Ingo Müller

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...

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....

Figure 1A from the paper shows the distribution of black-headed (western) and rose-breasted grosbeaks (eastern) throughout North America. Small illustrations of males of each species are shown. Black-headed has a rusty orange breast and black head, while rose-breasted has a small reddish bib with a bright white belly. There is an inset map of South Dakota showing the transect across the hybrid zone

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...

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

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/...

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

ggplot2 4.0.0 A new major version of ggplot2 has been released on CRAN. Find out what is new here.

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

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

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

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...

Why do speciation rates vary across the tree of life?
Some of the best yet most underappreciated places for this investigation are natural hybrid zones.
This preprint takes you to the hybrid zones in the origin of species to find a clue. 👉 shorturl.at/N7FXE
#Speciation #Evolution #hybridization

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...

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...

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...

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...

😎👇

Check out my poster here: doi.org/10.13140/RG....

Interested in eukaryotic algal evolution, metagenomics, new plastid diversity, and more? Check out my poster (P175) today at #eseb2025 ! #protistsonsky

If you're at #ESEB2025 drop by my poster today and let's chat about Birds-of-Paradise and their potential ring-like speciation history!

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...

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!

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...

For folks interested in hybrid zones / introgression / speciation, this looks interesting:

doi.org/10.1101/2025...

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...

*PhD position* 🦉

Would you like to do a PhD with Indo-Pacific birds and evolutionary genomics? Join us in Stockholm:

<deadline>
05 September 2025, 23:59

PhD student in Evolution of Indo-Pacific birds
recruit.visma.com/spa/public/a...

Opinion: Why Sex‐Based Genomic Differentiation Should Not Be Overlooked in Population Genetics Sex-specific genomic differentiation is a crucial yet frequently overlooked factor in population genetics. In this opinion piece, we leverage the substantial genomic resources available for the great...

onlinelibrary.wiley.com/doi/full/10....

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/...

The molecular evolutionary basis of species formation revisited How do new species arise? This is among the most fundamental questions in evolutionary biology. The first genetic model for how reproductive barriers lead to the origin of new species was proposed nea...

The molecular evolutionary basis of species formation revisited
www.cell.com/trends/genet...

A model-free method for genealogical inference without phasing and its application for topology weighting https://www.biorxiv.org/content/10.1101/2025.07.22.666161v1

🚨 Wanted: PhD student excited about population genomics, Natural History Collections and birds!
📍 Museum für Naturkunde, Berlin, Germany
🕒 3 Years, fully funded by the Leibniz Junior Researchgroup program

Details and Application portal 👇

jobs.museumfuernaturkunde.berlin/jobposting/8...

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/...

🧵5 Top Free Alternatives to BioRender for Scientific Illustrations!

These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs.

Save and share the post!

Very happy to share a new paper open access in Syst Biol. Introgression is commonly reported in phylogenomic studies, but whether these patterns are caused by ancestral or contemporary gene flow is rarely understood. Here we took a stab at this problem using parapatric tinkerbirds as a model (1/10)

Replicate geographic transects across a hybrid zone reveal parallelism and differences in the genetic architecture of reproductive isolation Abstract. Determining the genetic architecture of traits involved in adaptation and speciation is one of the key components of understanding the evolutiona

happy to see our study on genetic parallelism of reproductive isolation in chickadee hybrid zones out in @evolletters.bsky.social—great work led by Georgy Semenov & Scott Taylor: doi.org/10.1093/evle...

Now published! We examine how female competition shapes movement ecology. We provide the first genetic evidence of female philopatry and male-biased dispersal in a socially polyandrous bird species!

doi.org/10.1093/evol...
@journal-evo.bsky.social

Four images to illustrate some prominent single-gene myths. Top left shows a photograph of a person deftly rolling their tongue into a U-shape. Top right shows a photograph of a person’s ear, highlighting the shape and features of the earlobe and cartilage. Bottom left shows a close-up photograph of a person’s eye, with a vivid blue colouration. Bottom right shows a photograph of a person poised to write with their left hand on the blank white page of a spiral-bound notebook.

Remember when you first learned about genetics at school? All those fascinating examples of human traits that are each apparently determined by just a single gene? Time to check in on some of your favourites to see how they’re doing. 🧬🧵🧪 1/n

A complete and dynamic tree of birds - out today in PNAS! Teamwork with @eliotmiller.bsky.social and others at
@birdsoftheworld.bsky.social and Open Tree of Life to put together current relationships across all birds. www.pnas.org/doi/10.1073/...