Franz Baumdicker

1/6 Excited to share our review 🚀
🧬 CRISPR–Cas therapies targeting bacteria!
#MicroSky

The PopSim Consortium wants you! Please join us on zoom on May 27 at noon Eastern Time (1600 UTC) to tell us you would like to see in the next version of stdpopsim! DM me for meeting link, or just sign up for our email list: lists.uoregon.edu/mailman/list... (1/3)

Abstract deadline for @eseb2025.bsky.social extended to 5 May! Still time to submit your abstract for the evolution of microbial pangenomes ⬇️

If you are interested in microbial #pangenomes, join us at @eseb2025.bsky.social in Barcelona with @bjesseshapiro.bsky.social and @annadewar.bsky.social
Only two days left to submit your abstract!
eseb2025.com/call-for-abs...

Join our symposium The evolution of microbial pangenomes at @eseb2025.bsky.social with @bjesseshapiro.bsky.social and @annadewar.bsky.social (co-organized with @fbaumdicker.bsky.social and Jaime Iranzo) eseb2025.com/call-for-abs...

Accessible, realistic genome simulation with selection using stdpopsim Selection is a fundamental evolutionary force that shapes patterns of genetic variation across species. However, simulations incorporating realistic selection along heterogeneous genomes in complex de...

stdpopsim v0.3.0 is out! You can now mix and match your simulations of different demographic histories with published distributions of fitness effects along with gene annotations, and you can even throw in sweeps for good measure. Check out the new manuscript for more info: doi.org/10.1101/2025...

Using genomics to explore the ecology and evolution of plant-associated microbial populations and communities? 🌿

Submit an abstract by March 11 and join us in Cologne this July for #ISMPMI2025! We serve cool science + cold German beer 🍻 Join the party: buff.ly/uqEfN6O

Save the date for the second conference on Machine Learning for Evolutionary Genomics Data!

YouTube video by Eberhard Karls Universität Tübingen Thesencheck - Über diese 11 Behauptungen zur Klimapolitik lässt sich streiten

In unserer neuen "Thesencheck" Episode diskutiert Politikwissenschaftlerin Dr. Melanie Nagel 11 populäre Thesen zur Klimapolitik.💦🌞🌬️💻 youtu.be/xcjqTgDsfC0

Damit ist sie die 5. Tübinger Forscherin, die im "Thesencheck" in der Öffentlichkeit herumwabernde Aussagen mit ihrer Expertise betrachtet.🔍👩‍🔬

PopGen Seminar Series Summer Term 2025 04.03.25 – Lutz Becks (Univ. of Konstanz, DE)
The evolutionary dynamics of novel endosymbiosis. 11.03.25 – Ilkka Kronholm (Univ. of Jyväskylä, FI)
How chromatin structure influences genetic and epigenetic variation. 18.03.25 – Katja Hoedjes (Vrije Univ. Amsterdam, NL)
Understanding functional impact of genetic variation on complex traits at a single nucleotide resolution. 25.03.25 – Sophie Armitage (Freie Univ. of Berlin, DE)
Evolutionary ecology of host-pathogen interactions. 01.04.25 – Matthew Rockman (New York Univ., US)
Developmental evolution is a population-genetics problem. 08.04.25 – Wen-Juan Ma (Vrije Univ. Brussels, BE)
The evolution of sex chromosomes and sex determination in frogs. 15.04.25 – Almorò Scarpa (Vetmeduni, AT)
Two centuries of transposable element invasions in Drosophila melanogaster 22.04.25 – Julia Kreiner (Univ. of Chicago, US)
The mode and tempo of genomic adaptation to contemporary agriculture. 29.04.25 – Martin Kaltenpoth (Max Planck Inst. for Chemical Ecology, DE)
Microbial symbionts as sources of evolutionary innovations in beetles. 06.05.25 – Luisa Pallares (Friedrich Miescher Laboratory, DE)
Phenotypic robustness across the genotype-phenotype map, from genes to environment and back. 13.05.25 – Diana Rennison (Univ. of Calif., San Diego, US)
Understanding the predictability of evolutionary trajectories using threespine stickleback.

20.05.25 – Filipa Sousa (Univ. of Vienna, AT)
Bioenergetics Evolution: The link between Earth’s and Life’s history. 27.05.25 – Yun Song (Univ. of California, Berkeley, US)
Learning and applying complex probability distributions over biological sequences. 03.06.25 – April Wei (Cornell Univ., US)
Enabling efficient analysis of biobank-scale data with genotype representation graphs. ALT TEXT OUT OF SPACE, GO TO https://www.popgen-vienna.at/news/seminars/

The PopGen Vienna Seminar series schedule is ready for the next term (Mar-Jun). It's jam-packed with fantastic speakers in #evolution, #genetics, #genomics, #popgen, and more! Details and streaming link signup can be found on our website www.popgen-vienna.at/news/seminars/

Folge 2: Paleomycin: Wiederbelebung eines Urantibiotikums Inside CMFI: Potenziale der Mikrobiomforschung · Episode

#Podcast Release!

🎙️Folge 2: 𝗣𝗮𝗹𝗲𝗼𝗺𝘆𝗰𝗶𝗻: 𝗪𝗶𝗲𝗱𝗲𝗿𝗯𝗲𝗹𝗲𝗯𝘂𝗻𝗴 𝗲𝗶𝗻𝗲𝘀 𝗨𝗿𝗮𝗻𝘁𝗶𝗯𝗶𝗼𝘁𝗶𝗸𝘂𝗺𝘀

Kommt mit uns auf eine Schatzsuche nach einem Millionen Jahre alten #Urantibiotikum – dringend benötigt angesichts ansteigender #Antibiotikaresistenzen.

tinyurl.com/yc7vv58j

@nadineziemert.bsky.social & Evi Stegmann

Join our symposium The evolution of microbial pangenomes at @eseb2025.bsky.social with @bjesseshapiro.bsky.social @annadewar.bsky.social (co-organized with @fbaumdicker.bsky.social and Jaime Iranzo)

Neural networks for self-adjusting mutation rate estimation when the recombination rate is unknown Author summary single-layer feedforward neural networks learn the established model-based linear estimators for high and low recombination rates neural networks learn good estimators for intermedi...

Cool! This relates to our site frequency spectrum based neural network to estimate mutation rates. We always assumed that our network implicitly learned the underlying recombination rate based on the smoothness of the SFS but did not check it in detail dx.plos.org/10.1371/jour...

We have an open position PhD position in a project aiming to develop novel methodologies for phylogenomic reconstruction of plasmid evolution. See details and how to apply in the Ad. Candidates who will review the relevant literature (see Ad) have a higher chance to write a successful application.

I am looking for graduate students interested in investigating bacterial genome evolution, esp. pangenomes and intergenic regions, and the relative importance of genetic drift! https://buff.ly/3UPVcQ9

I recently used chatGPT to create a list of people working on a certain concept. The list was quite good, but the tool refused to provide their emails (which is probably a good thing) and I did not try to provide an abstract.

SBI hackathon is back! Join us in Tübingen for the 4th edition, make the toolbox better, brainstorm new direction, have fun!

Sketch of IBD segments linking Medieval genomes from the Black Death (1350 CE) to modern Europeans. Logo of ERC-funded research.

PhD opportunity in computational population genetics at @MPI_EVA_Leipzig:
Join our fully funded project to develop IBD-segment tools, connecting high-quality genomes from 500 Black Death victims to modern Europeans. 🌍💻🧬
Please spread the word! 📢🙌 #aDNA #PopGen

www.eva.mpg.de/de/karriere/...

A chromosomal mutation is superior to a plasmid-encoded mutation for plasmid fitness cost compensation Plasmids spread important traits in microbiomes but impose fitness costs on their hosts. This study of the ecological consequences of plasmid-bacterial compensatory evolution reveals benefits to bacte...

🆕New in @plosbiology.bsky.social: we show compensatory mutations make plasmids play Rock-Paper-Scissors and turn conjugation into a weapon🛡️💫✂️🦠

w/Rosanna Wright, Jamie Wood, @mbottery.bsky.social, @kmudz.bsky.social, @scottishwormboy.bsky.social, Ellie Harrison & @brockhurstlab.bsky.social #MicroSky

Only a few days left to apply!

GitHub - fbaumdicker/SpacerPlacer: ancestral reconstruction and likelihood analysis for CRISPR spacer arrays ancestral reconstruction and likelihood analysis for CRISPR spacer arrays - fbaumdicker/SpacerPlacer

It is crucial to use reconstructed arrays to see these deletion patterns in the database, as the position of spacers shifts toward the trailer end over time. I will post more details about our reconstruction tool SpacerPlacer at a later time. But you can find it here: https://buff.ly/40QdDId

Finally, across multiple CRISPR-Cas types and genera, we found no significant difference in deletion rates or lengths, suggesting that spacer deletions are likely not modulated by Cas proteins.

CRISPR spacer deletions might be more common at the leader due to
a) reconstruction errors (we correct for this)
b) mutations of the last repeat
c) recently acquired spacers lacking a long-term benefit
d) benefits of changing the spacers at the first most expressed positions
e) all of the above

The spacer deletions at the very first and last positions of CRISPR arrays deviate from a symmetric boundary effect. The reconstructed deletion rate is higher at the first positions compared to the losses at the last positions. This might have multiple reasons ...

Ignoring the boundary effect, we observe no gradient of deletion frequencies along arrays. CRISPR arrays evolve surely not neutrally, but our results hint at either weak selection pressures to delete specific spacers or an equally strong selection along the array to maintain spacers. However, ...

Consistent with this mechanism, we observe a “boundary effect”: Spacer deletions are less frequent near the leader and trailer ends of the array, potentially due to fewer neighboring repeats for alignment, while the middle of the array sees the most deletions.

Interestingly, besides the loss of a single spacer, deletions occur often in blocks, involving an average of 2.7 spacers per event. This block deletion aligns with theories of replication slippage, where nearby repeats misalign, leading to multiple spacer deletions.

Spacer deletions in CRISPR arrays follow fascinating patterns. Using our tool SpacerPlacer, we found that deletion events are 374x more frequent than single-nucleotide mutations, making immunity loss by spacer loss much more likely than by mutations.

SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions Abstract. Bacteria employ CRISPR-Cas systems for defense by integrating invader-derived sequences, termed spacers, into the CRISPR array, which constitutes

CRISPR arrays store "immune memories" of past invaders as spacers. But these memories aren’t permanent— frequent spacer deletions reshape the array.
We investigated the spacer deletion dynamics with our new reconstruction tool and learned a lot... 🧵
https://buff.ly/4fS4Iu3

Applications are open for the Microbial Population Biology GRS and GRC!

The GRS is a fun day for grad students and postdocs to network before the full GRC starts, and is co-chaired this year by me and Laura Suttenfield

Get your applications in by Jan 15! #evosky 🦠🧪

www.grc.org/microbial-po...