One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential.
www.biorxiv.org/content/10.1...
2. I don’t quite get this. My theoretical work computes expected psi for a single snp/mutation, so I don’t see how molecular clock (based on accumulation of mutations?) work here. I’ve linked the preprint in another post which gives more details.
1. For coalescent computations it is enough to consider 2 samples from A and 2 samples from B, which is what I did. With data, really you can use as much as you want to compute frequencies.
me with my poster))
please come see my poster today 🥺🥺🥺 #smbe2025
new preprint from me!
did you know that psi index is a hyperbolic tangent of the difference in drift between the two populations?
Flybase lost all of the NIH support overnight - it is a disaster for the community. Please consider donating. I just did! www.philanthropy.cam.ac.uk/give-to-camb...
How is functional variation at large-effect loci maintained in natural populations?
Thrilled to share our work showing how beneficial dominance reversal helps fruit flies maintain a resistance polymorphism as selection varies in their environment! A thread 🧵 1/n
www.biorxiv.org/content/10.1...
really happy to have participated in this project! this figure proves that a chromosome-scale sweep happened based on the time series of allele frequencies during the sweep (and even shows loci which have potentially swept independently).
new photo posts!!
www.lappo.photo
anyway, try it out and let me know what you think! i would appreciate any feedback and/or bug reports uwu
4/4
the main caveat is that slim-runner can only currently deal with tabular output in the csv format. it will work great if you are recording a set of quantities per cycle or per simulation. but, it won't help you directly if you are trying to e.g. keep track of tree sequences
3/
this wrapper is inspired by @vsbuffalo.bsky.social's slimflow, but has two main differences:
a) it's not based on snakemake and therefore can easily handle 10s or 100s of millions of simulations, and
b) it batches output to disk so you don't end up with millions of tiny files
2/
did you ever need to run many SLiM simulations to understand the behavior of some popgen quantity?
i have released a rust-based wrapper for SLiM that takes care of large-scale parallel runs over parameter grids!
github.com/EgorLappo/sl...
1/
Thrilled to share a new lab pre-print from graduate student Tris Dodge! Tris & co elegantly uncover the genetic underpinnings and fitness consequences of a sexual mimicry polymorphism in Xiphophorus birchmanni: www.biorxiv.org/content/10.1...
hanging out at #tagc2024
It's conference application season! We in the Rosenberg Lab recently assembled a list of conferences and I thought it could be helpful for other folks doing theoretical population biology. List is below -- feel free to add any we missed!
my work on cultural evolution and transmission biases in chess is out today in Proceedings B!
royalsocietypublishing.org/doi/10.1098/...
humsci.stanford.edu/feature/stud...
beach photo on film
i've been slacking off reading about phylogenetic networks and f-statistics, and instead posted some film photos from my trip to Melbourne
egorlappo.me/posts/2023-0...
Beautiful crow against a black background
It seems to me that the time is ripe for a Bluesky thread about how—and maybe even why—to befriend crows.
(1/n)
one of my film photos from high school: a house and a very dirty dark sky
decided to start posting some of my film photos online!
check them out here
https://egorlappo.me/posts/2023-08-12-old-photos.html
