Alex Mackintosh

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...