Jukka-Pekka Verta

Preprint alert: We adopt a cheap & rapid WGS protocol for vertebrate sized genomes, and use it to sequence nearly 1K whitefish genomes to low/med coverage for lake-wide pop genomics of adults + larvae for species assignment, habitat use, decline & selection: www.biorxiv.org/content/10.6...

#PopGen

Transgenerational plasticity affects fitness and mediates local adaptation https://www.biorxiv.org/content/10.1101/2025.11.23.690023v1

Evening views from home, morning views from the office

CDFW: 'Salmon Everywhere' One Year After Klamath River Dam Removal A little more than a year after the historic removal of four hydroelectric dams on the Klamath River, California Department of Fish and Wildlife (CDFW) scientists are seeing salmon reoccupying just ab...

A beautiful story of success amid all the carnage. Turn a river loose and it heals.

CDFW: 'Salmon Everywhere' One Year After Klamath River Dam Removal www.dailykos.com/stories/2025... || #rivers

Genuinely one of the most important and interesting papers I have been a part of! Relevant to fundamental questions regarding the predictability of adaptation, as well as the applications of genomic data. Congrats to @j-smiley-rhodes.bsky.social and all co-authors for such a masterpiece!

North of the Arctic Circle it’s winter wonderland already

Excited to share our review on alternative splicing evolution, with @peterinnes1.bsky.social and Nolan Kane!

Join Us The lab of Nina Overgaard Therkildsen in the Department of Natural Resources and the Environment at Cornell University invites applications for a PhD position starting in Fall 2026. Our group works...

Excited to recruit a new PhD student for Fall 2026 in my lab at Cornell! Looking for someone interested in evolutionary genomics + fisheries/conservation applications. Quick timeline this year—reach out soon. More details: www.therkildsenlab.org/join-us.html

New paper from the lab: we’re using long-read sequencing to disentangle isoform complexity at allele-specific loci 🧬💡
Here, we combine the PacBio Iso-Seq workflow with the established WhatsHap phasing approach to assign long reads to the correct allele in polymorphic F1 mouse hybrids.

Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...

Interested in doing a PhD in how extinction processes can inform conservation? Do you see yourself working at the intersection of genomics, museums, conservation and butterfly biology. If so consider applying for the ILESLA PhD programme at Oxford Brookes: www.brookes.ac.uk/courses/rese...

This was such a shocking thing to hear, even having already been told how bad it was...

Big Biology guest Dr. Katie Lotterhos reads out the banned word list given to a federal scientist. ❌ 😶 📋

Learn more about the impacts of federal and state policies on science since January 2025 by listening to the full episode with Katie: bigbiology.substack.com/p/vulnerabil.... 🎧

#science #bio

Monty Python understood p-hacking

Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...

One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential.

www.biorxiv.org/content/10.1...

They might not be giants: The genetics behind why some fish remain tiny Imagine you are a kind of fish called a goby, part of a huge family of more than 2,000 species. Maybe you're of average size for a goby, about three to four inches long.

Certain goby fish species remain miniature by overexpressing genes that inhibit growth, a genetic mechanism conserved for over 50 million years and shared across diverse vertebrates. doi.org/g97pqp

I'll be reviewing applications for this in a few days, so there's still time to get touch if you're interested.

💥 Another fruitful collaboration!

Along with @obog.bsky.social & Juan Tena’s teams we provide a multiomics study of zebrafish spermatogenesis
🐟#meiosis

👇
www.embopress.org/doi/full/10....

PhD OPPORTUNITY! 🔬🔖

Still one more day to apply for our fully-funded PhD position in Norway!

Please share widely 🙏

Inversions 😊

www.biorxiv.org/content/10.1...

Thank you so much Rob!

One week to apply for our fully funded PhD position in Norway! This is a really exciting project in collab. with University of Helsinki and Benchmark Genetics.

Samples are ready - you do (read: learn) everything - functional genomics, bioinformatics, genotype-phenotype associations 🤩

Please RT!

By extending the comparative model we can assay the evolutionary signal in evolvability itself and test a number of biologically interesting trait configurations (codivergence, contra-divergence, ceiling effects, phenotypic integrations and more!)

First northern lights since the sun started setting again here above the Arctic Circle

Jane Goodall, ethologist and conservationist, has died. She was 91

Surprised and excited that Atlantic salmon testis is a fertile ground for uncharacterized transcripts!

Huge thanks to my supervisors @fishcongen.bsky.social and @jpverta.bsky.social and all coauthors for their support. Grateful to have our first paper from my PhD out!

bsky.app/profile/fish...

A comprehensive analysis of Atlantic salmon gonad and pituitary transcriptomes identifies novel players in sexual maturation - BMC Genomics Sexual maturation is a key developmental process important for reproductive success. Understanding the molecular mechanisms behind variation in sexual maturation can provide insights into reproductive biology and how life history variation is encoded in the genome. Atlantic salmon (Salmo salar) has become an excellent sexual maturation research model due to its diversity of life history strategies and its ecological and economic importance. A major challenge has been the lack of a comprehensive transcriptional investigation of reproductive tissues that captures the dynamic transcriptional changes across individuals, tissues, and developmental stages. Long non-coding RNAs (lncRNAs) also play crucial roles in maturation, yet their functions in salmon maturation remain underexplored. In this study, we sequenced 98 transcriptomes and found substantial transcriptomic complexity in the gonad and pituitary tissues of Atlantic salmon. We identified transcripts corresponding to 2,364 putative newly characterized protein-coding genes and 4,421 putative long intergenic non-coding RNAs (lincRNAs), many with tissue-specific expression. Gene co-expression network analysis (WGCNA) revealed tissue-specific gene network modules, linked to GO terms including Wnt signaling in immature testis, lipid metabolism, and cilia assembly in mature testis, ribosome biogenesis and DNA repair in the ovary, and hormone activity in pituitary. We identified new copies of known genes, such as gh1, pou3f2, and ier5 associated with the regulation of gonadal and pituitary functions. Some lncRNAs and their nearest genes showed correlated expression within modules, suggesting potential regulatory roles. Candidate lincRNAs indicated cis-acting regulatory potential on genes like tnfrsf11b and fgl1, which are implicated in immune privilege during gonadal development and sperm quality control. Our study provides a comprehensive transcriptomic analysis of Atlantic salmon gonad and pituitary tissues, significantly improving the functional annotation of the Atlantic salmon genome. These findings reveal key regulatory pathways and novel molecular players involved in sexual maturation, particularly in the testis. Importantly, our study highlights the regulatory potential of lncRNAs in reproductive biology and maturation age variation, advancing our understanding of the molecular mechanisms governing sexual maturation. They further unlock future gene expression analyses and regulatory network reconstruction for dissecting the roles of lncRNAs in Atlantic salmon life history variation.

Surprise 🤗 So many uncharacterized transcripts in Atlantic salmon, including super interesting long non-coding RNAs!

Proud to share the 1st publication of Xindi Huang:

link.springer.com/article/10.1...

With @fishcongen.bsky.social

🖥️🧬🦑

Predicting the structural impact of human alternative splicing. #AlternativeSplicing #GenomeBiology
genomebiology.biomedcentral.com/articles/10....

Strong but diffuse genetic divergence underlies differentiation in an incipient species of marine stickleback https://www.biorxiv.org/content/10.1101/2025.09.19.677379v1