Ingo Müller
@ingomue.bsky.social
Currently a postdoc @ Uppsala University | Bioinformatics, population genomics, phylogeography | First gen | 🇵🇱x🇩🇪 Hybrid | Occasional nerdy arts
Reposted by Ingo Müller
I mean, the title says it all: Genetic confirmation of an “uncommon mourningthroat” (Geothlypis philadelphia × G. trichas): A rare but persistent hybrid warbler. Fun stuff with @kevinfpbennett.bsky.social and Kurt Gielow, OA in @wilsonornithsoc.bsky.social!
🦉 🧪
www.tandfonline.com/doi/full/10....
🦉 🧪
www.tandfonline.com/doi/full/10....
November 21, 2025 at 2:34 PM
I mean, the title says it all: Genetic confirmation of an “uncommon mourningthroat” (Geothlypis philadelphia × G. trichas): A rare but persistent hybrid warbler. Fun stuff with @kevinfpbennett.bsky.social and Kurt Gielow, OA in @wilsonornithsoc.bsky.social!
🦉 🧪
www.tandfonline.com/doi/full/10....
🦉 🧪
www.tandfonline.com/doi/full/10....
Reposted by Ingo Müller
If you use GMail, AI (Gemini) was turned on yesterday by default and now scans all of your content for machine learning. To turn off, go to Settings>General and scroll down. Uncheck the box for "Smart features."
There's other "Smart" add-ons as well, but that's the one that reads your content.
There's other "Smart" add-ons as well, but that's the one that reads your content.
November 20, 2025 at 5:32 PM
If you use GMail, AI (Gemini) was turned on yesterday by default and now scans all of your content for machine learning. To turn off, go to Settings>General and scroll down. Uncheck the box for "Smart features."
There's other "Smart" add-ons as well, but that's the one that reads your content.
There's other "Smart" add-ons as well, but that's the one that reads your content.
Reposted by Ingo Müller
Changing Views on Speciation onlinelibrary.wiley.com/doi/10.1111/...
Changing Views on Speciation
Our understanding of speciation processes is constantly changing. Two important concepts that have influenced thinking over the long term are the isolation and the genic views of speciation. However,...
onlinelibrary.wiley.com
November 18, 2025 at 6:45 PM
Changing Views on Speciation onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Ingo Müller
Our new @science.org paper is out! Cuckoos and hosts are locked in a coevolutionary arms race over egg mimicry.
But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!
doi.org/10.1126/scie...
🧵1/6
But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!
doi.org/10.1126/scie...
🧵1/6
Genomic architecture of egg mimicry and its consequences for speciation in parasitic cuckoos
Host-parasite arms races facilitate rapid evolution and can fuel speciation. Cuculus cuckoos are deceptive egg mimics that exhibit a broad diversity of counterfeit egg phenotypes, representing host-ad...
doi.org
October 30, 2025 at 7:15 PM
Our new @science.org paper is out! Cuckoos and hosts are locked in a coevolutionary arms race over egg mimicry.
But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!
doi.org/10.1126/scie...
🧵1/6
But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!
doi.org/10.1126/scie...
🧵1/6
Reposted by Ingo Müller
Happy to see my former @nbis.se advisory program student Zach Nolen's new pipeline PopGLen for analyses of short-read data using genotype-likelihood based methods out!
Github: github.com/zjnolen/PopG...
Paper: academic.oup.com/bioinformati...
Github: github.com/zjnolen/PopG...
Paper: academic.oup.com/bioinformati...
PopGLen—A Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods
AbstractSummary. PopGLen is a Snakemake workflow for performing population genomic analyses within a genotype-likelihood framework, integrating steps for r
academic.oup.com
March 20, 2025 at 7:52 AM
Happy to see my former @nbis.se advisory program student Zach Nolen's new pipeline PopGLen for analyses of short-read data using genotype-likelihood based methods out!
Github: github.com/zjnolen/PopG...
Paper: academic.oup.com/bioinformati...
Github: github.com/zjnolen/PopG...
Paper: academic.oup.com/bioinformati...
Reposted by Ingo Müller
New review out! With students in my lab, we explore how population size shapes speciation—from drift in small populations to selection in large ones. Do small or large populations speciate faster? The answer is more nuanced than you might think.
esj-journals.onlinelibrary.wiley.com/doi/full/10....
esj-journals.onlinelibrary.wiley.com/doi/full/10....
Speciation Through the Lens of Population Dynamics: A Theoretical Primer on How Small and Large Populations Diverge
Population size and dynamics fundamentally shape speciation by influencing genetic drift, founder events, and adaptive potential. Small populations may speciate rapidly due to stronger drift, whereas...
esj-journals.onlinelibrary.wiley.com
October 14, 2025 at 11:25 PM
New review out! With students in my lab, we explore how population size shapes speciation—from drift in small populations to selection in large ones. Do small or large populations speciate faster? The answer is more nuanced than you might think.
esj-journals.onlinelibrary.wiley.com/doi/full/10....
esj-journals.onlinelibrary.wiley.com/doi/full/10....
Reposted by Ingo Müller
The first Aguillon Lab paper is officially out in early view at Evolution!! Led by postdoc @devonderaad.bsky.social, we’ve explored the hybrid zone between black-headed and rose-breasted grosbeaks in the Great Plains. #ornithology #hybridization #speciation #evolution doi.org/10.1093/evol...
September 12, 2025 at 3:49 PM
The first Aguillon Lab paper is officially out in early view at Evolution!! Led by postdoc @devonderaad.bsky.social, we’ve explored the hybrid zone between black-headed and rose-breasted grosbeaks in the Great Plains. #ornithology #hybridization #speciation #evolution doi.org/10.1093/evol...
Reposted by Ingo Müller
Just published: Conservation genomics of two
endangered buntings reveal genetic diversity
before and after severe population declines. doi.org/10.1186/s129... Despite severe population declines, both species retained high genetic diversity but experienced increased inbreeding. #ornithology #birds
endangered buntings reveal genetic diversity
before and after severe population declines. doi.org/10.1186/s129... Despite severe population declines, both species retained high genetic diversity but experienced increased inbreeding. #ornithology #birds
October 1, 2025 at 7:50 PM
Just published: Conservation genomics of two
endangered buntings reveal genetic diversity
before and after severe population declines. doi.org/10.1186/s129... Despite severe population declines, both species retained high genetic diversity but experienced increased inbreeding. #ornithology #birds
endangered buntings reveal genetic diversity
before and after severe population declines. doi.org/10.1186/s129... Despite severe population declines, both species retained high genetic diversity but experienced increased inbreeding. #ornithology #birds
Reposted by Ingo Müller
We have a new paper out in Molecular Ecology, led by @devinbendixsen.bsky.social ! Reproductive isolation due to divergent ecological selection is accompanied by vast genomic instability in experimentally evolved yeast populations onlinelibrary.wiley.com/doi/10.1111/...
September 18, 2025 at 8:56 AM
We have a new paper out in Molecular Ecology, led by @devinbendixsen.bsky.social ! Reproductive isolation due to divergent ecological selection is accompanied by vast genomic instability in experimentally evolved yeast populations onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Ingo Müller
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
Reposted by Ingo Müller
I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN.
It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package.
Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats
It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package.
Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
www.tidyverse.org
September 11, 2025 at 11:20 AM
Reposted by Ingo Müller
Hybridization and introgression are major evolutionary processes. Since the 1940s, the prevailing view has been that they shape plants far more than animals. In our new study (www.science.org/doi/10.1126/...
), we find the opposite: animals exchange genes more, and for longer, than plants
), we find the opposite: animals exchange genes more, and for longer, than plants
September 12, 2025 at 7:55 AM
Hybridization and introgression are major evolutionary processes. Since the 1940s, the prevailing view has been that they shape plants far more than animals. In our new study (www.science.org/doi/10.1126/...
), we find the opposite: animals exchange genes more, and for longer, than plants
), we find the opposite: animals exchange genes more, and for longer, than plants
Reposted by Ingo Müller
The paper for my R package is published! This has been a fun process learning more about hybrid zones and triangle plots. Thanks everyone who has contributed and tested it out already!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
triangulaR: an R package for identifying AIMs and building triangle plots using SNP data from hybrid zones - Heredity
Heredity - triangulaR: an R package for identifying AIMs and building triangle plots using SNP data from hybrid zones
www.nature.com
April 14, 2025 at 2:17 PM
The paper for my R package is published! This has been a fun process learning more about hybrid zones and triangle plots. Thanks everyone who has contributed and tested it out already!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ingo Müller
New rock dove paper!🕊️
Bit by bit, we are disentangling their evolutionary history and adding evidence to recognise the elusive West African rock doves as a different species
*please ignore the little typo in the title, livia should be lowercase
@trstngnthr.bsky.social
doi.org/10.1002/ece3...
Bit by bit, we are disentangling their evolutionary history and adding evidence to recognise the elusive West African rock doves as a different species
*please ignore the little typo in the title, livia should be lowercase
@trstngnthr.bsky.social
doi.org/10.1002/ece3...
Gone With the Wind: Exploring a Vanished Rock Dove, Columba Livia, Hybrid Zone in the Sahara Desert
In this study, we tested the hypothesis of the existence of a hybrid zone between two differentiated rock dove lineages, which may contribute significantly to their divergence. By analyzing newly gen...
doi.org
August 28, 2025 at 9:16 AM
New rock dove paper!🕊️
Bit by bit, we are disentangling their evolutionary history and adding evidence to recognise the elusive West African rock doves as a different species
*please ignore the little typo in the title, livia should be lowercase
@trstngnthr.bsky.social
doi.org/10.1002/ece3...
Bit by bit, we are disentangling their evolutionary history and adding evidence to recognise the elusive West African rock doves as a different species
*please ignore the little typo in the title, livia should be lowercase
@trstngnthr.bsky.social
doi.org/10.1002/ece3...
Reposted by Ingo Müller
My very first post on here.
I am stoked to share lab's latest paper led by @ethantolman.bsky.social. Ethan developed a highly scalable pipeline to differentiate between various gene flow models, including ghost introgression in phylogenomic datasets. Check it out! www.biorxiv.org/content/10.1...
I am stoked to share lab's latest paper led by @ethantolman.bsky.social. Ethan developed a highly scalable pipeline to differentiate between various gene flow models, including ghost introgression in phylogenomic datasets. Check it out! www.biorxiv.org/content/10.1...
GhostParser: A highly scalable phylogenomic approach for the identification of ghost introgression
A growing body of empirical research shows that interspecific gene flow is a widespread biological force that shapes evolutionary histories across the Tree of Life. Computational approaches designed t...
www.biorxiv.org
August 23, 2025 at 11:52 PM
My very first post on here.
I am stoked to share lab's latest paper led by @ethantolman.bsky.social. Ethan developed a highly scalable pipeline to differentiate between various gene flow models, including ghost introgression in phylogenomic datasets. Check it out! www.biorxiv.org/content/10.1...
I am stoked to share lab's latest paper led by @ethantolman.bsky.social. Ethan developed a highly scalable pipeline to differentiate between various gene flow models, including ghost introgression in phylogenomic datasets. Check it out! www.biorxiv.org/content/10.1...
Reposted by Ingo Müller
August 22, 2025 at 4:17 PM
Reposted by Ingo Müller
Interested in eukaryotic algal evolution, metagenomics, new plastid diversity, and more? Check out my poster (P175) today at #eseb2025 ! #protistsonsky
August 21, 2025 at 8:50 AM
Interested in eukaryotic algal evolution, metagenomics, new plastid diversity, and more? Check out my poster (P175) today at #eseb2025 ! #protistsonsky
Reposted by Ingo Müller
Our genetic kinship estimation tool “DeepKin” is now available! Our neural network models trained on simulated data work effectively on real ancient data from diverse backgrounds and often outperform available tools. @compevohumang.bsky.social onlinelibrary.wiley.com/doi/10.1111/...
DeepKin: Predicting Relatedness From Low‐Coverage Genomes and Palaeogenomes With Convolutional Neural Networks
DeepKin is a novel tool designed to predict relatedness from genomic data using convolutional neural networks (CNNs). Traditional methods for estimating relatedness often struggle when genomic data i...
onlinelibrary.wiley.com
August 18, 2025 at 12:07 PM
Our genetic kinship estimation tool “DeepKin” is now available! Our neural network models trained on simulated data work effectively on real ancient data from diverse backgrounds and often outperform available tools. @compevohumang.bsky.social onlinelibrary.wiley.com/doi/10.1111/...
Thanks a lot @jenteo.bsky.social for discussing our paper on your blog!
New story on the Avian Hybrids blog!
Reversed speciation in New Guinean Honeyeaters?
avianhybrids.wordpress.com/2025/08/13/r...
Based on the Molecular Ecology study by Ingo Müller and his colleagues | #ornithology
Reversed speciation in New Guinean Honeyeaters?
avianhybrids.wordpress.com/2025/08/13/r...
Based on the Molecular Ecology study by Ingo Müller and his colleagues | #ornithology
Reversed speciation in New Guinean Honeyeaters?
Genetic analyses suggest an ephemeral speciation model.
avianhybrids.wordpress.com
August 14, 2025 at 11:19 AM
Thanks a lot @jenteo.bsky.social for discussing our paper on your blog!
Reposted by Ingo Müller
For folks interested in hybrid zones / introgression / speciation, this looks interesting:
doi.org/10.1101/2025...
doi.org/10.1101/2025...
Replicate avian hybrid zones reveal the progression of genetic and trait introgression through time
Replicate hybrid zones between the same taxa provide a unique opportunity to assess the repeatability of interspecific matings by uncovering recurrent genomic and phenotypic introgression patterns. Re...
doi.org
August 13, 2025 at 2:36 PM
For folks interested in hybrid zones / introgression / speciation, this looks interesting:
doi.org/10.1101/2025...
doi.org/10.1101/2025...
Reposted by Ingo Müller
*PhD position* 🦉
Would you like to do a PhD with Indo-Pacific birds and evolutionary genomics? Join us in Stockholm:
05 September 2025, 23:59
PhD student in Evolution of Indo-Pacific birds
recruit.visma.com/spa/public/a...
Would you like to do a PhD with Indo-Pacific birds and evolutionary genomics? Join us in Stockholm:
05 September 2025, 23:59
PhD student in Evolution of Indo-Pacific birds
recruit.visma.com/spa/public/a...
PhD student in Evolution of Indo-Pacific birds
The Department of Bioinformatics and Genetics is offering a four-year PhD position focused on analyzing population-level genomic data from museum bird samples. The project will employ cutting-edge gen...
recruit.visma.com
August 10, 2025 at 2:02 PM
*PhD position* 🦉
Would you like to do a PhD with Indo-Pacific birds and evolutionary genomics? Join us in Stockholm:
05 September 2025, 23:59
PhD student in Evolution of Indo-Pacific birds
recruit.visma.com/spa/public/a...
Would you like to do a PhD with Indo-Pacific birds and evolutionary genomics? Join us in Stockholm:
05 September 2025, 23:59
PhD student in Evolution of Indo-Pacific birds
recruit.visma.com/spa/public/a...
Reposted by Ingo Müller
Reposted by Ingo Müller
Very excited to have our study come out looking at multiple plant mosaic hybrid zones and their implications for hybrids to act as "sutures" of species ranges. We use genomic data to project shifts into future climates and discuss impacts on conservation/management.
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
July 30, 2025 at 4:14 PM
Very excited to have our study come out looking at multiple plant mosaic hybrid zones and their implications for hybrids to act as "sutures" of species ranges. We use genomic data to project shifts into future climates and discuss impacts on conservation/management.
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...