Check out our newest preprint! 📝 We find that adaptation on coevolutionary fitness landscapes is highly repeatable, but landscape-specific, and intergenomic epistasis creates coevolutionary fitness load for interacting species due to frequent fitness trade-offs 🏋️
Repeatability of adaptation in interacting species https://www.biorxiv.org/content/10.64898/2026.04.01.715933v1
April 7, 2026 at 7:20 AM
Check out our newest preprint! 📝 We find that adaptation on coevolutionary fitness landscapes is highly repeatable, but landscape-specific, and intergenomic epistasis creates coevolutionary fitness load for interacting species due to frequent fitness trade-offs 🏋️
Coevolutionary diversification between #hosts and their nutritional #symbionts in #phytophagous #hemipterans
doi.org/10.1016/j.co...
#SymbioSky
doi.org/10.1016/j.co...
#SymbioSky
Redirecting
doi.org
September 28, 2026 at 9:49 AM
Coevolutionary diversification between #hosts and their nutritional #symbionts in #phytophagous #hemipterans
doi.org/10.1016/j.co...
#SymbioSky
doi.org/10.1016/j.co...
#SymbioSky
Remarkable new human proteome-wide effort to predict protein-protein interactions using coevolutionary signals and deep learning. From Qian Cong in the Eugene McDermott Center at UT Southwestern.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Predicting protein-protein interactions in the human proteome
Protein-protein interactions (PPI) are essential for biological function. Coevolutionary analysis and deep learning (DL) based protein structure prediction have enabled comprehensive PPI identificatio...
www.science.org
September 25, 2025 at 6:26 PM
Remarkable new human proteome-wide effort to predict protein-protein interactions using coevolutionary signals and deep learning. From Qian Cong in the Eugene McDermott Center at UT Southwestern.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Anthropogenic Habitat Loss and Fragmentation May Alter Coevolutionary Progress as Examined in a Brood Parasitism Model | doi.org/10.1002/ece3... | Ecology and Evolution | #ornithology 🪶
July 18, 2025 at 11:30 AM
Anthropogenic Habitat Loss and Fragmentation May Alter Coevolutionary Progress as Examined in a Brood Parasitism Model | doi.org/10.1002/ece3... | Ecology and Evolution | #ornithology 🪶
🧵
[1/n] Does AlphaFold3 "know" biophysics and the physics of protein folding? Are protein language models (pLMs) learning coevolutionary patterns? You can try to guess the answer to these questions using mechanistic interpretability.
[1/n] Does AlphaFold3 "know" biophysics and the physics of protein folding? Are protein language models (pLMs) learning coevolutionary patterns? You can try to guess the answer to these questions using mechanistic interpretability.
December 12, 2024 at 10:50 PM
🧵
[1/n] Does AlphaFold3 "know" biophysics and the physics of protein folding? Are protein language models (pLMs) learning coevolutionary patterns? You can try to guess the answer to these questions using mechanistic interpretability.
[1/n] Does AlphaFold3 "know" biophysics and the physics of protein folding? Are protein language models (pLMs) learning coevolutionary patterns? You can try to guess the answer to these questions using mechanistic interpretability.
Proud to announce a new publication from the lab: EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals
www.nature.com/articles/s41...
www.nature.com/articles/s41...
EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals - Nature Communications
Despite having structures for most proteins, we still do not know their function. Here, authors introduce EvoWeaver, a de novo method to identify genes working together using evolutionary information....
www.nature.com
April 28, 2025 at 1:47 PM
Proud to announce a new publication from the lab: EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Super proud of Daniel Kim, whose paper on coevolutionary cycling and the evolution of virulence has just been published in @journal-evo.bsky.social. Daniel was in high school when he did this research and has just started his undergraduate degree @kebleoxford.bsky.social.
doi.org/10.1093/evol...
doi.org/10.1093/evol...
Coevolutionary cycling in allele frequencies and the evolution of virulence
Abstract. Coevolutionary cycling in allele frequencies due to negative frequency-dependent selection—sometimes referred to as Red Queen Dynamics—is a key p
doi.org
October 31, 2025 at 9:10 PM
Super proud of Daniel Kim, whose paper on coevolutionary cycling and the evolution of virulence has just been published in @journal-evo.bsky.social. Daniel was in high school when he did this research and has just started his undergraduate degree @kebleoxford.bsky.social.
doi.org/10.1093/evol...
doi.org/10.1093/evol...
Delighted to share news that our collaborative study with @justinmeyer.bsky.social
'Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics'
is now officially out in Virus Evolution:
academic.oup.com/ve/article/1...
'Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics'
is now officially out in Virus Evolution:
academic.oup.com/ve/article/1...
Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics
Abstract. The enormous diversity of bacteriophages and their bacterial hosts presents a significant challenge to predict which phages infect a focal set of
academic.oup.com
January 7, 2025 at 12:07 AM
Delighted to share news that our collaborative study with @justinmeyer.bsky.social
'Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics'
is now officially out in Virus Evolution:
academic.oup.com/ve/article/1...
'Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics'
is now officially out in Virus Evolution:
academic.oup.com/ve/article/1...
For 40+ years, evolutionary ecologist Craig Benkman has tracked crossbills across North America—showing how these finches & conifers evolved together in a remarkable coevolutionary dance. 🌲🕊️
Their bill shapes even match the cones they feed on.
Full story: www.allaboutbirds.org/news/craig-b...
Their bill shapes even match the cones they feed on.
Full story: www.allaboutbirds.org/news/craig-b...
November 3, 2025 at 7:51 PM
For 40+ years, evolutionary ecologist Craig Benkman has tracked crossbills across North America—showing how these finches & conifers evolved together in a remarkable coevolutionary dance. 🌲🕊️
Their bill shapes even match the cones they feed on.
Full story: www.allaboutbirds.org/news/craig-b...
Their bill shapes even match the cones they feed on.
Full story: www.allaboutbirds.org/news/craig-b...
‘If we don’t end up cooperating, we lose out on future beneficial interaction.’
Commitment and cooperation: a coevolutionary relationship
Commitment and cooperation: a coevolutionary relationship
Commitment and cooperation: a coevolutionary relationship | Aeon Essays
Though natural selection favours self-interest, humans are extraordinarily good at cooperating with one another. Why?
buff.ly
February 20, 2025 at 3:36 PM
‘If we don’t end up cooperating, we lose out on future beneficial interaction.’
Commitment and cooperation: a coevolutionary relationship
Commitment and cooperation: a coevolutionary relationship
Coevolutionary phage training expands phage host range: Driven by tail fiber mutations in Pseudomonas aeruginosa lytic phage?
#phage #phagesky #mevosky
www.sciencedirect.com/science/arti...
#phage #phagesky #mevosky
www.sciencedirect.com/science/arti...
Coevolutionary phage training expands phage host range: Driven by tail fiber mutations in Pseudomonas aeruginosa lytic phage?
The rise of antibiotic-resistant bacteria, particularly multidrug-resistant Pseudomonas aeruginosa (P. aeruginosa), represents a critical challenge to…
www.sciencedirect.com
August 31, 2025 at 7:19 AM
Coevolutionary phage training expands phage host range: Driven by tail fiber mutations in Pseudomonas aeruginosa lytic phage?
#phage #phagesky #mevosky
www.sciencedirect.com/science/arti...
#phage #phagesky #mevosky
www.sciencedirect.com/science/arti...
Host Competitive Asymmetries Accelerate Viral Evolution in a Microbe–Virus Coevolutionary System - Liaghat - 2025 - Ecology Letters - Wiley Online Library onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
June 20, 2025 at 3:29 PM
Host Competitive Asymmetries Accelerate Viral Evolution in a Microbe–Virus Coevolutionary System - Liaghat - 2025 - Ecology Letters - Wiley Online Library onlinelibrary.wiley.com/doi/10.1111/...
EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals www.nature.com/articles/s41... 🧬🖥️🧪 #Rstats bioconductor.org/packages/Syn...
April 25, 2025 at 8:00 PM
EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals www.nature.com/articles/s41... 🧬🖥️🧪 #Rstats bioconductor.org/packages/Syn...
I’ll never look at avocados in quite the same way: The latest from UC Berkeley Miller Fellow Jeff Groh who sits in my lab and Ben Blackman’s lab. He works on balancing selection and molecular mechanisms underlying the coevolutionary phenomenon of mating type alternation (PhD with Graham Koop).
Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado https://www.biorxiv.org/content/10.64898/2025.12.22.695989v1
December 25, 2025 at 3:23 PM
I’ll never look at avocados in quite the same way: The latest from UC Berkeley Miller Fellow Jeff Groh who sits in my lab and Ben Blackman’s lab. He works on balancing selection and molecular mechanisms underlying the coevolutionary phenomenon of mating type alternation (PhD with Graham Koop).
GhostFold: Accurate protein structure prediction using structure-constrained synthetic coevolutionary signals www.biorxiv.org/content/10.1... #jcampubs
October 15, 2025 at 3:31 PM
GhostFold: Accurate protein structure prediction using structure-constrained synthetic coevolutionary signals www.biorxiv.org/content/10.1... #jcampubs
☕️ Do you know the origins of your cup of coffee? 🤔💭
When UC Berkeley professor Noah Whiteman opens a cabinet, he sees not just ingredients but the products of a four-billion-year-long coevolutionary war between plants and animals.
🔗 youtu.be/qf1WoW35BeQ?...
When UC Berkeley professor Noah Whiteman opens a cabinet, he sees not just ingredients but the products of a four-billion-year-long coevolutionary war between plants and animals.
🔗 youtu.be/qf1WoW35BeQ?...
Professor: Coevolutionary war gave us caffeine | 101 in 101
YouTube video by UC Berkeley
youtu.be
February 19, 2025 at 8:36 PM
☕️ Do you know the origins of your cup of coffee? 🤔💭
When UC Berkeley professor Noah Whiteman opens a cabinet, he sees not just ingredients but the products of a four-billion-year-long coevolutionary war between plants and animals.
🔗 youtu.be/qf1WoW35BeQ?...
When UC Berkeley professor Noah Whiteman opens a cabinet, he sees not just ingredients but the products of a four-billion-year-long coevolutionary war between plants and animals.
🔗 youtu.be/qf1WoW35BeQ?...
The commitment to collaborate. Though natural selection favours self-interest, humans are extraordinarily good at cooperating with one another [well, let’s hope so!]. Why? aeon.co/essays/commi...
Commitment and cooperation: a coevolutionary relationship | Aeon Essays
Though natural selection favours self-interest, humans are extraordinarily good at cooperating with one another. Why?
aeon.co
February 23, 2025 at 3:28 PM
The commitment to collaborate. Though natural selection favours self-interest, humans are extraordinarily good at cooperating with one another [well, let’s hope so!]. Why? aeon.co/essays/commi...
Can mutualists evolve stronger cooperation when partners keep changing? Experimental evolution in yeast shows that stable partnerships accelerate mutualistic benefits, even when they don't produce specialists. academic.oup.com/evlett/advan...
Temporal partner heterogeneity constrains the evolution of mutualistic benefits
Abstract. Evolutionary theory predicts that coevolutionary specialization between mutualistic lineages is beneficial, increasing the evolution of cooperati
academic.oup.com
September 25, 2026 at 2:48 PM
Can mutualists evolve stronger cooperation when partners keep changing? Experimental evolution in yeast shows that stable partnerships accelerate mutualistic benefits, even when they don't produce specialists. academic.oup.com/evlett/advan...
Why are juveniles often more vulnerable to infection? A new coevolutionary model shows pathogens can drive age-specific specialization in both infection and host resistance academic.oup.com/evlett/advan...
Pathogens pull hardest in the coevolutionary arms race to determine innate age-specific transmission biases
From humans to plants, juvenile individuals often represent a highly susceptible pool of hosts for infectious diseases. Surprisingly, recent work has sugge
academic.oup.com
September 21, 2026 at 1:36 PM
Why are juveniles often more vulnerable to infection? A new coevolutionary model shows pathogens can drive age-specific specialization in both infection and host resistance academic.oup.com/evlett/advan...
Delighted to share this paper out via Virus Evolution:
academic.oup.com/ve/advance-a...
in which we develop and assess a quantitative method to infer phage and bacterial mutations driving changes in infection phenotypes arising in coevolutionary dynamics.
a 🧵 about people (and some science)
academic.oup.com/ve/advance-a...
in which we develop and assess a quantitative method to infer phage and bacterial mutations driving changes in infection phenotypes arising in coevolutionary dynamics.
a 🧵 about people (and some science)
December 2, 2024 at 2:44 PM
Delighted to share this paper out via Virus Evolution:
academic.oup.com/ve/advance-a...
in which we develop and assess a quantitative method to infer phage and bacterial mutations driving changes in infection phenotypes arising in coevolutionary dynamics.
a 🧵 about people (and some science)
academic.oup.com/ve/advance-a...
in which we develop and assess a quantitative method to infer phage and bacterial mutations driving changes in infection phenotypes arising in coevolutionary dynamics.
a 🧵 about people (and some science)
The Purple-throated Carib females’ bills are longer and more curved than males. This sexual dimorphism has produced a coevolutionary relationship with bihai and caribbaea species of Heliconia plant, with each flower evolving color morphs that best attract their primary pollinator.
#huevember #birds
#huevember #birds
November 14, 2025 at 6:03 PM
The Purple-throated Carib females’ bills are longer and more curved than males. This sexual dimorphism has produced a coevolutionary relationship with bihai and caribbaea species of Heliconia plant, with each flower evolving color morphs that best attract their primary pollinator.
#huevember #birds
#huevember #birds
Why do species' ranges stop where they do? New theory shows that matching habitat choice can sharpen range boundaries and reinforce limits imposed by competition academic.oup.com/evlett/advan...
By Shirani and @benjaminfreeman.bsky.social
By Shirani and @benjaminfreeman.bsky.social
Coevolution of species’ range borders: Interactions between interspecific competition, gene flow, and matching habitat choice
Abstract. Existing theory examining the coevolutionary dynamics of species’ range borders assumes random dispersal, which causes maladaptive gene flow from
academic.oup.com
June 10, 2026 at 1:22 PM
Why do species' ranges stop where they do? New theory shows that matching habitat choice can sharpen range boundaries and reinforce limits imposed by competition academic.oup.com/evlett/advan...
By Shirani and @benjaminfreeman.bsky.social
By Shirani and @benjaminfreeman.bsky.social
Lack of coevolution should be default assumption, but it’s not, because it’s easy to imagine coevolutionary scenarios
But most microbial populations live very complicated lives
Multi level selection is hard when generation times orders of magnitude different and microbial environments are complex
But most microbial populations live very complicated lives
Multi level selection is hard when generation times orders of magnitude different and microbial environments are complex
February 14, 2026 at 7:15 PM
Lack of coevolution should be default assumption, but it’s not, because it’s easy to imagine coevolutionary scenarios
But most microbial populations live very complicated lives
Multi level selection is hard when generation times orders of magnitude different and microbial environments are complex
But most microbial populations live very complicated lives
Multi level selection is hard when generation times orders of magnitude different and microbial environments are complex
Our new @science.org paper is out! Cuckoos and hosts are locked in a coevolutionary arms race over egg mimicry.
But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!
doi.org/10.1126/scie...
🧵1/6
But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!
doi.org/10.1126/scie...
🧵1/6
Genomic architecture of egg mimicry and its consequences for speciation in parasitic cuckoos
Host-parasite arms races facilitate rapid evolution and can fuel speciation. Cuculus cuckoos are deceptive egg mimics that exhibit a broad diversity of counterfeit egg phenotypes, representing host-ad...
doi.org
October 30, 2025 at 7:15 PM
Our new @science.org paper is out! Cuckoos and hosts are locked in a coevolutionary arms race over egg mimicry.
But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!
doi.org/10.1126/scie...
🧵1/6
But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!
doi.org/10.1126/scie...
🧵1/6
Coevolutionary cycling in allele frequencies and the evolution of virulence https://www.biorxiv.org/content/10.1101/2025.05.22.655598v1
May 27, 2025 at 7:33 PM
Coevolutionary cycling in allele frequencies and the evolution of virulence https://www.biorxiv.org/content/10.1101/2025.05.22.655598v1