Yann Bourgeois
@bourgeoisyann.bsky.social
Evolutionary biologist at the French National Research Institute for Development in Montpellier
https://yannbourgeois.github.io/
https://yannbourgeois.github.io/
A nice work, I think.
doi.org/10.1111/mec....
doi.org/10.1111/mec....
doi.org
November 29, 2025 at 4:52 PM
A nice work, I think.
doi.org/10.1111/mec....
doi.org/10.1111/mec....
From experience, using whatshap to build small blocks then phasing with those as priors usually seems to work well. + sanity check with phase-insensitive methods like SMC++
Robustness of Ancestral Recombination Graph Inference Tools to Phasing Errors https://www.biorxiv.org/content/10.1101/2025.11.24.690249v1
November 26, 2025 at 7:57 AM
From experience, using whatshap to build small blocks then phasing with those as priors usually seems to work well. + sanity check with phase-insensitive methods like SMC++
Reposted by Yann Bourgeois
Robustness of Ancestral Recombination Graph Inference Tools to Phasing Errors https://www.biorxiv.org/content/10.1101/2025.11.24.690249v1
November 26, 2025 at 7:31 AM
Robustness of Ancestral Recombination Graph Inference Tools to Phasing Errors https://www.biorxiv.org/content/10.1101/2025.11.24.690249v1
Reposted by Yann Bourgeois
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
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
October 7, 2025 at 9:55 PM
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
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
Really cool www.biorxiv.org/content/10.1...
www.biorxiv.org
September 20, 2025 at 10:58 PM
Really cool www.biorxiv.org/content/10.1...
Cool news from the former lab.
www.pnas.org/doi/10.1073/...
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
September 11, 2025 at 2:14 PM
Cool news from the former lab.
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Reposted by Yann Bourgeois
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...
🔹 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
August 26, 2025 at 2:48 PM
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...
🔹 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...
Nice!
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...
🔹 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
August 28, 2025 at 8:16 PM
Nice!
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?
August 25, 2025 at 9:28 AM
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?
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
August 22, 2025 at 12:46 PM
Cool! doi.org/10.1093/molb...
Reposted by Yann Bourgeois
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!
August 21, 2025 at 9:08 AM
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!
Reposted by Yann Bourgeois
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
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
August 21, 2025 at 9:22 AM
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
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
Reposted by Yann Bourgeois
Relaxed Purifying Selection is Associated with an Accumulation of Transposable Elements in Flies
academic.oup.com/mbe/article/...
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
July 7, 2025 at 1:11 PM
Relaxed Purifying Selection is Associated with an Accumulation of Transposable Elements in Flies
academic.oup.com/mbe/article/...
academic.oup.com/mbe/article/...
Reposted by Yann Bourgeois
*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...
"Signals of consistent genetic diversity decline are not yet measurable in global meta-analysis" doi.org/10.1101/2025...
August 4, 2025 at 6:35 PM
*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...
"Signals of consistent genetic diversity decline are not yet measurable in global meta-analysis" doi.org/10.1101/2025...
Reposted by Yann Bourgeois
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
SWIF-TE: identifying novel transposable element insertions from short read data https://www.biorxiv.org/content/10.1101/2025.07.30.667279v1
August 2, 2025 at 6:42 PM
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
Reposted by Yann Bourgeois
SWIF-TE: identifying novel transposable element insertions from short read data https://www.biorxiv.org/content/10.1101/2025.07.30.667279v1
August 2, 2025 at 5:48 AM
SWIF-TE: identifying novel transposable element insertions from short read data https://www.biorxiv.org/content/10.1101/2025.07.30.667279v1
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...
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
August 2, 2025 at 9:44 AM
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...
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...
Reposted by Yann Bourgeois
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
June 12, 2025 at 7:57 PM
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...
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
July 30, 2025 at 7:48 AM
Where we look at anoles in the city doi.org/10.1111/mec....
Reposted by Yann Bourgeois
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
July 23, 2025 at 10:27 PM
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