Ingo Müller

An Evolving View of Species Tree Inference Abstract. Nearly all modern studies that address evolutionary questions require consideration of the phylogenetic relationships among species. But what, ex

An Evolving View of Species Tree Inference
academic.oup.com/sysbio/advan...

Ancestral‐area algorithms are unreliable We examine two standard phylogenetic–biogeographic patterns and how these are interpreted by current ancestral-area algorithms. In the first pattern, a basal, paraphyletic grade is restricted to one ...

Ancestral-area algorithms are unreliable
onlinelibrary.wiley.com/doi/10.1111/...

Pangenomes: new tools for ecological and evolutionary genomics Genomic structural variation is an important component of genetic variation in natural populations. By assembling and analyzing multiple high-quality genomes within a species or clade, pangenomes capt...

www.cell.com/trends/ecolo...

Check out our cover article by @timjanicke.bsky.social and colleagues about the role of sexual selection in animal speciation. academic.oup.com/evlett/artic.... The beautiful illustration is by Katharina Bóth.

📰 Starting this friday with some positive news:

Our publication "Pangenomes as a framework for adaptive radiation, speciation, and adaptation" came out today in the American Journal of Botany!

bsapubs.onlinelibrary.wiley.com/journal/1537...

I have a new preprint demonstrating a genome-architecture-aware approach to inferring species trees and introgression landscapes from a small number of genomes. If you are interested in phylogenomics, birds, or hybridization, this is for you! www.biorxiv.org/content/10.1...

A five panel figure, with four showing photographs of a putative hybrid warbler between a mourning warbler and a common yellowthroat. The final panel shows an illustration of the bird by David Sibley

A three panel figure showing the genetic composition of the hybrid and the putative parental species. Two panels show points on a principal components analysis, with the hybrid falling intermediate. The final panel shows bars illustrating genome-wide admixture, with the hybrid having intermediate ancestry between the two.

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....

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.

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,...

Changing Views on Speciation onlinelibrary.wiley.com/doi/10.1111/...

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...

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

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

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...

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...

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....