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Alex Mackintosh

@thymelicus.bsky.social
252 followers 233 following 12 posts

Population genetics | Uppsala

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Reposted by Alex Mackintosh
KamilSJaron.bsky.social @kamilsjaron.bsky.social · 18/09/2026
I am so excited to see this preprint out. I started working on springtails with @laurarossevo.bsky.social in 2019, but this pinnacle of our efforts manifested only with heroric leadership of Sam Ebdon! So, what's the deal? 👇
Globular springtail Allacma fusca. Female, one of the samples in the linked preprint.
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Ana Ignatieva @anaignatieva.bsky.social · 14/09/2026
We are advertising a 3 year postdoc position for a project on ARGs and structural variation! Based at Oxford stats. Closing date noon 12 October, full details here: my.corehr.com/pls/uoxrecru...
my.corehr.com
Job Details
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Ryan Gutenkunst @ryangutenkunst.bsky.social · 09/09/2026
Increasingly powerful methods are enabling increasing complex models of ancient human history to be inferred from population genomic data. In a recent review, I highlight two blind spots in these inferences: limitations of the methods and choices of models to fit. arxiv.org/abs/2608.27591
arxiv.org
Two blind spots in the demographic inference of human origins from genomic data
Ancient DNA and new inference methods have transformed the study of human origins, but consensus has not followed. Evidence increasingly indicates that hominin populations were pervasively structured ...
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 26/08/2026
For folks interested I just posted my keynote on ARGs from #PEQG26 on youtube (with permission). Thanks again to @genetics-gsa.bsky.social and organizers for what was a wonderful conference (except for the 24hrs prior to my talk when I was too nervous to sleep or think straight) youtu.be/ntJOdZd0mwc
youtu.be
PEQG Keynote 2026
YouTube video by Jeffrey Ross-Ibarra
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Alex Mackintosh @thymelicus.bsky.social · 19/07/2026
New preprint on the effect of ancient admixture / structure on genealogical trees. I introduce a new way of summarising reconstructed genealogies that captures a clear signal of ancient gene flow into the ancestors of modern humans. Feedback welcome!
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Leeban Yusuf @leebanhy.bsky.social · 06/07/2026
How do coevolutionary interactions begin in nature, and what are the first steps of reciprocal adaptation? Our preprint investigates these questions in a natural experiment: an introduced cricket (T. oceanicus) and its acoustically hunting parasitoid (O. ochracea) in Hawaii. shorturl.at/7llsA 1/n
shorturl.at
Ecological genomics of a novel host-parasitoid arms-race in nature
Novel antagonistic interactions between species are expected to drive especially rapid coevolution. However, little is known about the genomic basis of such coevolution in nature because novel inter-s...
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Genome Biology and Evolution @genomebiolevol.bsky.social · 05/06/2026
The June 2026 cover of GBE features our newest Perspective by Brault et al., who propose guidelines and best practices for calculating population genetics summary statistics. 🔗 academic.oup.com/gbe/issue/18/6 #genome #evolution #societyjournal
Genome Biology and Evolution | June 2026 cover
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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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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 11/04/2026
Computing coalescence rates for complex demographies and sampling configurations www.biorxiv.org/content/10.64898/20…
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Evolutionary Biology at Uppsala University @evobiouppsala.bsky.social · 24/03/2026
PREPRINT ALERT! Determinants of chromosomal rearrangements in holocentric Leptidea butterflies www.biorxiv.org/content/10.6... Massive #chromosome reshuffling in Leptidea #butterflies reveals how satellite DNA, rDNA, and duplications—not #transposons, shape the architecture of #genomeevolution.
biorxiv.org
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bioRxivpreprint @biorxivpreprint.bsky.social · 20/02/2026
diempy: fast and reference-free genome polarisation www.biorxiv.org/content/10.64898/20…
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bioRxiv Genetics @biorxiv-genetic.bsky.social · 03/02/2026
The genetic architecture of local adaptation is historically contingent www.biorxiv.org/content/10.64898/20…
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Leeban Yusuf @leebanhy.bsky.social · 15/01/2026
New paper out: “allopatric” Drosophila species aren’t so allopatric after all. We show that most currently allopatric species pairs probably overlapped in the past and exchanged genes at levels similar to sympatric pairs. @evolletters.bsky.social doi.org/10.1093/evle... [1/6]
doi.org
Genomic analyses in Drosophila do not support the classic allopatric model of speciation
Abstract. The allopatric model of speciation has dominated our understanding of speciation biology and biogeography since the Modern Synthesis. It is uncon
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José Cerca @naturalselection.bsky.social · 14/01/2026
Hit me up if you'd like to apply to a Data-driven postdoc fellowship with me in Sweden. 2 year salary, excellent community. Deadline March 31. I have a project idea on reference bias vs pangenome, but keen on hearing ideas. Please share broadly. www.scilifelab.se/data-driven/...
scilifelab.se
DDLS Research School Postdoc call 2026
Call for Academic and Industrial Postdoctoral Fellowships in Data-Driven Life Science 2026 Generic Description of the DDLS Postdoc Program The SciLifeLab and Wallenberg National Program for Data-Drive...
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Katie Abson @katieabson.bsky.social · 06/01/2026
I'm excited to share that our preprint is now available on bioRxiv! Our study challenges the widespread use of molecular genetic diversity as a predictor adaptive potential, with important implications for how genetic data is used to inform conservation decisions. www.biorxiv.org/content/10.6...
biorxiv.org
Nucleotide diversity is a poor predictor of short-term adaptive potential
A capacity to adapt is essential for a population to avoid extinction in a changing world and is recognised as a global conservation priority. Adaptation requires additive (heritable) genetic variatio...
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Ryan Gutenkunst @ryangutenkunst.bsky.social · 15/12/2025
Congratulations to the winners of the 2025 Genomic History Inference Strategies Tournament challenges! Among the 9 challenges, we had five winners: @alwaysrong.bsky.social, @adaigle.bsky.social, @andrewhvaughn.bsky.social, @thymelicus.bsky.social, @rgollnisch.bsky.social
GHIST logo
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Leyan Wang @leyan-wang.bsky.social · 26/11/2025
We are excited to share our recent work on the surprising robustness of Ancestral Recombination Graph (ARG) inference tools to computational phasing errors, now available on BioRxiv: biorxiv.org/content/10.1.... This work is co-advised by @yundeng.bsky.social and Rasmus Nielsen. 1/7
biorxiv.org
Robustness of Ancestral Recombination Graph Inference Tools to Phasing Errors
Ancestral Recombination Graphs (ARGs) are fundamental population genetic structures that encode the genealogical history of a sample of haplotypes along the genome. They have recently received substan...
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Vincent CASTRIC @vincentcastric.bsky.social · 29/09/2025
Very happy to announce that the next POPGROUP meeting will take place in Lille on 7-9 January ! Follow ‪@popgroup2026.bsky.social for all updates. 📢 Please share widely ! 📢‬
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Bob Muscarella @bobmuscarella.bsky.social · 20/08/2025
🚨New paper out in PNAS🚨 Soil eDNA reflects regionally dominant species rather than local composition of tropical tree communities 🧬🌿🌳🌺🧬 We asked about the spatial scale of biodiversity captured by samples of DNA from tropical soils #Luquillo #eDNA. A short 🧵.... www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 26/07/2025
A model-free method for genealogical inference without phasing and its application for topology weighting www.biorxiv.org/content/10.1101/202…
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Alex Mackintosh @thymelicus.bsky.social · 07/07/2025
Our new work on estimation of background selection (BGS) is up on bioRxiv. We investigated the problem using simulations and also developed a method for joint inference of BGS, demography and partial selfing from windowed site frequency spectra along the genome. Feedback is welcome. #BGS
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Alex Mackintosh @thymelicus.bsky.social · 07/07/2025
Our new work on estimation of background selection (BGS) is up on bioRxiv. We investigated the problem using simulations and also developed a method for joint inference of BGS, demography and partial selfing from windowed site frequency spectra along the genome. Feedback is welcome. #BGS
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Nicolas Bierne @couplingdmi.bsky.social · 01/07/2025
#PopGen New preprint of the team on the discovery of a very high rate of polymorphic duplication in a marine bivalve. Imagine looking at the distribution of the allelic coverage fraction at heterozygous calls in an indivdual and getting this distribution 👇 😱😱😱
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Benoit Nabholz @benoitevol.bsky.social · 28/04/2025
Speciation genomics in scarce swallowtails Iphiclides podalirius and I . feisthamelii : dx.plos.org/10.1371/jour...
dx.plos.org
Genomic regions of current low hybridisation mark long-term barriers to gene flow in scarce swallowtail butterflies
Author summary Efforts to understand how new species evolve typically approach the problem through either: 1) investigating patterns of genetic exchange across ‘hybrid zones’ — where closely related s...
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 17/03/2025
The 229 chromosomes of the Atlas blue butterfly reveal rules constraining chromosome evolution in Lepidoptera www.biorxiv.org/content/10.1101/202…
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 28/02/2025
Likelihoods for a general class of ARGs under the SMC www.biorxiv.org/content/10.1101/202…
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KamilSJaron.bsky.social @kamilsjaron.bsky.social · 31/01/2025
🚨Registration open🚨 1st - 6th of June, me, Katie Jenike, @rayanchikhi.bsky.social and Gene Myers will run a week long workshop on k-mers for biodiversity genomics organised by @connectingscience.bsky.social at @sangerinstitute.bsky.social. Join us & get equipped to wrestle large genomic datasets!
https://coursesandconferences.wellcomeconnectingscience.org/event/k-mer-workshop-for-biodiversity-genomics-20250601/
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Alex Mackintosh @thymelicus.bsky.social · 12/12/2024
My and Derek Setter's work on gene flow is now published in the latest issue of Genetics. We show that it is possible to detect past gene flow between two populations by summarising the asymmetry in pop-specific external branch lengths. 1/2 tinyurl.com/5ff8ch9e
tinyurl.com
Genealogical asymmetry under the isolation with migration model and a two-taxon test for gene flow
Abstract. Methods for detecting gene flow between populations often rely on asymmetry in the average length of particular genealogical branches, with the A
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jim mallet @wtf-r-species.bsky.social · 20/11/2024
A new case of hybrid speciation? www.biorxiv.org/content/10.1...
Aricia species photos
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