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Ingo Müller

@ingomue.bsky.social
218 followers 180 following 7 posts

Postdoc @ Uppsala University | Bioinformatics, population genomics, adaptation, mainly in 🐦 | First gen | 🇵🇱x🇩🇪 Hybrid | Occasional nerdy arts

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Reposted by Ingo Müller
David Díez del Molino 🇪🇸🇸🇪🏳️‍🌈 @indianadiez.bsky.social · 24/09/2026
New research in @molecularecolup.bsky.social! Museum collections help us understand the genomic consequences of the insect biodiversity crisis 🐝🧬🏛️ We analyzed specimens spanning 150 years to track genomic diversity in the common carder bee in Sweden. OA onlinelibrary.wiley.com/doi/full/10....
Sampling details
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José Cerca @naturalselection.bsky.social · 22/09/2026
V happy about this one (@brentcemerson.bsky.social @biodiversitysmns.bsky.social @hernmoral.bsky.social)et al Species have survived on oceanic islands for Mya despite occupying small geographic areas, facing environmental calamities and having low Ne. We discuss this w/ a focus on conservation. 1/2
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Jente Ottenburghs | Avian Hybrids @jenteo.bsky.social · 15/09/2026
Your daily Avian Hybrids story! Genomic confirmation of intergeneric hybrids between Birds-of-Paradise species avianhybrids.wordpress.com/2025/03/05/g... #ornithology
avianhybrids.wordpress.com
Genomic confirmation of intergeneric hybrids between Birds-of-Paradise species
Why does reproductive isolation break down between these species?
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Markus Stetter @mgstetter.bsky.social · 18/09/2026
New preprint! 🎉 How do populations adapt to a changing environment? We show how standing genetic variation enables polygenic adaptation, while the speed and magnitude of environmental change can determine whether populations adapt—or go extinct. www.biorxiv.org/content/10.6...
biorxiv.org
Standing genetic variation drives polygenic adaptation to different environmental shifts
Most organisms are well adapted to the environment they have been exposed to for many generations. However, changing environments pose existential threats to populations, unless they are able to adapt...
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Christian Landry @christianlandry.bsky.social · 04/08/2026
Our latest contribution on #regulatoryevolution in which we show that the shape of fitness functions and the distribution of mutational effect sizes jointly limit adaptation by regulatory mutations. Led by @simonaube.bsky.social www.nature.com/articles/s41...
nature.com
The shape of fitness functions and the distribution of mutational effect sizes jointly limit adaptation by regulatory mutations - Nature Ecology & Evolution
Saturation mutagenesis of the FCY1 promoter in budding yeast shows that adaptation to 5-fluorocytosine is not accessible through single cis-regulatory mutations, despite large mutational effects on pr...
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Evolutionary Journal of the Linnean Society @evojlinnsoc.bsky.social · 29/07/2026
Renowned Evolutionary biologists Peter & Rosemary Grant are back with new research on adaptive radiation in Geospiza finches on Daphne Major, looking at the long term impacts of hybridization on 3 species of ground finch! You can read the full paper below 👇 🧪 (1/2) doi.org/10.1093/evol...
doi.org
Fission, fusion and the generation of novelty in Geospiza species on Daphne Major Island, Galápagos
Abstract. Early stages in the adaptive radiation of Darwin’s finches are characterized by divergence (fission) and convergence (fusion) caused by natural s
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Darren Irwin (he / him) @darrenirwin.bsky.social · 25/07/2026
Magic traits, search costs, and the persistence of species in secondary contact Jack R. Farley, Darren Irwin bioRxiv 2026.07.23.740407 www.biorxiv.org/content/10.6...
biorxiv.org
Magic traits, search costs, and the persistence of species in secondary contact
When two populations come into secondary contact, assortative mating can act as a barrier to gene flow. However, when assortative mating is incomplete, associations between preference and cue loci can...
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Ferran Sayol @ferransayol.bsky.social · 24/07/2026
New paper out! 🖨️ Glad to be part of this study, out in Science Advances: "Emergent patterns of island biodiversity in the Anthropocene" www.science.org/doi/10.1126/... Much of what looks natural in island biodiversity is a legacy of human impacts going back millennia. See main findings 👇🧵 (1/8)
science.org
Emergent patterns of island biodiversity in the Anthropocene
Human impacts substantially affect our ability to detect and understand natural biodiversity patterns.
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Thibault (Tibo) Leroy @tiboleroyinen.bsky.social · 07/07/2026
Happy to share that Maëva Gabrielli's latest work on Zosterops borbonicus is now published in Evolution! Interested by identifying barrier loci with genomic data? I hope you will find this piece of work interesting! ⬇️ academic.oup.com/evolut/advan...
academic.oup.com
Accounting for recombination rate variation improves inference of barrier loci and reveals the role of both natural and sexual selection in an incipient bird radiation
Abstract. Examining genomic patterns of differentiation across lineage pairs at different stages of the speciation continuum, in combination with recombina
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José Cerca @naturalselection.bsky.social · 15/07/2026
We published a new paper, which was a fun side quest of mine ➡️ 🧭❓🗺️ : Hybridization with wild individuals fuels reindeer domestication. royalsocietypublishing.org/rspb/article...
royalsocietypublishing.org
Hybridization with wild individuals fuels reindeer feralization
Abstract. Domestication has profoundly influenced the development of human agriculture, and is characterized by intense artificial selection. Feralization
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Andy Lee, PhD @andylee.bsky.social · 12/07/2026
In our Viewpoint (onlinelibrary.wiley.com/doi/abs/10.1...) we synthesize the gametic definition (outlined by Janicke et al below) and other definitions of sex (e.g., multivariate definition). We contend that is NO consensus on “biological sex” (maybe a consensus isn’t actually necessary…)
onlinelibrary.wiley.com
There is No Consensus on Biological Sex
At this critical moment when misinformation about sex is being applied to policy globally, scientific clarification on the definition of biological sex is valuable. Here, we evaluate the primary appr...
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Jun Ishigohoka @junishigohoka.bsky.social · 16/06/2026
Paper alert!🧬🐦💻 Divergent selection is the textbook explanation for narrow inversion clines. Our blackcap inversion cline doesn't fit: it is wide, and the inversion is always the rarer arrangement. We show that negative frequency-dependent selection shifting between populations underlies this!
onlinelibrary.wiley.com
Shifting Balancing Selection Underlies an Inversion Cline in Eurasian Blackcap
We investigated what factor contributes to a cline of a chromosomal inversion of the Eurasian blackcap, which differs from typical inversion clines maintained by divergent selection. Using a simulati...
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Tom Mathers @tom-mathers.bsky.social · 15/06/2026
Bit late posting this... MicroFinder is now published in GigaScience: academic.oup.com/gigascience/....
academic.oup.com
MicroFinder: conserved gene-set mapping and assembly ordering for manual curation of bird dot microchromosomes
AbstractBackground. Obtaining chromosomally complete genome assemblies across the tree of life is an important goal of biodiversity genomics. However, some
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Heng Li @lh3lh3.bsky.social · 16/06/2026
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
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Katharina Hoff @katharinahoff.bsky.social · 11/04/2026
1/ BRAKER4 hatched! The Earth BioGenome Project is on track to sequence ~1.5M eukaryotic species. Every one needs a structural annotation. No Perl monolith was going to survive that. So we rewrote BRAKER from the ground up. github.com/Gaius-August...
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José Cerca @naturalselection.bsky.social · 02/06/2026
🧨 New publication out (I think this one is 🌶️ ): Cerca & @stelkens.bsky.social - "The identity crisis of speciation genomics". academic.oup.com/evolinnean/a...
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Susan Johnston @susanjohnston.bsky.social · 01/06/2026
📣🧬 Postdoc Alert🧬📣 We are hiring a 2+ year NERC-funded postdoc at Edinburgh Uni investigating causes and consequences of sex differences in recombination in house sparrows in Norway. Informal enquiries welcome at Susan.Johnston@ed.ac.uk 🙂 Details here: elxw.fa.em3.oraclecloud.com/hcmUI/Candid...
A female and male sparrow stand on a wooden post. Photo by Peter S. Ranke.
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Heng Li @lh3lh3.bsky.social · 30/05/2026
Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...
biorxiv.org
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Molecular Biology and Evolution @molbioevol.bsky.social · 25/05/2026
Wong et al. present IQ-TREE version 3, with new features including mixture models, gene and site concordance factors, integration with phylogenomic divergence time estimation, and a fully featured sequence simulator. 🔗 doi.org/10.1093/molbev/msag117 #evobio #molbio #compbio
MBE | IQ-TREE 3: phylogenomic inference software using complex evolutionary models
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 12/05/2026
Love this quote: "We used to make fun of Edgar Anderson by saying that he was finding hybrids under every bush. Then we realized that even the bushes were hybrids." academic.oup.com/jeb/article/...
academic.oup.com
Hybridization and speciation*
Abstract. Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow a
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Mozes Blom @moosblom.bsky.social · 11/05/2026
⏰⏰⏰ 6 days more to apply!! Don't be shy if you feel like you don't fit all criteria; motivation, curiosity and fun to work with, are the most important traits that we are looking for! ⏰⏰⏰
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Plant Science Spotlight @plant-sci.bsky.social · 05/05/2026
Don’t reach for ChatGPT Images or Nano Banana as your first option when creating scientific images There are multiple free and open-source images, icons, and tools for creating scientific illustrations. #plantscience @stephenturner.us blog.stephenturner.us/p/free-open-...
blog.stephenturner.us
Free and open-source images, icons, and tools for creating scientific illustrations
Phylopic, NIH Bioart, Bioicons, Scidraw, Open Science Art, Health Icons, Servier Medical Art, Biodiversity Heritage Library, the Noun Project, Segment Anything, Excalidraw, draw.io, Biographics
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Lukas Musher @lukemusher.bsky.social · 22/04/2026
New simulation study with Ethan Gyllenhaal highlighting a potentially big problem for biogeographic inference. royalsocietypublishing.org/rspb/article...
royalsocietypublishing.org
Spatial impacts on gene flow may hinder linking phylogeographic data to macroevolutionary patterns
Abstract. Biogeography relies on estimates of phylogeny and gene flow to test hypotheses. Established theory posits: (i) gene flow varies non-randomly with
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Scott V. Edwards @scottvedwards.bsky.social · 22/04/2026
Ver excited to share my just-published Darwin Review with @lh3lh3.bsky.social on population-scale long-read sequencing! royalsocietypublishing.org/rspb/article...
royalsocietypublishing.org
Population-scale long-read DNA sequencing: peering under the hood of the new evolutionary genomics
Abstract. Population-scale long-read DNA sequencing (PLRS) is rapidly reshaping our understanding of genomic variation in humans and non-model species. In
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EvolDir @evoldir.bsky.social · 21/04/2026
📣 EvolDir is now managed by @eseb.bsky.social! We are delighted to be taking the reins and express our gratitude to both Brian Golding who began this service to the community in the mid-1980s and to @rdmpage.bsky.social who ran this account until now 👏 You can now find evoldir here: evoldir.net
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Simon J. Greenhill @simongreenhill.bsky.social · 16/04/2026
This is lovely: www.theguardian.com/environment/... #science #biology
theguardian.com
In the footsteps of Linnaeus: scientists share their passion for species from tiny wasps to hairy plants – in pictures
For his project ‘De Oförtrutna’ (The Relentless), photographer Christer Björkman pictured Swedish scientists working in the spirit of Carl Linneaus, the botanist who created the modern taxonomic syste...
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Pilar Herrera Egoavil @tikaevolutiva.bsky.social · 16/04/2026
The first chapter of my PhD thesis is out: doi.org/10.1111/mec.... !!! This comparative study explores the presence and maintenance of a joint contact zone among three important forest tree species (formed during recolonisation after the LGM). Trees, genetics and evolution, just a perfect combo!
doi.org
When South Meets North: A Joint Contact Zone Coinciding With Environmental Gradients in Three Boreal Tree Species
Post-glacial recolonisation of Fennoscandia created secondary contact zones in many species, offering opportunities to study how gene flow and selection contribute to their establishment and maintena....
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Olivia Ghosh @oliviamghosh.bsky.social · 30/03/2026
Really excited that this major work from my PhD is finally published in @plosbiology.org ! In it, we were trying to tackle a fundamental question in evolution - how do genetic mutations map onto evolutionary fitness? (1/n) journals.plos.org/plosbiology/...
journals.plos.org
Genotype-fitness mapping of adaptive mutants reveals shifting low-dimensional structure across divergent environments
Predicting the effect of a genetic mutation on fitness is a major challenge in evolutionary biology. This study uses fitness effects of a large collection of adaptive yeast mutants in multiple lab env...
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Laura Bertola @lauradbertola.bsky.social · 05/03/2026
An Evolving View of Species Tree Inference academic.oup.com/sysbio/advan...
academic.oup.com
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
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Ingo Müller @ingomue.bsky.social · 30/12/2025
Ancestral-area algorithms are unreliable onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
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 ...
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Dr Mark E Hauber @thecowbirdlab.bsky.social · 26/12/2025
www.cell.com/trends/ecolo...
cell.com
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...
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Evolution Letters @evolletters.bsky.social · 04/12/2025
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.
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José Cerca @naturalselection.bsky.social · 05/12/2025
📰 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...
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Lukas Musher @lukemusher.bsky.social · 01/12/2025
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...
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David Toews @davetoews.bsky.social · 21/11/2025
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....
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.
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Jesper Boman @jesperboman.bsky.social · 18/11/2025
Changing Views on Speciation onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
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,...
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Justin Merondun @merondun.bsky.social · 30/10/2025
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
doi.org
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...
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Verena Kutschera @vekutschera.bsky.social · 20/03/2025
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...
academic.oup.com
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
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Ryo Yamaguchi @r-yamaguchi.bsky.social · 15/10/2025
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
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...
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Dr. Stepfanie Aguillón 😷 @s-m-aguillon.bsky.social · 12/09/2025
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...
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
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Per Alström @peralstrom.bsky.social · 01/10/2025
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 · 18/09/2025
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 · 15/09/2025
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 · 11/09/2025
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
tidyverse.org
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
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Camille Roux @crouxevo.bsky.social · 12/09/2025
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 · 14/04/2025
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...
nature.com
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
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Germán Hernández-Alonso @germanha.bsky.social · 28/08/2025
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...
doi.org
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...
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Anton Suvorov @antonsuvorov.bsky.social · 24/08/2025
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...
biorxiv.org
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...
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Freja Lindstedt @frejalindstedt.bsky.social · 22/08/2025
😎👇 Check out my poster here: doi.org/10.13140/RG....
doi.org
(PDF) Gene copy number variations in Brassicaceae
PDF | On Aug 19, 2025, Freja Lindstedt and others published Gene copy number variations in Brassicaceae | Find, read and cite all the research you need on ResearchGate
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