Alex Mackintosh

Passionate about studying the genomics of local adaptation? Join us for a fully funded 4-year PhD at Uppsala University, Sweden. Enjoy competitive salaries, full employment benefits, and a vibrant research community surrounded by nature. Apply here bit.ly/4gAsHyn

European butterflies have been studied intensely by scientists and naturalists for centuries. It is therefore with some surprise that we wish to report the discovery of a European hybrid lineage of butterflies that has persisted for more than 50,000 years. (THREAD)

Genomic regions of current low hybridisation mark long-term barriers to gene flow in scarce swallowtail butterflies biorxiv.org/cgi/content/sh… #biorxiv_evobio

Genealogical asymmetry under the IM model and a two-taxon test for gene flow biorxiv.org/cgi/content/sh… #biorxiv_evobio

@ethanblinck There is a power analysis for inferring a bottleneck in Bunnefeld et al. 2015 (see Figs 3 and 4) academic.oup.com/genetics/artic…

looking for a good example of a power analysis in empirical population genomics—ideally in the context of demographic inference, but open to other applications. any leads?

@3rdreviewer @DavidEnard pyrho actually outputs values of c, not rho. Users will assume that is what is being estimated. Given that c, Ne and mu all vary along the genome, I don't think rho should be rescaled to c. But, in the case of pyrho, it is!

@DavidEnard I'm not sure I understand: these methods are all explicitly estimating rho (=4Nc), so they are population recombination measures. There is no bias to estimates of meiotic recombination rate (c), because they don't estimate that. 1/2

PopGenomics twitter, I am looking for examples of papers where the authors fit a demographic model to a pair of species and the maximum likelihood estimate of migration rate was 0. Anyone have any suggestions? There should be loads... (retweets appreciated)

Evolution of hybrid inviability associated with chromosome fusions biorxiv.org/cgi/content/sh… #biorxiv_evobio

@RegevSchweiger I also noticed that FitCoal fails to infer a simulated ancient bottleneck that was added to a non-African history (bottleneck III), yet other SMC-based methods pick it up quite well (Fig 3C). This seems at odds with the idea that FitCoal can infer bottlenecks others can't.

FitCoal correctly infers a bottleneck on simulated data - as do previous methods, if slightly less accurately. But for real data, the discrepancy between FitCoal and others is much larger than in simulations. Why? Is it possible to simulate data with such large differences? 4/

A new paper by Hu et al. just out, with wide media coverage. The authors infer a previously undetected very narrow bottleneck in human prehistory around ~0.9Mya, lasting for around 100,000 years, effective pop size ~1300. science.org/doi/10.1126/sc… 1/

@RealRockatansky youtu.be/S3O4qTGHBZ0?si…

Thanks for all the great feedback on the Time Travel episode! Now I gotta find another time travel story so Titor and Mad Mike can be a part of a trilogy.

There's no shame in eating a whole tub of rocky road ice cream doi.org/10.1101/2023.0…

PHD CONTRACT ON BUTTERFLY GENOMICS The Butterfly Diversity & Evolution Lab in Barcelona offers a 4-year PhD contract. If you are interested, please send to Roger Vila (roger.vila@csic.es) a brief letter of motivation, CV, and the BS and MS academic record (with average grades).

@TiBoLeroyInEn @BenoitNabholz Interesting. I didn't feel so confident either, but might try again (with some simulations to boost confidence) in future projects.

@TiBoLeroyInEn @BenoitNabholz Hi Thibault, how well do you think iSMC worked on Oak genomes? I really like the method and tried it out on some butterfly genomes a couple of years ago (tinyurl.com/4fmzvtnr), but think that the true ρ / θ may be too high.

Inversions, ARGs and seahorses !

I'm advertising a @darwintreelife postdoc to work at @EdinburghUni @SBSatEd on comparative #plant genomics! 16 months to use chromosomal level genome assemblies to investigate genomic diversity in British native flowering plants. Collab with @RBGE_Science. 🌲☘️🌼 Please RT.

Large-scale phylogenomics uncovers a complex evolutionary history and extensive ancestral gene flow in an African primate radiation dlvr.it/Sr3XVB

Do chromosome rearrangements fix by genetic drift or natural selection? A test in Brenthis butterflies biorxiv.org/cgi/content/sh… #biorxiv_evobio