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Pedro Ribeiro @pedrogribeiro.bsky.social · 49m

Thanks a lot, Nick!

Pedro Ribeiro @pedrogribeiro.bsky.social · 21d

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

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Pedro Ribeiro @pedrogribeiro.bsky.social · 21d

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!

Pável Matos @pavelmatosm.bsky.social · 22d

Our lab is celebrating! 🥳 Pedro Ribeiro @pedrogribeiro.bsky.social has excellently defended his PhD thesis: theses.cz/id/9gnm91/

Pedro has used genome data to study the evolution of butterflies and their endosymbiont bacteria Wolbachia.

We wish you all the best, Dr. Pedro! 🦋

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Pedro Ribeiro @pedrogribeiro.bsky.social · Aug 18

@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/

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…

pavelmatos.wordpress.com

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Reposted by Pedro Ribeiro

Rob Waterhouse @rmwaterhouse.bsky.social · Jul 4

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-...

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...

www.erga-biodiversity.eu

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Pedro Ribeiro @pedrogribeiro.bsky.social · Jun 30

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

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Pedro Ribeiro @pedrogribeiro.bsky.social · Jun 25

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

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Reposted by Pedro Ribeiro

Christopher Wheat @chriswheat.bsky.social · Jun 22

🚨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

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.

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Reposted by Pedro Ribeiro

Alexis Stamatakis @stamatak.bsky.social · May 15

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/...

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

github.com

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Reposted by Pedro Ribeiro

Project Psyche @projectpsyche.bsky.social · Mar 20

(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 🧬

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Reposted by Pedro Ribeiro

Marc Somssich @somssich.bsky.social · Mar 12

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

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

academic.oup.com

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Reposted by Pedro Ribeiro

Charlotte Wright @charlottewright.bsky.social · Mar 8

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...

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Reposted by Pedro Ribeiro

Joana Meier @joanameier.bsky.social · Feb 24

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.

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...

docs.google.com

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Pedro Ribeiro @pedrogribeiro.bsky.social · Feb 24

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.

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Pedro Ribeiro @pedrogribeiro.bsky.social · Feb 21

I would like to be added! thanks a lot!

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Reposted by Pedro Ribeiro

Niklas Wahlberg @lepphylo.bsky.social · Feb 6

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/...

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

lu.varbi.com

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Reposted by Pedro Ribeiro

KamilSJaron.bsky.social @kamilsjaron.bsky.social · Jan 31

🚨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!

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

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Pedro Ribeiro @pedrogribeiro.bsky.social · Jan 10

@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!

Niklas Wahlberg @lepphylo.bsky.social · Jan 10

Happy to have hosted first author @pedrogribeiro.bsky.social in our lab in Lund that led to a cool paper on Wolbachia in a group of tropical skippers!

bmcmicrobiol.biomedcentral.com/articles/10....

Pervasive horizontal transmission of Wolbachia in natural populations of closely related and widespread tropical skipper butterflies - BMC Microbiology

Background The endosymbiotic relationship between Wolbachia bacteria and insects has been of interest for many years due to their diverse types of host reproductive phenotypic manipulation and potenti...

bmcmicrobiol.biomedcentral.com

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Pedro Ribeiro @pedrogribeiro.bsky.social · Jan 6

@everyjing.bsky.social maaaybe of interest?

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Reposted by Pedro Ribeiro

Niklas Wahlberg @lepphylo.bsky.social · Jan 3

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...

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.....

doi.org

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Pedro Ribeiro @pedrogribeiro.bsky.social · Dec 19

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!

Pedro Ribeiro @pedrogribeiro.bsky.social · Dec 19

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/

Blog – Matos Lab

Posts about Blog written by admin

pavelmatos.wordpress.com

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Pedro Ribeiro @pedrogribeiro.bsky.social · Dec 19

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!

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