Yiyuan (YY) Li
@yli19.bsky.social
Professor of Evolutionary Biology at Ningbo University. Interested in Host-symbionts Interactions, Coevolution Between Genomes, Insect Genomics, Environmental DNA https://yyli.weebly.com/
Reposted by Yiyuan (YY) Li
New work from @miyapan.bsky.social and our team, bringing ant, bee, and wasp labs together. @chuanxinyu.bsky.social shows that the ANTSR locus we discovered in ants has determined sex for 150+ My across bees and stinging wasps 🐜🐝, despite virtually no sequence conservation 😮 doi.org/10.1073/pnas...
January 6, 2026 at 3:01 AM
New work from @miyapan.bsky.social and our team, bringing ant, bee, and wasp labs together. @chuanxinyu.bsky.social shows that the ANTSR locus we discovered in ants has determined sex for 150+ My across bees and stinging wasps 🐜🐝, despite virtually no sequence conservation 😮 doi.org/10.1073/pnas...
Reposted by Yiyuan (YY) Li
I am looking for a PhD student to start in my lab at UCSB in Fall 2026, studying evolutionary biology. See attached flyer for more information. Please also share with potentially interested students. Thanks!
November 3, 2025 at 5:27 PM
I am looking for a PhD student to start in my lab at UCSB in Fall 2026, studying evolutionary biology. See attached flyer for more information. Please also share with potentially interested students. Thanks!
Reposted by Yiyuan (YY) Li
The Mexican honey wasp is a bit of an oddball: it makes and eats honey like a bee, but when it’s hankering for protein, instead of pollen, it eats other insects. A new study finds its gut microbiome is more like bees than wasps. Funded by USDA and NSF. journals.asm.org/doi/10.1128/...
October 3, 2025 at 2:46 PM
The Mexican honey wasp is a bit of an oddball: it makes and eats honey like a bee, but when it’s hankering for protein, instead of pollen, it eats other insects. A new study finds its gut microbiome is more like bees than wasps. Funded by USDA and NSF. journals.asm.org/doi/10.1128/...
Reposted by Yiyuan (YY) Li
Jo Holley led an undergrad team for this study, about wasps that are trying to be bees, using a new microbiome.
Honey wasps differ from other wasps in possessing large gut communities dominated by host-restricted bacteria | mBio
Honey-feeding social insects such as honey bees and bumble bees have conserved gut
bacterial communities that are transmitted among nestmates. These bacteria benefit
hosts by providing defense against...
journals.asm.org
October 3, 2025 at 11:16 PM
Jo Holley led an undergrad team for this study, about wasps that are trying to be bees, using a new microbiome.
Reposted by Yiyuan (YY) Li
Super excited to share the results of one of my favorite projects, out now in PNAS! We uncovered the mechanism of protection against fungal pathogens in the aphid-Fukatsuia symbiosis. (1/2)
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Heritable symbiont producing nonribosomal peptide confers extreme heat sensitivity and antifungal protection on its host | PNAS
Insects frequently form associations with maternally transmitted symbiotic bacteria.
This transmission mode ensures that symbiont-conferred effects...
www.pnas.org
June 30, 2025 at 1:23 AM
Super excited to share the results of one of my favorite projects, out now in PNAS! We uncovered the mechanism of protection against fungal pathogens in the aphid-Fukatsuia symbiosis. (1/2)
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Reposted by Yiyuan (YY) Li
super-happy, three TE invasions in Dmel during the last 30 years; the crazy thing - Transib1 spread in just 2-3years in global populations academic.oup.com/mbe/advance-... great work everyone @rpianezza.bsky.social @almoroscarpa.bsky.social @signor-molevol.bsky.social Anna Haider
Spatio-temporal tracking of three novel transposable element invasions in Drosophila melanogaster over the last 30 years
Abstract. Transposable elements (TEs) are repetitive sequences capable of mobilizing within genomes, exerting a sigfinificant influence on evolution throug
academic.oup.com
June 11, 2025 at 11:37 AM
super-happy, three TE invasions in Dmel during the last 30 years; the crazy thing - Transib1 spread in just 2-3years in global populations academic.oup.com/mbe/advance-... great work everyone @rpianezza.bsky.social @almoroscarpa.bsky.social @signor-molevol.bsky.social Anna Haider
Reposted by Yiyuan (YY) Li
🚨 Our GW paper is out in Nature Methods!🥲
GW is a fast genomics browser (up to 100x faster!)
github.com/kcleal/gw
Also, just released a Python interface for GW
github.com/kcleal/gwplot
📝 nature.com/articles/s4159…#Genomicsc#Bioinformaticscs
GW is a fast genomics browser (up to 100x faster!)
github.com/kcleal/gw
Also, just released a Python interface for GW
github.com/kcleal/gwplot
📝 nature.com/articles/s4159…#Genomicsc#Bioinformaticscs
GitHub - kcleal/gw: Genome browser and variant annotation
Genome browser and variant annotation. Contribute to kcleal/gw development by creating an account on GitHub.
github.com
June 26, 2025 at 2:47 PM
🚨 Our GW paper is out in Nature Methods!🥲
GW is a fast genomics browser (up to 100x faster!)
github.com/kcleal/gw
Also, just released a Python interface for GW
github.com/kcleal/gwplot
📝 nature.com/articles/s4159…#Genomicsc#Bioinformaticscs
GW is a fast genomics browser (up to 100x faster!)
github.com/kcleal/gw
Also, just released a Python interface for GW
github.com/kcleal/gwplot
📝 nature.com/articles/s4159…#Genomicsc#Bioinformaticscs
Reposted by Yiyuan (YY) Li
“The idea that taking walks, reading things unrelated to your research, and hanging out with strangers in a campus pub should be considered part of the serious process of thinking, but might well meet with skepticism in practice.”
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
The forgotten half of scientific thinking | PNAS
The forgotten half of scientific thinking
www.pnas.org
June 26, 2025 at 1:23 PM
“The idea that taking walks, reading things unrelated to your research, and hanging out with strangers in a campus pub should be considered part of the serious process of thinking, but might well meet with skepticism in practice.”
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Reposted by Yiyuan (YY) Li
New preprint ex @bolinabug.bsky.social (+ @daisukekageyama.bsky.social & @scottishwormboy.bsky.social) on the pronounced secondary expansion of Spiroplasma and Rickettsia genomes in lacewings doi.org/10.1101/2025... #symbiosky 1/2
Concerted genome expansion of heritable symbionts in an insect host
Maternally transmitted symbionts represent important components of arthropod biology, acting as both beneficial partners and as reproductive parasites. Their strict vertical transmission greatly reduc...
doi.org
May 12, 2025 at 8:14 AM
New preprint ex @bolinabug.bsky.social (+ @daisukekageyama.bsky.social & @scottishwormboy.bsky.social) on the pronounced secondary expansion of Spiroplasma and Rickettsia genomes in lacewings doi.org/10.1101/2025... #symbiosky 1/2
Reposted by Yiyuan (YY) Li
Interesting AI read. 15-23% of uncultivated microbes may engage in symbiotic relationships.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
A genomic catalog of Earth’s bacterial and archaeal symbionts
Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth, yet remains underexplored due to culturing challenges. This study employed machine learning (ML) to predict...
www.biorxiv.org
June 6, 2025 at 11:07 PM
Reposted by Yiyuan (YY) Li
An update on open postdoc positions, in my group and the adjacent group of Howard Ochman, here at UT-Austin. #SymbioSky
Mine: insect-bacterial symbiosis with emphasis on intracellular endosymbionts and molecular mechanisms.
web.biosci.utexas.edu/moran/contac...
Mine: insect-bacterial symbiosis with emphasis on intracellular endosymbionts and molecular mechanisms.
web.biosci.utexas.edu/moran/contac...
Nancy Moran Contact
web.biosci.utexas.edu
June 2, 2025 at 8:26 PM
An update on open postdoc positions, in my group and the adjacent group of Howard Ochman, here at UT-Austin. #SymbioSky
Mine: insect-bacterial symbiosis with emphasis on intracellular endosymbionts and molecular mechanisms.
web.biosci.utexas.edu/moran/contac...
Mine: insect-bacterial symbiosis with emphasis on intracellular endosymbionts and molecular mechanisms.
web.biosci.utexas.edu/moran/contac...
Reposted by Yiyuan (YY) Li
Struggling to find the tiny microchromosomes in draft bird genome assemblies?
Our new #preprint introducing MicroFinder can help: www.biorxiv.org/content/10.1...
🧵 below
(1/n)
@sangerinstitute.bsky.social
Our new #preprint introducing MicroFinder can help: www.biorxiv.org/content/10.1...
🧵 below
(1/n)
@sangerinstitute.bsky.social
May 16, 2025 at 10:07 AM
Struggling to find the tiny microchromosomes in draft bird genome assemblies?
Our new #preprint introducing MicroFinder can help: www.biorxiv.org/content/10.1...
🧵 below
(1/n)
@sangerinstitute.bsky.social
Our new #preprint introducing MicroFinder can help: www.biorxiv.org/content/10.1...
🧵 below
(1/n)
@sangerinstitute.bsky.social
Reposted by Yiyuan (YY) Li
collaborative effort involving almost all previous postdocs in the lab and many years, but it is out and it is a great story! @kamilsjaron.bsky.social @ajmongue.bsky.social and many others
Our mealybug B chromosome paper is finally out, a small cross-generational gem from @laurarossevo.bsky.social's lab. academic.oup.com/gbe/article/...
A few interesting things we found 👇
A few interesting things we found 👇
The B Chromosome of Pseudococcus viburni: A Selfish Chromosome that Exploits Whole-Genome Meiotic Drive
Abstract. Meiosis is generally a fair process: each chromosome has a 50% chance of being included into each gamete. However, meiosis can become aberrant wi
academic.oup.com
February 1, 2025 at 7:21 PM
collaborative effort involving almost all previous postdocs in the lab and many years, but it is out and it is a great story! @kamilsjaron.bsky.social @ajmongue.bsky.social and many others
Reposted by Yiyuan (YY) Li
Wow! CONSISTENT #genome annotations for 200 insect species from different families, including 85 species previously lacking annotations www.biorxiv.org/content/10.1...
Annotation of 200 Insect Genomes with BRAKER for Consistent Comparisons across Species
The annotation of genomes lags behind their sequencing and assembly. For example, of 5,092 insect species in GenBank, as one of the most widely used databases, only 375 currently have annotated genome...
www.biorxiv.org
April 21, 2025 at 12:55 PM
Wow! CONSISTENT #genome annotations for 200 insect species from different families, including 85 species previously lacking annotations www.biorxiv.org/content/10.1...
Reposted by Yiyuan (YY) Li
🔔 Join the ERGA Plenary this month to hear @tom-mathers.bsky.social from @sangerinstitute.bsky.social discuss his work on improving reference #genomes for challenging species.
📅 28/04 at 15:00 CEST
🔗 www.erga-biodiversity.eu/post/plenary...
#biodiversity #genomics #assemblies #chromosomes #Dtol
📅 28/04 at 15:00 CEST
🔗 www.erga-biodiversity.eu/post/plenary...
#biodiversity #genomics #assemblies #chromosomes #Dtol
Plenary talk - Chromosomally complete reference genomes for challenging species: overcoming sequencing dropout in bird microchromosomes
At this month's ERGA Plenary meeting, taking place on Monday, April 28 at 15:00 CEST, Dr. Thomas Mathers will present his work on a Tree of Life pilot project focused on improving reference genome ass...
www.erga-biodiversity.eu
April 17, 2025 at 8:59 AM
🔔 Join the ERGA Plenary this month to hear @tom-mathers.bsky.social from @sangerinstitute.bsky.social discuss his work on improving reference #genomes for challenging species.
📅 28/04 at 15:00 CEST
🔗 www.erga-biodiversity.eu/post/plenary...
#biodiversity #genomics #assemblies #chromosomes #Dtol
📅 28/04 at 15:00 CEST
🔗 www.erga-biodiversity.eu/post/plenary...
#biodiversity #genomics #assemblies #chromosomes #Dtol
Reposted by Yiyuan (YY) Li
🚨 New paper alert! 🚨
A robustly rooted tree of eukaryotes sheds light on their deep evolutionary ancestry—suggesting that the Last Eukaryotic Common Ancestor (LECA) may have had an excavate-like cell architecture. 🧵🔬 (1/) www.nature.com/articles/s41...
A robustly rooted tree of eukaryotes sheds light on their deep evolutionary ancestry—suggesting that the Last Eukaryotic Common Ancestor (LECA) may have had an excavate-like cell architecture. 🧵🔬 (1/) www.nature.com/articles/s41...
A robustly rooted tree of eukaryotes reveals their excavate ancestry - Nature
The root of the eukaryote Tree of Life is estimated from a new, larger dataset of mitochondrial proteins including all known eukaryotic supergroups, showing it lies between two multi-supergroup assemb...
www.nature.com
March 12, 2025 at 4:39 PM
🚨 New paper alert! 🚨
A robustly rooted tree of eukaryotes sheds light on their deep evolutionary ancestry—suggesting that the Last Eukaryotic Common Ancestor (LECA) may have had an excavate-like cell architecture. 🧵🔬 (1/) www.nature.com/articles/s41...
A robustly rooted tree of eukaryotes sheds light on their deep evolutionary ancestry—suggesting that the Last Eukaryotic Common Ancestor (LECA) may have had an excavate-like cell architecture. 🧵🔬 (1/) www.nature.com/articles/s41...
Reposted by Yiyuan (YY) Li
Just posting this to #popgen
Here's a link to my notes on population & quantitative genetics:
github.com/cooplab/popg...
Hoping to extend it more after the winter holidays, as I'm just finishing up teaching the undergrad version of class.
Here's a link to my notes on population & quantitative genetics:
github.com/cooplab/popg...
Hoping to extend it more after the winter holidays, as I'm just finishing up teaching the undergrad version of class.
Releases · cooplab/popgen-notes
Population genetics notes. Contribute to cooplab/popgen-notes development by creating an account on GitHub.
github.com
November 19, 2024 at 11:37 PM
Just posting this to #popgen
Here's a link to my notes on population & quantitative genetics:
github.com/cooplab/popg...
Hoping to extend it more after the winter holidays, as I'm just finishing up teaching the undergrad version of class.
Here's a link to my notes on population & quantitative genetics:
github.com/cooplab/popg...
Hoping to extend it more after the winter holidays, as I'm just finishing up teaching the undergrad version of class.
Reposted by Yiyuan (YY) Li
Out now, a comprehensive guide to metagenomics -- from sample collection to data analysis. This primer covers best practices, challenges, and applications in health, agriculture & environment. A roadmap for studying microbial communities 👇
www.nature.com/articles/s43...
www.nature.com/articles/s43...
January 27, 2025 at 9:53 PM
Out now, a comprehensive guide to metagenomics -- from sample collection to data analysis. This primer covers best practices, challenges, and applications in health, agriculture & environment. A roadmap for studying microbial communities 👇
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Reposted by Yiyuan (YY) Li
76 #arthropod #genomes, five haplodiploid lineages tested have fast-evolving mitochondrial #genes & fast-evolving nuclear #genes related to mitochondrial functions --- with YY @gwct.bio fringy et al. link.springer.com/article/10.1...
Rapid evolution of mitochondrion-related genes in haplodiploid arthropods - BMC Biology
Background Mitochondrial genes and nuclear genes cooperate closely to maintain the functions of mitochondria, especially in the oxidative phosphorylation (OXPHOS) pathway. However, mitochondrial genes...
link.springer.com
December 8, 2024 at 2:19 PM
76 #arthropod #genomes, five haplodiploid lineages tested have fast-evolving mitochondrial #genes & fast-evolving nuclear #genes related to mitochondrial functions --- with YY @gwct.bio fringy et al. link.springer.com/article/10.1...
Reposted by Yiyuan (YY) Li
🚨Postdoc position(s) alert🚨 If you like to develop new bioinformatic tools for *human* microbiome analysis, are interested by virus/phages, we (JGI Viral Genomics and Microbiome Data groups) may have a great position for you ! No official job posting yet, but email or DM if you are interested !
January 7, 2025 at 9:12 PM
🚨Postdoc position(s) alert🚨 If you like to develop new bioinformatic tools for *human* microbiome analysis, are interested by virus/phages, we (JGI Viral Genomics and Microbiome Data groups) may have a great position for you ! No official job posting yet, but email or DM if you are interested !