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Reposted by Yann Bourgeois

Joe Manthey @jdmanthey.bsky.social · 3d

Our paper on the temporal genomics of Ethiopian birds
has been highlighted (and gotten the cover) in @genomebiolevol.bsky.social
Article: doi.org/10.1093/gbe/evaf163
Highlight: doi.org/10.1093/gbe/evaf175

w/ @bourgeoisyann.bsky.social, @lcampillo.bsky.social, and others not on bsky

Genome Biology and Evolution October 2025 cover image with a photo of an Ethiopian White-eye.

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Yann Bourgeois @bourgeoisyann.bsky.social · 20d

Really cool www.biorxiv.org/content/10.1...

www.biorxiv.org

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Yann Bourgeois @bourgeoisyann.bsky.social · 26d

Cool. www.science.org/doi/10.1126/...

Rapid establishment of species barriers in plants compared with that in animals

Speciation, the process by which new reproductively isolated species emerge from ancestral populations, results from the gradual accumulation of barriers to gene flow within genomes. To date, the noti...

www.science.org

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Yann Bourgeois @bourgeoisyann.bsky.social · 29d

Cool news from the former lab.
www.pnas.org/doi/10.1073/...

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

www.pnas.org

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Reposted by Yann Bourgeois

Mathieu Gautier @mgda76.bsky.social · Aug 26

For those interested: 🚀 BayPass v3.1 released!
🔹 Improved MCMC adaptive phase
🔹 Computation reduced >6X with default (recommended) options, while keeping similar accuracy
🔹 Plus other minor edits

📖 Details in the manual / changelog
🔗 Repo: forge.inrae.fr/mathieu.gaut...

GAUTIER Mathieu / baypass public · GitLab

GitLab Community Edition

forge.inrae.fr

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Yann Bourgeois @bourgeoisyann.bsky.social · Aug 28

Nice!

Mathieu Gautier @mgda76.bsky.social · Aug 26

For those interested: 🚀 BayPass v3.1 released!
🔹 Improved MCMC adaptive phase
🔹 Computation reduced >6X with default (recommended) options, while keeping similar accuracy
🔹 Plus other minor edits

📖 Details in the manual / changelog
🔗 Repo: forge.inrae.fr/mathieu.gaut...

GAUTIER Mathieu / baypass public · GitLab

GitLab Community Edition

forge.inrae.fr

Yann Bourgeois @bourgeoisyann.bsky.social · Aug 25

Wondering whether there is work about the role of polymorphic, possibly long indels in explaining Lewontin's paradox? Wouldn't one expect reduction in Ne proportional to the frequency of the deletion? Possibly in combination with interference process?

Yann Bourgeois @bourgeoisyann.bsky.social · Aug 23

The latest paper on Ethiopian birds, led by @jdmanthey.bsky.social
doi.org/10.1093/gbe/...

Temporal genomics reveal a century of genomic diversity shifts across a biodiversity hotspot avian assemblage

Abstract. Biodiversity has experienced tremendous shifts in community, species, and genetic diversity during the Anthropocene. Understanding temporal diver

doi.org

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Yann Bourgeois @bourgeoisyann.bsky.social · Aug 22

Cool! doi.org/10.1093/molb...

How did evolution halve genome size during an oceanic island colonization?

Abstract. Red devil spiders of the genus Dysdera colonised the Canary Islands and underwent an extraordinary diversification. Notably, their genomes are ne

doi.org

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Reposted by Yann Bourgeois

Joris Bertrand @jorisbertrand.bsky.social · Aug 21

For whoever interrested in, Pascaline Salvado will eventually present her ongoing work on Ophrys orchids today on spot 359 at #ESEB2025. Do not hesitate to come and discuss about science and/or post-doc opportunities with us!

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Reposted by Yann Bourgeois

Alexa Sadier @aigverte.bsky.social · Aug 21

If you like evolutionary constraints, serial homology, teeth, bats or all of the above, come and see our talk and posters! 👇🏼
At 3:30 I will talk about the genomic and developmental foundation of adaptive tooth shape evolution in bats Room S09 rm 118-119 #ESEB2025

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Reposted by Yann Bourgeois

Gavin Woodruff @weirdworms.bsky.social · Jul 7

Relaxed Purifying Selection is Associated with an Accumulation of Transposable Elements in Flies

academic.oup.com/mbe/article/...

Relaxed Purifying Selection is Associated with an Accumulation of Transposable Elements in Flies

Abstract. Although the mechanisms driving genome size evolution are not yet fully understood, one potentially important factor is the dynamics of the accum

academic.oup.com

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Reposted by Yann Bourgeois

Moi Expósito-Alonso (MOILAB) @mexpositoalonso.bsky.social · Aug 4

*ALERT! GLOBAL GENETIC DIVERSITY TREND RE-ANALYSIS*

"Signals of consistent genetic diversity decline are not yet measurable in global meta-analysis" doi.org/10.1101/2025...

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Reposted by Yann Bourgeois

Claire Menard @clairecodes.bsky.social · Aug 2

My first first author manuscript has posted! I’m very excited to share SWIF-TE with yall. It is a fast, memory efficient tool to identify novel TE insertions from short-read data. 🧬 #TEworldwide #transposons

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Aug 2

SWIF-TE: identifying novel transposable element insertions from short read data https://www.biorxiv.org/content/10.1101/2025.07.30.667279v1

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Reposted by Yann Bourgeois

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Aug 2

SWIF-TE: identifying novel transposable element insertions from short read data https://www.biorxiv.org/content/10.1101/2025.07.30.667279v1

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Yann Bourgeois @bourgeoisyann.bsky.social · Aug 2

A couple of things:
I have a new website: yannbourgeois.github.io
The url www.methodspopgen.com now redirects to a dedicated methods section on the new website. As a complement, note that we have developed Physalia workshops that may be useful to newcomers in the field: github.com/PhysaliaIntr...

Yann X.C. Bourgeois

A simple, whitespace theme for academics. Based on [*folio](https://github.com/bogoli/-folio) design.

yannbourgeois.github.io

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Reposted by Yann Bourgeois

Emily Josephs @emjo.bsky.social · Jun 12

Hey, Miles' @milesroberts.bsky.social beautiful paper showing that sequence diversity missed by standard methods contributes to Lewontin's paradox is officially published in @evolletters.bsky.social. academic.oup.com/evlett/advan...

k-mer-based diversity scales with population size proxies more than nucleotide diversity in a meta-analysis of 98 plant species

Abstract. A key prediction of neutral theory is that the level of genetic diversity in a population should scale with population size. However, as was note

academic.oup.com

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Yann Bourgeois @bourgeoisyann.bsky.social · Jul 30

Where we look at anoles in the city doi.org/10.1111/mec....

Urban Life Shapes Genetic Diversity in the Green Anole, Anolis carolinensis

Urbanisation presents unique environmental pressures that drive rapid evolutionary adaptations, particularly in species inhabiting fragmented and anthropogenised landscapes. In this study, we investi....

doi.org

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Reposted by Yann Bourgeois

Christine N Meynard @cnmeynard.bsky.social · Jul 23

I just concluded two weeks of very productive work with my Argentinian colleagues at CEPAVE in La Plata. Thanks to them all! Great to see that people remain highly motivated to do science, despite the government de-funding, and expecting interesting results! Project with @cbgpmontpellier.bsky.social

Photo of myself and my Argentinian collaborators at CEPAVE in La Plata, Argentina

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Reposted by Yann Bourgeois

Thomas Lenormand @thomaslenormand.bsky.social · Jul 12

Interested to know more about a new theory relating the #evolution of #sexchromosomes to the rules of #speciation? Check out this paper that we published with Denis Roze in the last issue of #Science. PDF here: www.science.org/stoken/autho...

A single theory for the evolution of sex chromosomes and the two rules of speciation

Sex chromosomes are involved in three major empirical patterns: (i) Y (or W) chromosomes are often nonrecombining and degenerate; (ii) heterogametic offspring (XY or ZW) from interspecific crosses are...

www.science.org

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Reposted by Yann Bourgeois

Heng Li @lh3lh3.bsky.social · Jul 8

Preprint on "Finding easy regions for short-read variant calling from pangenome data": arxiv.org/abs/2507.03718

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Reposted by Yann Bourgeois

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Jul 8

The evolution of tandem repeat sequences under partial selfing and different modes of selection https://www.biorxiv.org/content/10.1101/2025.07.04.663195v1

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Yann Bourgeois @bourgeoisyann.bsky.social · Jul 7

Cool!
doi.org/10.1038/s414...

Accounting for population structure and data quality in demographic inference with linkage disequilibrium methods - Nature Communications

Accurate estimation of effective population size is critical for understanding population history but is often confounded by structure and data quality. Here, the authors show that GONE2 and currentNe...

doi.org

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Reposted by Yann Bourgeois

Joris Bertrand @jorisbertrand.bsky.social · Jun 30

Our proposal on the evolution of bee orchids will be funded by an #ANR project! With @bourgeoisyann.bsky.social, we will be recruiting two people to work on:
🌸 innovative/AI-powered phenotyping
🧬 genomic architecture of adaptive radiations
Get in touch and meet up at @eseb2025.bsky.social!

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Yann Bourgeois @bourgeoisyann.bsky.social · Jun 12

Merci Thibault !

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