Jukka-Pekka Verta

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

Symposium in Lund September 25th The cellular roots of evolutionary change Sep 25 14:30 - 17:00 Blå hallen, Ekologihuset, Sölvegatan 37, Lund How does cell- and developmental biology improve our understanding of the evolutionary process? Join us for an afternoon of discussions about cells, development and evolution. Program 14:30 Introduction 14:40 Arild Husby, Plasticity of a life history trade-off: from GRN to high level phenotypes 15:10 Markéta Kaucká, Cell type evolution 15:40 Coffee break 16:00 Gunter Wagner, From cells to tissues and organs: nothing in evolutionary biology makes sense except in the light of cell biology 16:30 Emilia Santos, Interplay between genetics and phenotypic plasticity in the adaptation to novel environments Bonus Sep 26: 09:00 Robin Pranter, Thesis defense - Neural crest cells and the evolution of a phenotypic syndrome Lund University

How does cell end developmental biology inform our understanding of evolution? Join us for an afternoon of discussion about #cells, #development, #plasticity and #evolution.
Zoomlink Sep 25th: lu-se.zoom.us/j/62473328732
Zoomlink Sep 26th: lu-se.zoom.us/j/67411449026
#EvoDevo @biologylu.bsky.social

Why do males and females often differ in traits?
The expected answer: selection.
But our new paper in GENETICS shows that genetic drift alone can generate sexual dimorphism — even when male & female optima are the same

There’s a leak - and a conceptual artist - at the Max Planck 👌

⏳ Only 2 weeks left to apply to our PhD in evolutionary prediction!

Very excited to see this work in press! I think there is a reason to believe that this is a common means of stabilizing large-effect polymorphisms in general and might be an important reason for why diploidy is so common. news.stanford.edu/stories/2025...

What we show here is that beneficial dominance reversal does operate for alleles of large effect in real natural systems under fluctuating selection and we argue that it should be common for many such systems. Hope this helps. n/n

Top: Dscam1 gene structure and isoform diversity in pancrustacean species. Top: Schematic diagrams of Drosophila melanogaster Dscam1 gene and protein structure. The variable exons or domains are shown in color, while the constant exons or domains are shown in gray. Middle: Phylogenetic distribution of Dscam1 isoform diversity. A phylogenetic tree of Pancrustacean species is shown in the lower panel. The upper panel shows distribution of the number of exons in variable exon 4, exon 6, or exon 9 clusters in Pancrustacean species, with variable exon clusters shown in different colors. The middle panel shows distribution of the number of potential ectodomains diversity, where species with a special number of diversities are highlighted. Bottom: Reducing the Dscam1 diversity affects adult survival upon Beauveria bassiana infection. Survival curves after Triton or B. bassiana infection for wild-type and exon 4 (left), exon 6 (middle), and exon 9 (right) mutants are shown, respectively. The Triton groups (control) are represented by solid lines, while the B. bassiana groups are represented by dashed lines.

The #Drosophila Dscam1 gene generates 10000s of isoforms, but only a small fraction supports neuronal functions. This study shows that #fitness & #immunity are the likely primary evolutionary drivers of Dscam1 isoform diversity in #arthropods @plosbiology.org 🧪 plos.io/4gp8cWd

Beyond supergenes: the diverse roles of inversions in trait evolution Chromosomal inversions are ubiquitous across the Tree of Life, with genome-wide studies revealing a bias toward smaller inversions, yet research has disproportionately focused on large, supergene-like...

Beyond supergenes: the diverse roles of inversions in trait evolution www.cell.com/trends/ecolo...

PhD position in Carrion & Invasive Species Ecology (283012) | Nord University Job title: PhD position in Carrion & Invasive Species Ecology (283012), Employer: Nord University, Deadline: Sunday, September 21, 2025

📢 Exciting PhD fellowship with a great mix of ecosystem ecology and invasion biologie in Northern Norway! www.jobbnorge.no/en/available...

Skreien er annerledes i dag enn for 100 år siden Torsken er ikke genmanipulert. Endringene er menneskeskapte, ifølge ny forskning.

Høyt fiskepress har endret alder for kjønnsmodning og genetisk sammensetning hos Barents-torsken, som er verdens største gjenværende torskebestand.

Også på Grand Banks gikk gytealderen ned før kollapsen var et faktum www.forskning.no/dna-fisk-hav...

How is this possible?

This ant can lay eggs of two different species, birthed by the same mother

🚨 We're hiring!
PhD position in Evolutionary Systems Biology at Stockholm University & SciLifeLab

🎓 Focus: evolution, development, computational & mathematical modeling, prediction
📍 Stockholm, Sweden
🕒 4 years, fully-funded
🔍 Details: su.varbi.com/en/what:job/...

Please share!

How do regulatory genes control alternative life histories? We have an open PhD position to answer this question using functional genomics in Atlantic salmon.

Apply by October 15th through www.jobbnorge.no/en/available...

Please share widely! 🧬🦑🖥️

I'm looking to recruit a PhD student to study patterns of local adaptation and introgression across the spruce hybrid zone in the Rockies near Calgary. Projects can include field work, bioinformatics, pop gen theory, or comparison to plant/ conifer species
yeamanlab.weebly.com/uploads/5/7/...