been very important to the project -- thank you!
Excited to contribute to this beautiful study led by @yukihaba.bsky.social and @lindymcbr.bsky.social!
How does life evolve to adapt to modern cities?
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
November 4, 2025 at 8:11 PM
Thank you so much Ryan!! From the Cpip samples from Iowa to our discussion at Kolymbari, your contributions have been very important to the project -- thank you!
Reposted by Yuki Haba
Excited to contribute to this beautiful study led by @yukihaba.bsky.social and @lindymcbr.bsky.social!
How does life evolve to adapt to modern cities?
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Ancient origin of an urban underground mosquito
Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. In this work, we investigate a widely cited example of urban adaptation, Culex pipie...
www.science.org
November 4, 2025 at 5:41 PM
Excited to contribute to this beautiful study led by @yukihaba.bsky.social and @lindymcbr.bsky.social!
Reposted by Yuki Haba
New study funded in part by our Rosemary Grant Advanced Award - congratulations @yukihaba.bsky.social !!
How does life evolve to adapt to modern cities?
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Ancient origin of an urban underground mosquito
Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. In this work, we investigate a widely cited example of urban adaptation, Culex pipie...
www.science.org
October 30, 2025 at 8:06 PM
New study funded in part by our Rosemary Grant Advanced Award - congratulations @yukihaba.bsky.social !!
Reposted by Yuki Haba
Thrilled that this paper is finally out and that I was able to contribute specimens from the metro Atlanta area. Congrats @yukihaba.bsky.social! 🦟🧬🔬
How does life evolve to adapt to modern cities?
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Ancient origin of an urban underground mosquito
Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. In this work, we investigate a widely cited example of urban adaptation, Culex pipie...
www.science.org
October 30, 2025 at 12:46 PM
Thrilled that this paper is finally out and that I was able to contribute specimens from the metro Atlanta area. Congrats @yukihaba.bsky.social! 🦟🧬🔬
Reposted by Yuki Haba
Do flies feel pain?
Spooky new preprint from our lab on the cells and circuits that mediate nociceptive behaviors in adult Drosophila, led by graduate student (and newly minted PhD!) @jonesjes.bsky.social.
🪰⚡👻🎃
www.biorxiv.org/content/10.1...
Spooky new preprint from our lab on the cells and circuits that mediate nociceptive behaviors in adult Drosophila, led by graduate student (and newly minted PhD!) @jonesjes.bsky.social.
🪰⚡👻🎃
www.biorxiv.org/content/10.1...
October 29, 2025 at 6:56 PM
Do flies feel pain?
Spooky new preprint from our lab on the cells and circuits that mediate nociceptive behaviors in adult Drosophila, led by graduate student (and newly minted PhD!) @jonesjes.bsky.social.
🪰⚡👻🎃
www.biorxiv.org/content/10.1...
Spooky new preprint from our lab on the cells and circuits that mediate nociceptive behaviors in adult Drosophila, led by graduate student (and newly minted PhD!) @jonesjes.bsky.social.
🪰⚡👻🎃
www.biorxiv.org/content/10.1...
Reposted by Yuki Haba
Thrilled to see this study out in Science! It was a privilege to have had the opportunity to contribute to PipPop alongside such a talented group. Congrats, Yuki, on your leadership and an exciting piece of work! 🌆🦟
How does life evolve to adapt to modern cities?
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Ancient origin of an urban underground mosquito
Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. In this work, we investigate a widely cited example of urban adaptation, Culex pipie...
www.science.org
October 28, 2025 at 5:51 PM
Thrilled to see this study out in Science! It was a privilege to have had the opportunity to contribute to PipPop alongside such a talented group. Congrats, Yuki, on your leadership and an exciting piece of work! 🌆🦟