Pedro Ribeiro

Thanks a lot, Nick!

Huge thanks also to main collaborators @lepphylo.bsky.social, @joanameier.bsky.social, @kaybiodiversity.bsky.social and many others!

That's it! On Monday I defended my PhD working with the genomics and evolutionary history of the relationship between butterflies and Wolbachia, with a comment on the use of genomics to conservation! Thanks a lot to @pavelmatosm.bsky.social for supervising and mentoring!

Join us Opportunities Below are the positions currently open in our lab. PhD position (full-time doctoral funding) We are seeking a highly motivated PhD student to join our team. The goal of the project is…

@pavelmatosm.bsky.social has a new PhD position opportunity to work with conservation genomics of European butterflies! The project involves very cool collaborations with @projectpsyche.bsky.social, @10klepgenomes.bsky.social and the LepEUConsortium!
Deadline Sep 12
pavelmatos.wordpress.com/join-us/

Faster identification of Transposable Elements in full genome assemblies This month's ERGA BioGenome Analysis & Applications Seminar will feature a talk by speaker Pío Sierra about a new tool, pantera, which allows faster identification of Transposable Elements in genome a...

This month's ERGA BioGenome Analysis & Applications Seminar will feature a talk by speaker Pío Sierra about a new tool, pantera, which allows faster identification of Transposable Elements in genome assemblies. www.erga-biodiversity.eu/post/faster-...

cool! thanks a lot for the tip, I will try that because so far no luck with that!

Anybody out there with BayesAss2 experience? I think we are not understanding each other about how the input file has to look like!

The aim of this proposal is to place population genomic insights into a comparative framework to gain fundamental insights into the determinants of evolutionary outcomes. The project will work within LepEU, the European Lepidopteran Population Genomics Consortium (https://lepeu.github.io/). LepEU provides access to field samples from European populations of diverse species. Chromosome-scale reference genomes are provided by Project Psyche (https://www.projectpsyche.org/). Networking during the postdoc will be facilitated by participation in the 10kLepGenomes COST Action (https://10klepgenomes.eu/). Existing datasets await analysis, while additional samples need DNA extraction and submission for sequencing. Functional validation capability (CRISPR/Cas9 gene manipulations) is also available to test emergent hypotheses of allele-to-phenotype impacts. Personal research interests of the postdoc will be important to determine the exact project, as the project has a generous sequencing budget.

The successful applicant should have a PhD (obtained within 6 years of the application deadline) in a suitable subject area, such as evolutionary biology or population genomics. A strong interest in population genomics, local adaptation, comparative analyses, and experience working with genomic-scale data is essential. The candidate must have a documented publication record demonstrating relevant skills. Experience working with bioinformatic pipelines (e.g., Snakemake), or working with butterflies is welcome but not essential. The net salary is 28,000 SEK/month (~2,430 Euro, not subject to Swedish income tax) and comes directly from the Carl-Trygger Foundation stipend, which is paid out directly to the postdoc. Only PhD candidates acquired outside of the host department can apply. Currently, the lab of Prof. Wheat consists of 3 postdoctoral researchers, while the Dept. of Zoology provides a vibrant and excellent research environment of active, dynamic researchers. Applications should include: i) a succinct description of research interests and experience, detailing your contribution to any relevant publications (max 1 page), ii) why you are the ideal candidate for this position in the lab (max 1 page); iii) a CV including a list of publications, and iv) the name and contact information of two personal references. Applications will be reviewed on a rolling basis with a deadline of 23 August 2025. The project is planned to start on 1 October, but flexibility in the starting date can be provided for a suitable candidate. Please contact Prof. Wheat for additional information.

🚨Postdoc opportunity🚨: LepEU postdoc: comparative population genomics of European scale adaptation in butterflies

2 year, full-time PD in my group, Stockholm Univ.

Applications assed on rolling basis, deadline: 23 August 2025. Planned start 1 Oct.

Details:
christopherwheatlab.wordpress.com

Release RAxML-NG v2.0-beta2 · amkozlov/raxml-ng Main new features Adaptive tree search heuristic (Togkousidis 2023) , (Togkousidis 2024) Multiple fast branch support measures Integrated model testing Full Changelog: 1.2.2...2.0-beta2

RAxML-NG v2.0 beta is here

github.com/amkozlov/rax...
Features
1. Difficulty prediction
academic.oup.com/mbe/article/...
2. Adaptive search academic.oup.com/mbe/article/...
3. Early Stop
www.biorxiv.org/content/10.1...
4. Model selection
5. Rapid bootstrapping academic.oup.com/mbe/article/...

(1/4) In its first year, #ProjectPsyche has engaged with the research community by creating networks with experts in moths and butterflies 🦋 Members of the project have also trained the research community in #GenomeCuration, a key step in the generation of genomes 🧬

A Message From the Editors-in-Chief We have been Co-Editor-in-Chiefs of Molecular Biology and Evolution (MBE) for 2 years now. In that time, we have learned a great deal about the science of

This Editorial by Brandon S. Gaut and Claudia A. M. Russo provides some nice insight into how #SocietyJournals work, and why it pays for Scientists to publish with #SocietyOwned Journals. 👇

A Message From the Editors-in-Chief
academic.oup.com/mbe/article/...

#PlantScience #SciencePublishing

It's been brilliant to discuss so many aspects of Project Psyche as a community and find ways to make Psyche even better! Big thank you to @lepphylo.bsky.social @lunduniversity.bsky.social for hosting us and COST for making this meeting possible! www.cost.eu/actions/CA23...

Darwin Tree of Life Impact Assessment This form is used to share information within DToL about case studies, ongoing research, and funding awards that demonstrate the impact the Darwin Tree of Life consortium project has had on Global and...

Do you use Darwin Tree of Life (DToL) genomes for your work or grant applications? If so, can you please fill out this form? docs.google.com/forms/d/e/1F... We are gathering info on how DToL genomes are used. It will help us raise money to continue producing publicly available high-quality genomes.

Official petition for using em-dash in scientific publication (is it used?). It feels to me a bit too flamboyant to use it in a paper, but honestly I see it as a stylish alternative to "i.e" or sometimes colons.

I would like to be added! thanks a lot!

Postdoctoral fellow in Noctuidae functional genomics Subject description The project will use a comparative functional genomes approach to study a species-rich group of moths, Noctuidae (Lepidoptera). Noctuidae have both a huge negative and positive imp

A postdoc opportunity to work on Noctuidae (Lepidoptera) functional genomics with me, @jadrankarota.bsky.social and @chriswheat.bsky.social in Lund, Sweden. We aim to leverage the amazing amount of data being generated by @projectpsyche.bsky.social and DToL projects.
lu.varbi.com/en/what:job/...

https://coursesandconferences.wellcomeconnectingscience.org/event/k-mer-workshop-for-biodiversity-genomics-20250601/

🚨Registration open🚨 1st - 6th of June, me, Katie Jenike, @rayanchikhi.bsky.social and Gene Myers will run a week long workshop on k-mers for biodiversity genomics organised by @connectingscience.bsky.social at @sangerinstitute.bsky.social. Join us & get equipped to wrestle large genomic datasets!

@lepphylo.bsky.social was ahead of me to post about our paper together with Pavel Matos, @joanameier.bsky.social and others!
I will come back to this to talk a bit more about it.
For me, this is the product of amazing collaborations with inspiring people!

@everyjing.bsky.social maaaybe of interest?

Phylogenomic insights into the relationship and the evolutionary history of planthoppers (Insecta: Hemiptera: Fulgoromorpha) Using genomic data from 285 species across 19 planthopper families, we conducted the first phylogenomic study targeting global planthoppers and inferred their phylogeny with the highest resolution s.....

Happy to have been part of this new article on planthopper (Fulgoromorpha) systematics! A great collaboration between Jagiellonian and Lund Universities!

doi.org/10.1111/syen...

a note on writing: if I could, I would definitely re-edit these articles 😅. I like them, but catch a buncha English mistakes, silly "catch" phrases I'd not use today, syntaxes I'd avoid.
Fun to read tho!

Blog – Matos Lab Posts about Blog written by admin

In our lab's website, we have a Blog section for more informal articles: our research, "philosophical" discussions from our meetings and journal clubs.
I've contributed to two of these blog posts:
- Are cryptic species real?
- Congresses attended by our [...]
pavelmatos.wordpress.com/category/blog/

Left ex-twitter today (finally). There I tried to maintain a strictly science-based profile.

Here I will try to be more flexible, bringing some readings, movies, music, personal life in general. But the aim is mostly to engage with researchers!

Cheers!