Alex Mackintosh
@thymelicus.bsky.social
Population genetics | Uppsala
Reposted by Alex Mackintosh
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/10.1093/evle... [1/6]
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
doi.org
January 15, 2026 at 11:58 AM
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/10.1093/evle... [1/6]
Reposted by Alex Mackintosh
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/...
www.scilifelab.se/data-driven/...
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...
www.scilifelab.se
January 14, 2026 at 12:31 PM
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/...
www.scilifelab.se/data-driven/...
Reposted by Alex Mackintosh
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...
www.biorxiv.org/content/10.6...
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...
www.biorxiv.org
January 6, 2026 at 8:26 AM
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...
www.biorxiv.org/content/10.6...
Reposted by Alex Mackintosh
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
Among the 9 challenges, we had five winners: @alwaysrong.bsky.social, @adaigle.bsky.social, @andrewhvaughn.bsky.social, @thymelicus.bsky.social, @rgollnisch.bsky.social
December 15, 2025 at 6:48 PM
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
Among the 9 challenges, we had five winners: @alwaysrong.bsky.social, @adaigle.bsky.social, @andrewhvaughn.bsky.social, @thymelicus.bsky.social, @rgollnisch.bsky.social
Reposted by Alex Mackintosh
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
This work is co-advised by @yundeng.bsky.social and Rasmus Nielsen.
1/7
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...
biorxiv.org
November 26, 2025 at 5:09 PM
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
This work is co-advised by @yundeng.bsky.social and Rasmus Nielsen.
1/7
Reposted by 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 ! 📢
Follow @popgroup2026.bsky.social for all updates.
📢 Please share widely ! 📢
Exciting news!
The next #PopGroup meeting will take place in Lille 🍟, France, 7–9 January 2026 – just 1 hour by train from London, Brussels, and Paris.
This year, PopGroup will also host ALPHY, the annual meeting of Evolutionary Genomics.
More info: populationgeneticsgroup.org.uk
See you there !
The next #PopGroup meeting will take place in Lille 🍟, France, 7–9 January 2026 – just 1 hour by train from London, Brussels, and Paris.
This year, PopGroup will also host ALPHY, the annual meeting of Evolutionary Genomics.
More info: populationgeneticsgroup.org.uk
See you there !
Population Genetics group 59
populationgeneticsgroup.org.uk
September 29, 2025 at 1:06 PM
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 ! 📢
Follow @popgroup2026.bsky.social for all updates.
📢 Please share widely ! 📢
Reposted by Alex Mackintosh
🚨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/...
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
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...
www.pnas.org
August 20, 2025 at 2:39 PM
🚨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/...
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/...
Reposted by Alex Mackintosh
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
July 26, 2025 at 5:32 AM
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
Reposted by Alex Mackintosh
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
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
Estimating the reduction in genetic diversity from background selection under non-equilibrium demography and partial selfing https://www.biorxiv.org/content/10.1101/2025.06.30.662370v1
July 7, 2025 at 10:11 AM
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
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
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
Estimating the reduction in genetic diversity from background selection under non-equilibrium demography and partial selfing https://www.biorxiv.org/content/10.1101/2025.06.30.662370v1
July 7, 2025 at 10:11 AM
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
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
Reposted by Alex Mackintosh
#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 👇 😱😱😱
Imagine looking at the distribution of the allelic coverage fraction at heterozygous calls in an indivdual and getting this distribution 👇 😱😱😱
July 1, 2025 at 12:47 PM
#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 👇 😱😱😱
Imagine looking at the distribution of the allelic coverage fraction at heterozygous calls in an indivdual and getting this distribution 👇 😱😱😱
Reposted by Alex Mackintosh
Speciation genomics in scarce swallowtails Iphiclides podalirius and I . feisthamelii : dx.plos.org/10.1371/jour...
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...
dx.plos.org
April 28, 2025 at 7:48 PM
Speciation genomics in scarce swallowtails Iphiclides podalirius and I . feisthamelii : dx.plos.org/10.1371/jour...
Reposted by Alex Mackintosh
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
March 17, 2025 at 7:32 PM
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
Reposted by Alex Mackintosh
Likelihoods for a general class of ARGs under the SMC https://www.biorxiv.org/content/10.1101/2025.02.24.639977v1
February 28, 2025 at 3:33 AM
Likelihoods for a general class of ARGs under the SMC https://www.biorxiv.org/content/10.1101/2025.02.24.639977v1
Reposted by Alex Mackintosh
🚨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!
January 31, 2025 at 3:17 PM
🚨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!
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/5ff8ch9e
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
tinyurl.com
December 12, 2024 at 2:17 PM
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/5ff8ch9e
Reposted by Alex Mackintosh
A new case of hybrid speciation? www.biorxiv.org/content/10.1...
November 20, 2024 at 3:41 PM
A new case of hybrid speciation? www.biorxiv.org/content/10.1...