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Ingo Müller

@ingomue.bsky.social

190 followers 160 following 6 posts

Fresh off my PhD in museomics studying New Guinean birds @ Naturhistoriska Riksmuseet & Stockholm University | Bioinformatics, population genomics, phylogeography | First gen | 🇵🇱x🇩🇪 Hybrid | Occasional nerdy arts

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Ingo Müller @ingomue.bsky.social · Dec 13

Quick introduction 👋
I'm Ingo, I am in the last months of my PhD on avian museomics at the Swedish Museum of Natural History and Stockholm University. If you'd like a teaser of my work here's the publication to my first thesis chapter:
journals.plos.org/plosone/arti...

(more to come soon™️)

Species-specific dynamics may cause deviations from general biogeographical predictions – evidence from a population genomics study of a New Guinean endemic passerine bird family (Melampittidae)

The family Melampittidae is endemic to New Guinea and consists of two monotypic genera: Melampitta lugubris (Lesser Melampitta) and Megalampitta gigantea (Greater Melampitta). Both Melampitta species ...

journals.plos.org

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Per Alström @peralstrom.bsky.social · 7d

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

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Rike Stelkens @stelkens.bsky.social · 20d

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/...

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James Bonfield @jbonfield.bsky.social · 23d

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

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Thomas Lin Pedersen @thomasp85.com · 27d

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

ggplot2 4.0.0

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

www.tidyverse.org

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Camille Roux @crouxevo.bsky.social · 26d

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

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Ben Wiens @omys-omics.bsky.social · Apr 14

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...

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

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Silu Wang (she/her)🇨🇦 @siluwang.bsky.social · Aug 30

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

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Germán Hernández-Alonso @germanha.bsky.social · Aug 28

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...

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

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Anton Suvorov @antonsuvorov.bsky.social · Aug 23

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...

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

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Freja Lindstedt @frejalindstedt.bsky.social · Aug 22

😎👇

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

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Mahwash Jamy @mjamy.bsky.social · Aug 21

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

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Ingo Müller @ingomue.bsky.social · Aug 21

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!

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Merve Nur Güler @meerf.bsky.social · Aug 18

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

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Ingo Müller @ingomue.bsky.social · Aug 14

Thanks a lot @jenteo.bsky.social for discussing our paper on your blog!

Jente Ottenburghs | Avian Hybrids @jenteo.bsky.social · Aug 13

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?

Genetic analyses suggest an ephemeral speciation model.

avianhybrids.wordpress.com

Reposted by Ingo Müller

Darren Irwin (he / him) @darrenirwin.bsky.social · Aug 13

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

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

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José Cerca @naturalselection.bsky.social · Aug 10

*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...

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

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Sara Lipshutz (she/her) @jacanamama.bsky.social · Aug 10

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

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

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Trevor Faske @trevorfaske.bsky.social · Jul 30

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/...

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Laura Bertola @lauradbertola.bsky.social · Aug 9

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

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...

www.cell.com

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bioRxiv Genomics @biorxiv-genomic.bsky.social · Jul 26

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

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Mozes Blom @moosblom.bsky.social · May 22

🚨 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...

14/2025 PhD student (f/m/d)

jobs.museumfuernaturkunde.berlin

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Alexis Stamatakis @stamatak.bsky.social · May 15

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/...

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

github.com

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Rafeeque Mavoor @rafeeque.com · May 13

🧵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!

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Loïs Rancilhac @loisrancilhac.bsky.social · May 14

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)

academic.oup.com

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Ethan Linck @elinck.bsky.social · May 12

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...

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

doi.org

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