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Haoran Cai

@haorancai.bsky.social
430 followers 329 following 31 posts

Evolutionary and Quantitative Genetics | Evolutionary Systems Biology | GP map | Complex trait | haorancai.github.io Post-doc @UCLA EEB

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Reposted by Haoran Cai
Alejandro Fábregas-Tejeda @alejandrofabregastejeda.com · 11/08/2026
As simulations grow in complexity, a set of non-trivial issues emerge: diminished identifiability as free parameters become too numerous relative to exp. constraints & difficulties grasping causality. In our new 📄, we point to potential avenues to move #CellBio forward 👇 arxiv.org/abs/2608.06998
arxiv.org
Simulating is not always understanding: When model complexity obscures biology
In cell biology, computational models of biological systems range from minimal representations with a handful of parameters to whole-cell simulations tracking thousands of molecular species across a c...
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Molecular Biology and Evolution @molbioevol.bsky.social · 16/09/2026
@haorancai.bsky.social @kgslab.bsky.social & @evodaveo.bsky.social show that genetic correlations are more environmentally stable when driven by polygenic background correlation across many loci, vs. a few large-effect pleiotropic outliers 🔗 academic.oup.com/mbe/article/... #societyjournal #evobio
academic.oup.com
Consistent and idiosyncratic pleiotropy in shaping genetic correlations
Abstract. Pleiotropy, the phenomenon where a single mutation influences multiple phenotypic traits, creates genetic correlations that can constrain evoluti
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Graham Coop @gcbias.bsky.social · 10/09/2026
I’m looking to hire an NIH funded postdoc to join our lab here at Davis (please RT). Ongoing areas of interest include: 1) polygenic signals of selection from time series, ARGs, GWAS, etc 2) The interpretation of GWAS, polygenic scores, & sources of confounding
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Luis-Miguel Chevin @lmchev.bsky.social · 09/09/2026
Now out in PNAS: our latest exploration of the interplay between interspecific interactions and adaptation to a changing abiotic environment! This time it’s about predator-prey interactions. www.pnas.org/doi/10.1073/...
pnas.org
Coadapting but not static predators facilitate prey adaptation to a fluctuating environment | PNAS
Understanding how between-species interactions influence adaptation and population persistence in the face of environmental change is one of the gr...
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Alejandro Fábregas-Tejeda @alejandrofabregastejeda.com · 08/09/2026
Interesting 📰 @theguardian.com by @samanthsubramanian.bsky.social on non-neural cognition: www.theguardian.com/news/ng-inte... Confronted with this polarizing debate, @philosobio.bsky.social & I wrote a balanced take on basal #cognition from an #evobio lens 👇 link.springer.com/article/10.1... #HPS
theguardian.com
‘This is dangerous’: slime moulds and the bitter debate over the nature of intelligence
The long read: Scientists are battling over whether supposedly simple organisms should be considered ‘intelligent’. The outcome could reshape our understanding of the natural world – and our own place...
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Sam Yeaman @samyeaman.bsky.social · 08/09/2026
I'm looking to hire a postdoc to work on the RepAdapt + MacroMar projects, analysing genomic data from >130 species of plants, animals, and fungi (VCFs are processed, ready to go). Lots of potential for creativity and collaboration! yeamanlab.weebly.com/uploads/5/7/...
Picture shows fireweed in foreground and Mt. Lougheed in background
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Altmetric @altmetric.com · 08/09/2026
Update: The academic flight from Twitter is now complete and appears permanent. April 2023, after the pandemic research surge, we recorded 2,234,307 posts sharing research on Twitter. As of April this year, "X" had 896,741 posts about research. That's a 60% drop in traffic.
Graph showing cumulative research sharing across platforms, including Twitter - April 2023Graph of April 2026 cumulative research sharing including "X". One third of what it was.
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Thomas Lenormand @thomaslenormand.bsky.social · 01/09/2026
🚨Interested in #evolutionary #genomics and #popgen #theory? My lab just opened a 1+ year #postdoc position to work on sex chromosome dosage compensation. At #CEFE in beautiful Montpellier. Deadline soon, don't be shy, apply, theory is exciting! 👉 bit.ly/4eMWDIh
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David Lowry @davidlowry.bsky.social · 31/08/2026
I am currently searching for a postdoc to work on the evolution of adaptations, cold acclimation, and freezing tolerance in switchgrass. The position entails lab, growth facility, bioinformatics, and fieldwork. careers.msu.edu/jobs/postdoc...
careers.msu.edu
Postdoctoral Scholar-Fixed Term - East Lansing, Michigan, United States
Position Summary The Lowry Lab at Michigan State University is searching for a postdoctoral research associate to conduct field and laboratory experiments to understand the causes of genetic variation...
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MEPGT @mepgt.bsky.social · 30/08/2026
Very important paper by @phylogenetrips.bsky.social "Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale" | PNAS www.pnas.org/doi/10.1073/...
pnas.org
Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale | PNAS
Adaptation in protein-coding sequences can be detected from multiple sequence alignments across species or alternatively by leveraging polymorphism...
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Haoran Cai @haorancai.bsky.social · 27/08/2026
Now out @molbioevol.bsky.socialGenetic correlations summarize how traits covary, but they can hide different underlying architectures. Distinguishing those architectures can reveal distinct mechanisms generating—and potentially constraining—trait–trait relationships. academic.oup.com/mbe/advance-...
academic.oup.com
Consistent and idiosyncratic pleiotropy in shaping genetic correlations
Abstract. Pleiotropy, the phenomenon where a single mutation influences multiple phenotypic traits, creates genetic correlations that can constrain evoluti
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Matthew Hahn @3rdreviewer.bsky.social · 31/07/2026
Very cool pair of papers demonstrating little link between amount of additive genetic variation and amount of nucleotide variation within species: journals.plos.org/plosbiology/... www.pnas.org/doi/10.1073/...
journals.plos.org
Levels of additive genetic variation vary substantially between species
Adaptive potential determines how populations respond to environmental change. This study compiles evolvability estimates from over 170 multicellular species, revealing substantial variation across th...
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 29/07/2026
We remind the SMBE community that applications for the second edition of the SMBE Fellows Program are ongoing. Apply before August 15. 🔗 smbe.org/smbe-fellows-program #society
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 01/07/2026
Two journals, two editorial boards, the same service to science. The SMBE and our research community as a whole are indebted to our colleagues who dedicate their effort and expertise to handling manuscripts in the service of MBE and GBE. #society #societyjournal #SMBE2026
SMBE 2026 | MBE Editorial BoardSMBE 2026 | GBE Editorial Board
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Pedro Andrade @evopaa.bsky.social · 29/06/2026
The new SMBE Fellows call is now live! Early career researchers (PhD students or postdocs) interested in #scicomm can apply before August 15. If you're at #SMBE2026 and considering joining, let's meet up and chat 🙂
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Dave Des Marais @evodaveo.bsky.social · 24/06/2026
news.mit.edu/2026/tenured...
news.mit.edu
The tenured engineers of 2026
MIT School of Engineering faculty Jacob Andreas, Zachary Cordero, Christina Delimitrou, Sili Deng, David Des Marais, Carmen Guerra-Garcia, Laura Lewis, Tami Lieberman, Kevin O’Brien, and Wim van Rees ...
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Haoran Cai @haorancai.bsky.social · 25/06/2026
New paper out @pnas.org: We explore why fly wings evolve along "lines of least resistance" and reconcile the "rate paradox" between population variation and divergence. Check out how a low dimensional model of selection on size explains it all: www.pnas.org/doi/full/10....
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Itai Yanai @itaiyanai.bsky.social · 24/06/2026
Real science: 1. Is not correlated with the amount of funding 2. Progresses slowly, usually taking many years 3. Leads to more questions than it answers 4. Advances when we disengage a bit and have improvisational discussions 5. Is too serious a thing to be done in a non-playful way
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PLOS Biology @plosbiology.org · 19/06/2026
How do species differ in their ability to #adapt to environmental change? This study by Lillith Zijmers, Adam Eyre-Walker &co estimates #evolvability from over 170 multicellular species, revealing that #plants exhibit greater adaptive potential than animals. 🧪#AcademicSky plos.io/4vk2TON
The predicted evolvability from the authors' model for a linear, morphological trait estimated from a wild population for each species, plotted across the phylogeny with their 95% credible intervals. Evolvability estimates for plants are higher than for other groups.
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Chuliang Song @clsong.com · 16/06/2026
Spent the last two years developing a new Intro to Physics course for undergrad biology majors. It features tons of examples from biology (especially Ecology & Evolution!) and requires only middle school-level math. Lecture note here shorturl.at/0PiVp Any comments or feedback are highly welcome!
drive.google.com
physics_for_biologists.pdf
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Jitka Polechová @polejit.bsky.social · 12/06/2026
Are you looking for a PhD on the intersection between evolutionary and ecological theory? Join us @univie. Fully funded PhD position in fundamental eco-evolutionary theory, open to international students. Apply by 13.7.2026: ecoevo.owlstown.net/search Reposting appreciated. #evolbio #evoeco #ecology
ecoevo.owlstown.net
Jitka's EcoEvo Lab - Jobs
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John Stinchcombe @johnstinchcombe.bsky.social · 07/06/2026
Why are leaves the shape that they are? What controls intraspecific, genetic variation in leaf shape? New from my lab, in collaboration with many others, led by PhD student Amanda Peake: mapping the leaf shape polymorphism in Ipomoea hederacea.
Homozygous recessive entire leaf of Ivyleaf morning gloryHomozygous dominant, lobed leaf of Ivyleaf morning glory
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American Naturalist / ASN 🐌 @asn-amnat.bsky.social · 19/03/2026
Exploring the Genotype-to-Phenotype Map Using Quantifiable Patterns in Metazoan Genomic and Morphological Data by Peterson et al. Available now ahead of print! www.journals.uchicago.edu/doi/10.1086/...
The American Naturalist classic cover
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Genome Biology and Evolution @genomebiolevol.bsky.social · 27/05/2026
For this month's GBE Highlight, SMBE Fellow Haoran Cai delves into Adey et al., who investigated the role of pervasive transcription in the human genome. @haorancai.bsky.social 🔗 doi.org/10.1093/gbe/evag104 #genome #evolution #highlight
GBE | Highlight: “Dark” or “Junk”? Functional Roles of Pervasive Transcription in the Human Genome
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Sasha Gusev @sashagusevposts.bsky.social · 23/05/2026
I assigned random gender/ethnicity labels to scientific abstracts from the literature and then asked Claude to do a thematic analysis. Claude identified a clinical versus computational split for female/male authors and a DEI focus for Black/URM authors. All in completely random data.
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Daohan "Rex" Jiang @rexjiang.bsky.social · 22/05/2026
I'm presenting this study for the virtual meeting of @evolmtg.bsky.social on May 22 at 6:15 PM Eastern Time. Please come!
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Evolution @journal-evo.bsky.social · 18/05/2026
Be sure to read the Invited Commentary by Brian Charlesworth, "How is variation in fitness maintained?" academic.oup.com/evolut/artic...
academic.oup.com
How is variation in fitness maintained?
Abstract. The existence of substantial additive genetic variance in fitness poses a long-standing question for evolutionary geneticists. A new theoretical
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Kevin Bird @stairwaytokevin.bsky.social · 18/05/2026
First real post on the new blog! If you follow human genetics, you've likely of "missing heritability". If you look at twins to estimate heritability, you get values much larger than what molecular genomic methods produce. IQ, for example, goes from 50-80% heritability to 10-15%. Which is right?
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Genome Biology and Evolution @genomebiolevol.bsky.social · 18/05/2026
This article is the focus of this month's GBE Highlight, written by SMBE Fellow Haoran Cai. @haorancai.bsky.social “Dark” or “Junk”? Functional Roles of Pervasive Transcription in the Human Genome 🔗 doi.org/10.1093/gbe/evag104
doi.org
“Dark” or “Junk”? Functional Roles of Pervasive Transcription in the Human Genome
Highlights editor: Laura A. Katz, Maud Tenaillon
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Haoran Cai @haorancai.bsky.social · 18/05/2026
I’m looking forward to presenting my project on the puzzles of fly wings evolution at the Evol-Mut-Circle seminar Tuesday, May 19th at 11:00 AM EDT/3:00 PM UTC molevol.org/2025/12/08/e... DM me for the Zoom info, or reach out to Arlin Stoltzfus (evolarlin@gmail.com) to sign up for the email list!
molevol.org
evol-mut-circle
evol-mut-circle is an international group of scientists, philosophers, and historians interested in research on the role of mutation in evolution, particularly as a dispositional factor. The group …
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Alex Cope, PhD (he/him) @alexcope241.bsky.social · 13/05/2026
I'm looking for postdoc opportunities for the 2026-2027 academic year. If you're looking for a postdoc with a broad skill set spanning evolutionary genetics, bioinformatics, and various omics methods, feel free to reach out. Some recent pubs: (1) doi.org/10.1126/scie... (2) doi.org/10.1073/pnas...
doi.org
Macroevolutionary divergence of gene expression driven by selection on protein abundance
The regulation of messenger RNA (mRNA) and protein abundances is well-studied, but less is known about the evolutionary processes shaping their relationship. To address this, we derived a new phylogen...
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Jae Young Choi @jychoi.bsky.social · 30/04/2026
I'm looking to hire a postdoc. Please share if you can!
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Mauricio González-Forero @mauriciogforero.bsky.social · 27/02/2026
New preprint: "A mathematical synthesis of genetics, development, and evolution". This work addresses the longstanding challenge of integrating these and finds a way. I think it has broad implications and offers exciting opportunities. Feedback welcome! www.biorxiv.org/content/10.6...
biorxiv.org
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Genome Biology and Evolution @genomebiolevol.bsky.social · 24/04/2026
This month's GBE Highlight by SMBE @haorancai.bsky.social focuses on the recent paper by Bastian, Enard & Lartillot on the nearly neutral theory. "Bridging Micro- and Macroevolution: Phylogenomic Evidence for the Nearly Neutral Theory in Mammals" 🔗 doi.org/10.1093/gbe/evag074 #genome #evolution
GBE Highlight | Bridging Micro- and Macroevolution: Phylogenomic Evidence for the Nearly Neutral Theory in Mammals
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PolyAdapt STN @polyadapt-stn.bsky.social · 13/04/2026
Join us for a seminar by Dr. Francois Mallard (Institute de Biologie, École Normale Supérieure, Paris-France) about 'The genetic architecture of phenotypic plasticity' on 30th April, 2026, 3 pm CET. Zoom link here: polygenic-adaptation-network.org/seminars/
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Genome Biology and Evolution @genomebiolevol.bsky.social · 09/04/2026
@haorancai.bsky.social and Des Marais investigated gene expression variability in duplicate genes, suggesting a mechanism facilitating gene expression divergence, functional gains, and duplicate retention following small-scale duplications. 🔗 doi.org/10.1093/gbe/evag077 #genome #evolution
doi.org
Dynamics of Expression Variability Contribute to Retention of Small-Scale vs. Whole-Genome Duplicates
Abstract. Genome analyses reveal that gene duplication in eukaryotes is pervasive, providing a primary source for the emergence of new genes. Nevertheless,
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Genome Biology and Evolution @genomebiolevol.bsky.social · 06/04/2026
Bastian, Enard & Lartillot tested predictions of the nearly-neutral theory of molecular evolution across time scales, confirming the role of effective population size in tuning selection efficacy in placental mammals. 🖌️ Léa Backory 🔗 doi.org/10.1093/gbe/evag030 #genome #evolution
GBE | Empirical Validation of the Nearly Neutral Theory at Divergence and Population-Genomic Scales Using 144 Placental Mammal Genomes

Figure credit: Léa Backory, Instagram: @lea_faitdesvagues
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Haoran Cai @haorancai.bsky.social · 05/04/2026
🚨 New Paper 🚨 Thrilled to share new work with @evodaveo.bsky.social eo.bsky.social! We dive into the evolution of gene duplicates and demonstrate how expression variability might contribute to retention following duplication. Read the full article here: academic.oup.com/gbe/article/...
academic.oup.com
Dynamics of Expression Variability Contribute to Retention of Small-Scale vs. Whole-Genome Duplicates
Abstract. Genome analyses reveal that gene duplication in eukaryotes is pervasive, providing a primary source for the emergence of new genes. Nevertheless,
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Sergey Kryazhimskiy @skryazhi.bsky.social · 04/04/2026
We posted a new theory preprint. I am very interested to hear what the community thinks about it. We looked at the dynamics of evolution on several (simple) models of modular genotype-phenotype-fitness maps and found that populations approach a quasi-steady state we call "module-selection balance".
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Quentin Horta @quentinevo.bsky.social · 02/04/2026
Our work as Editor's choice in @evolletters.bsky.social !✨️ Developmental biases & micro- to macroevution in the lizard skull 🦎 academic.oup.com/evlett/advan...
Lizard head on the journal
cover
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Kim Cooper @ucsdcooperlab.bsky.social · 29/03/2026
The Cooper lab is hiring a postdoc with a strong background in mouse genetics and molecular biology to advance.our gene drive work. Must be extremely organized, engineering-minded, and outcomes-oriented. Spread the word and have interested candidates email me directly.
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Nora Martin @n-martin.bsky.social · 17/03/2026
New group website: www.noramartin-lab.com Get in touch if you are interested in joining the group, or know anyone who might be 📮
noramartin-lab.com
HOME | Martin Lab
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Lisandro Milocco @milocco.bsky.social · 12/03/2026
How does development shape the variation evolution can act on? In our new paper in @pnas.org , we bridge developmental dynamics and quantitative genetics, linking dynamical models of phenotype formation with the statistical parameters used to study evolutionary change www.pnas.org/doi/10.1073/...
pnas.org
Bridging developmental and statistical approaches to variation and evolution | PNAS
Phenotypic variation is the raw material for evolutionary diversification and adaptation. However, a critical gap remains in evolutionary theory be...
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Neda Barghi @nedabarghi.bsky.social · 12/03/2026
Join us for this exciting seminar and hear about redundancy in genome-wide epistatic interactions!
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Robin Pranter @robinpranter.bsky.social · 27/02/2026
How does development affect the evolutionary process? Join our symposium at www.evodevoconference26.com in Glasgow this June. We have a strong lineup of invited speakers, chaired by me and @milocco.bsky.social Submit your abstract before Thursday! ⏰
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Masahito Tsuboi @masahitotsuboi.bsky.social · 08/07/2025
Now online ‪Communications Biology!‬ We showed that variation aligns across biological levels. We proposed that #macroevolution mould #developmentalbias with a cascading effect on variation. #Microevolution, then, may be a result—not a cause of—macroevolution. nature.com/articles/s42...
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David Lowry @davidlowry.bsky.social · 02/03/2026
Weighted Gene Co-expression Network Analysis (WGCNA) has been the go to program for analysis of gene expression modules for nearly two decades but it is a difficult to implement. To make it easier to use WGCNA, I used Codex to build a human in the loop agentic workflow. github.com/lowrylab/WGC...
github.com
GitHub - lowrylab/WGCNA_agent
Contribute to lowrylab/WGCNA_agent development by creating an account on GitHub.
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Lee Hsiang Liow (廖珕庠) @lhliow.bsky.social · 28/02/2026
2 PhD & 1 postdoc available at BioM in Oslo www.uio.no/english/rese... Interdisciplinary methods to model and govern biodiversity under uncertainty. Re-post widely! Work with statistical ecologists Olav Skarpaas (Natural History Museum Oslo @uio.no) @t-ergon.bsky.social
uio.no
Methods for knowledge-based biodiversity monitoring and management under uncertainty (BioM) - UiO:Life Science
BioM develops new interdisciplinary methods to model and govern biodiversity under uncertainty, combining ecology, statistics, and philosophy. The project delivers predictive tools, normative framewor...
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Jenn Coughlan @jenncoughlan.bsky.social · 25/02/2026
Promises to be poppin (🍿) BUT SRSLY PLEASE REGISTER, WE ARE SO EXCITED!!!!!!!!!!!!
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