Alex Mackintosh

diempy: fast and reference-free genome polarisation https://www.biorxiv.org/content/10.64898/2026.02.18.706591v1

The genetic architecture of local adaptation is historically contingent https://www.biorxiv.org/content/10.64898/2026.02.01.703099v1

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

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]

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...

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/...

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...

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...

GHIST logo

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

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...

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.
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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 ! 📢‬

You went to preschool with Naoyuki Takahata?!

HiC. Not particularly cheap, but it is probably the only (non-trio) method where you can accurately phase SNPs across a whole chromosome.

🚨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/...

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

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

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

#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 👇 😱😱😱

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...

Speciation genomics in scarce swallowtails Iphiclides podalirius and I . feisthamelii : dx.plos.org/10.1371/jour...

The 229 chromosomes of the Atlas blue butterfly reveal rules constraining chromosome evolution in Lepidoptera https://www.biorxiv.org/content/10.1101/2025.03.14.642909v1

Likelihoods for a general class of ARGs under the SMC https://www.biorxiv.org/content/10.1101/2025.02.24.639977v1

https://coursesandconferences.wellcomeconnectingscience.org/event/k-mer-workshop-for-biodiversity-genomics-20250601/

🚨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!

The test requires just one unphased diploid from each population and makes few assumptions about the underlying demographic history. I hope that others find the paper/method useful. 2/2

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

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

Sadly I am no longer working on butterfly genomics. I am currently focused on popgen methods with application to plant genomes (mostly simulated plant genomes for now...) Perhaps I'll return one day 🦋

Aricia species photos

A new case of hybrid speciation? www.biorxiv.org/content/10.1...