Alex Mackintosh

🌱PhD position in my lab at the University of Edinburgh to study adaptation to novel environments during plant range shifts: e5-dtp.ed.ac.uk/project?item... Competition for funding through the E5 Doctoral Training Partnership, apply by December 2nd. Please send me an email if you'd like to discuss!

Exciting postdoc position on adaptive introgression in butterflies just announced by Konrad Lohse: elxw.fa.em3.oraclecloud.com/hcmUI/Candid... I can highly recommend working together with him and Simon Martin in Edinburgh.

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? 👇

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...

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

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

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!

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

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

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!

Computing coalescence rates for complex demographies and sampling configurations https://www.biorxiv.org/content/10.64898/2026.04.09.717519v1

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.

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

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]

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/...

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...

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

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

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 ! 📢‬

🚨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 👇 😱😱😱

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

🚨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!

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