23 July 2023

 

 

Here are my picks of papers for the week:

 

Emergent coexistence in multispecies microbial communities. Álvaro Sánchez does some pretty neat, elegant work showing that if you break down a stable synthetic microbial community by studying all pairwise interactions of its members, almost every single time you’ll get one member of the pair outcompeting and excluding the other. The point of doing this is to show that ecological complexity isn’t a consequence of coexistence, but rather that coexistence is a consequence of ecological complexity. Not the first time I see this idea explored, but it’s a cool one. https://www.science.org/doi/10.1126/science.adg0727, or open access here: https://europepmc.org/article/MED/37471535

 

Sequential mutations in exponentially growing populations. This theoretical paper seems to have some useful approaches to estimate the number of mutants in an exponentially growing population using branching processes. I’ve banged my head against the wall with this for my own simulations, so I’m glad to see someone else figure it out. Pretty relevant for everything from cancer to pathogen infections to adaptability in ecology, math is fun. https://arxiv.org/abs/2208.02088

 

Using big sequencing data to identify chronic SARS-Coronavirus-2 infections. It’s pretty crazy we have the sequencing depth to make studies like this possible. These folks were able to find publicly available covid genomes that seemed to correspond to the same individual sampled at multiple points over the course of a long-term infection. They confirm at scale what had been observed in manually-found chronic cases (hat tip to the legend, Ryan Hisner): within-host immune selection pressure seems to be predictive of future population-level evolution. They cap it off by training a language model to detect chronic infections from a single genome sequence, which could be a useful way of guiding control efforts (as well as more windows into the future, as they suggest). https://www.biorxiv.org/content/10.1101/2023.07.16.549184v1

 

Dating the origin and spread of specialization on human hosts in Aedes aegypti mosquitoes. This paper has been out for a while but just got reviews published now, following eLife’s new model. They show how mosquito (the viral fever kind, not malaria kind) adaptation to human hosts has occurred in two waves: one 5000 years ago driven by the climatic changes that created the Sahara (yes, the Sahara is only 5000 years old!) and the second driven by urbanization in the past half century.

https://elifesciences.org/articles/83524

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