Alex Mackintosh

Postdoc working on population genetics | 🦋🐥🌱

[Gabriela Montejo-Kovacevich 🇪🇺 @gmkov]

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 https://t.co/Csl5sHDSaC

[Jesper Boman @JesperBoman]

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)

[bioRxiv Evobio @biorxiv_evobio]

Genomic regions of current low hybridisation mark long-term barriers to gene flow in scarce swallowtail butterflies https://t.co/ozmZ7GQ4DI #biorxiv_evobio

[bioRxiv Evobio @biorxiv_evobio]

Genealogical asymmetry under the IM model and a two-taxon test for gene flow https://t.co/NwdQEWgtz6 #biorxiv_evobio

[Alex Mackintosh @Thymelicus]

@ethanblinck There is a power analysis for inferring a bottleneck in Bunnefeld et al. 2015 (see Figs 3 and 4) https://t.co/hZnKKt4JoB

[Alex Mackintosh @Thymelicus]

@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!

[Alex Mackintosh @Thymelicus]

https://t.co/N0SxC5r0WA

[Alex Mackintosh @Thymelicus]

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)

[bioRxiv Evobio @biorxiv_evobio]

Evolution of hybrid inviability associated with chromosome fusions https://t.co/QIqSVlKKWi #biorxiv_evobio

[Alex Mackintosh @Thymelicus]

@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.

[Alex Mackintosh @Thymelicus]

@RealRockatansky https://t.co/Z8Gd9RW0tR

[Butterfly Diversity & Evolution Lab @RogerVila_Lab]

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 ([email protected]) a brief letter of motivation, CV, and the BS and MS academic record (with average grades).

[Alex Mackintosh @Thymelicus]

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

[Alex Mackintosh @Thymelicus]

@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 (https://t.co/Y9POidZxqF), but think that the true ρ / θ may be too high.

[Alex Mackintosh @Thymelicus]

Inversions, ARGs and seahorses !

[bioRxiv Genomics @biorxiv_genomic]

Divergence and gene flow history at two large chromosomal inversions involved in long-snouted seahorse ecotype formation https://t.co/tjntJD6SaD #biorxiv_genomic

[Alex Twyford @alex_twyford]

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.

[Introgression Papers @_introgression]

Large-scale phylogenomics uncovers a complex evolutionary history and extensive ancestral gene flow in an African primate radiation https://t.co/NWKfsS1Hbn

[bioRxiv Evobio @biorxiv_evobio]

Do chromosome rearrangements fix by genetic drift or natural selection? A test in Brenthis butterflies https://t.co/D7eZ3bR6AE #biorxiv_evobio