Afra Salazar
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salazarafra.bsky.social
Afra Salazar
@salazarafra.bsky.social
150 followers 190 following 17 posts
PhD student in microbial ecology and evolution at the University of Lausanne salazarafra.github.io | Literary fiction, philosophy & cinema
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Reposted by Afra Salazar
brockhurstlab.bsky.social
New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

www.biorxiv.org/content/10.1...
Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages
Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...
www.biorxiv.org
October 6, 2025 at 6:27 AM
Reposted by Afra Salazar
kepatitis-c.bsky.social
What is the best strategy to win any contest?

Eliminate your opponents of course.

Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.

www.biorxiv.org/content/10.1...
November 20, 2025 at 10:12 PM
Reposted by Afra Salazar
baym.lol
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Reposted by Afra Salazar
ellinoralseth.bsky.social
Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky

journals.plos.org/plosbiology/...
Bacterial immune systems as causes and consequences of microbiome structure
Bacterial immune systems have evolved in response to diverse molecular "parasites", yet their ecological roles remain poorly understood. This Essay explores how interactions between mobile genetic ele...
journals.plos.org
November 19, 2025 at 6:35 PM
Reposted by Afra Salazar
natecoevo.nature.com
Population genetics simulations and analysis of experimental datasets in yeast, Drosophila and E. coli show that beneficial mutations are abundant but transient, as they become deleterious after environmental turnover (antagonistic pleiotropy)🧪 www.nature.com/articles/s41...
Adaptive tracking with antagonistic pleiotropy results in seemingly neutral molecular evolution - Nature Ecology & Evolution
Population genetics simulations and analysis of experimental datasets in yeast, Drosophila and E. coli show that beneficial mutations are abundant but transient, as they become deleterious after envir...
www.nature.com
November 20, 2025 at 4:31 PM
Reposted by Afra Salazar
tatianadimitriu.bsky.social
PhD studentship opportunity! Join us at St Andrews to study the factors controlling plasmid transmission in the gut. Competition-funded as part of the EASTBIO DTP, co-supervised with Dr Jaclyn Pearson. Please share & pass on to anyone interested! 🦠🧫 Deadline 15th December👇
www.findaphd.com
November 18, 2025 at 11:41 AM
Reposted by Afra Salazar
jpjhall.bsky.social
🚨#PhD studentship opportunity! Plasmids provide bacteria with antimicrobial resistance, but do they have more fundamental effects on behaviour? 🧫🦠💫🧟‍♂️

Apply for a 4y funded MRC DiMeN position with me and Jamie Wheeler @livuni-ives.bsky.social www.findaphd.com/phds/project...
MRC DiMeN Doctoral Training Partnership: Resistant zombies: how drug-resistance plasmids manipulate the behaviour of the opportunistic pathogen Pseudomonas aeruginosa at University of Liverpool on Fin...
PhD Project - MRC DiMeN Doctoral Training Partnership: Resistant zombies: how drug-resistance plasmids manipulate the behaviour of the opportunistic pathogen Pseudomonas aeruginosa at University of Li...
www.findaphd.com
November 18, 2025 at 9:38 AM
Reposted by Afra Salazar
filipruzicka.bsky.social
Modestly, we decided to review a century's worth of theories of balancing selection :) onlinelibrary.wiley.com/doi/10.1111/...
A century of theories of balancing selection
Traits that affect organismal fitness are often highly genetically variable. This genetic variation is vital for populations to adapt to their environments, but it is also surprising given that natur...
onlinelibrary.wiley.com
November 14, 2025 at 2:31 PM
Reposted by Afra Salazar
plosbiology.org
When colonizing a new habitat, organisms adapt to maximize their reproductive success via #LifeHistory #evolution. @ecoevodevolab.bsky.social @cbank.bsky.social show that life history evolution facilitates niche diversification across a range of theoretical models @plosbiology.org 🧪 plos.io/4p7YT0a
An eco-evolutionary feedback loop promoting diversity. Ecological diversification is common in complex landscapes composed of multiple ecosystems connected by dispersal (e.g., fish radiations across multiple lakes or bird radiations across island archipelagos). After colonization of a novel environment, local adaptation in life history results in stronger intraspecific competition, which, in the presence of ecological opportunity, induces disruptive selection. As a consequence, ecological diversification driven by niche specialization occurs, increasing phenotypic diversity within populations or species diversity in case barriers to gene flow evolve. In either case, functional diversity is enhanced, which, in turn, can positively influence dispersal and thereby the rate of colonization of novel environments. Although our model does not explicitly incorporate spatial structure, the evolutionary trajectories are assumed to begin from a colonization event, which is implicitly linked to dispersal across the landscape.
November 13, 2025 at 10:02 AM
Reposted by Afra Salazar
benkawam.bsky.social
New paper!

We propose a framework to empirically study animal social relationships by modelling social network (SN) data as time-series—that is, without the need to aggregate them over time.

www.biorxiv.org/content/10.1...
Each dyad (a, b) moves through four discrete states over time, represented by coloured circles. The dyad remains in a given state for a certain duration, or "holding time", before transitioning to a new state according to state-specific transition probabilities, indicated by arrows showing all possible (non-zero) transitions. Paintings by Sofia M. Pereira & Judith von Nordheim.
November 12, 2025 at 11:56 AM
Reposted by Afra Salazar
jaguilarrod.bsky.social
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...
Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation
The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...
www.biorxiv.org
October 22, 2025 at 5:46 PM
Reposted by Afra Salazar
sophiejwalton.bsky.social
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 11, 2025 at 5:15 PM
salazarafra.bsky.social
"I've been in 160 films, and I feel I'm nearing the end, but of all of the films I have been in, Harakiri, taken as a whole, is my favourite of them all."

Tatsuya Nakadai, the immortal.
letterboxd.social Letterboxd @letterboxd.social · 13d
Tatsuya Nakadai (1932–2025)
November 11, 2025 at 5:42 PM
Reposted by Afra Salazar
mfwhite2.bsky.social
Thinking about your first steps to independent research? We'd love to hear from you. More details below, or contact me directly for details - reposts appreciated!

www.nature.com/naturecareer...
Biomolecular Science Fellowship Day - St Andrews, Fife (GB) job with UNIVERSITY OF ST ANDREWS | 12848597
The School of Biology at the University of St Andrews is inviting applications from outstanding visionary Research Fellow and Future Leader candida...
www.nature.com
November 10, 2025 at 4:44 PM
Reposted by Afra Salazar
tanjastadler.bsky.social
Open position at the Swiss Institute of Bioinformatics:
We are looking for a Director of the Center of Pathogen Bioinformatics
apply.refline.ch/499599/0346/...
I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and
Director, Center for Pathogen Bioinformatics
The Centre for Pathogen Bioinformatics (CPB) is a unit of SIB which offers expertise and services in pathogen bioinformatics, computational molecular epidemiology and related multi-site project manage...
apply.refline.ch
October 25, 2025 at 1:03 PM
Reposted by Afra Salazar
pengellab.bsky.social
🐝🦠 New paper: rdcu.be/eOf7A
Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social
Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota - Nature Communications
Authors analyse paired viral and bacterial shotgun metagenomics data from individual honeybee guts, revealing modular, nested phage–bacteria networks, with viral diversity mirroring bacterial strain c...
www.nature.com
November 4, 2025 at 8:36 PM
Reposted by Afra Salazar
arvidagren.bsky.social
*NEW PAPER*

How much of a threat are within-organism conflicts, really?

In Biology & Philosophy, @martijnschenkel.bsky.social, Manus Patten, and I present a mathematical framework to measure evolutionary individuality in the face of internal conflicts. link.springer.com/article/10.1...
Screenshot of the abstract. It reads In biology, individuals can be identified at various levels of organization, ranging from the molecular and cellular—e.g., viruses and protists—to the organismal and societal—e.g., termites and termite colonies. This nested biological hierarchy results from evolutionary transitions in individuality, in which lower-lying entities (particles) come together to form higher-level entities (collectives). These collectives are then taken to be individuals in their own right, capable of being the units on which selection acts and where adaptations may reside. Challenges arise, however, when we recognize the possibility for internal conflict, for example from selfish genetic elements within organisms. Here we develop a quantitative approach to biological individuality, in which collectives qualify as individuals to the extent that their particles possess a unity of purpose—i.e., that they possess aligned fitness interests. We propose a mathematical framework that measures the degree of individuality exhibited by organisms and other biological collectives in the presence of internal conflicts. This framework not only helps pinpoint where in the hierarchy biological individuality sits, but also identifies the level at which adaptation may reside. We develop two metrics: fitness unity, which measures the threat posed by internal conflicts to a collective individual’s status as an optimizing agent; and trait unity, which measures differences in optimal strategies among its particles. Finally, we consider cases where internal conflicts become so disruptive to individualized biological collectives so that it no longer makes sense to think of them as individuals, but instead as compromises of multiple competing particles.
October 31, 2025 at 1:24 PM
Reposted by Afra Salazar
olimeacock.bsky.social
I am excited to announce two PhD opportunities! Come and join our interdisciplinary team in Sheffield, UK.
- Destroying forever chemicals with microbes and cold plasma: tinyurl.com/mth8ymx5
- Learning how motile bacteria make decisions: tinyurl.com/2hmc9a8u
UK and overseas students welcome to apply!
ECOSOLUTIONS DFA - Harnessing microbes and cold plasma to concentrate and destroy ‘forever chemicals’ in food associated ecosystems at University of Sheffield on FindAPhD.com
PhD Project - ECOSOLUTIONS DFA - Harnessing microbes and cold plasma to concentrate and destroy ‘forever chemicals’ in food associated ecosystems at University of Sheffield, listed on Find...
tinyurl.com
October 30, 2025 at 11:53 AM
Reposted by Afra Salazar
cbank.bsky.social
We have an open PhD position (application deadline 9 January 2026) in "Theory of fitness landscapes" at @unibe.ch 🤓⛰️📊👩‍💻🎓: banklab.github.io/positions/

Please share widely!

#QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED
October 28, 2025 at 4:22 PM
Reposted by Afra Salazar
paulbrainey.bsky.social
@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎

www.pnas.org/doi/10.1073/...
Jumbo phage–mediated transduction of genomic islands | PNAS
Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages, and c...
www.pnas.org
October 28, 2025 at 6:36 PM
Reposted by Afra Salazar
kostchristian.bsky.social
#microsky #mevosky @spp2389.bsky.social

A PhD position is available in my lab to work on:

Emergence and self-organisation of bacterial metabolism in consortia of cross-feeding bacteria.

Please RT

Deadline: 12.11.25

More infos 👇
shorturl.at/rAKAT
October 28, 2025 at 8:43 AM
Reposted by Afra Salazar
lucasoldini.bsky.social
(1/9) Join us in Bern, Switzerland (8–11 Feb 2026) for our EMBO Workshop on Molecular Mechanisms of Selfish Elements and Strategies!

Organized with Tanja Schwander, Laura Ross (@laurarossevo.bsky.social) and Axel Imhof.

meetings.embo.org/event/26-sel...

#EMBOselfishElements #EMBOevents
Molecular mechanisms of selfish elements and strategies
Certain genes, chromosomes, organelles, or entire sets of chromosomes can bias their transmission to the next generation, propagating themselves at the expense of the rest of the genome. Referred to …
meetings.embo.org
October 27, 2025 at 5:37 PM
Reposted by Afra Salazar
craigmaclean.bsky.social
New pre-print: Plasmid dependent phage effectively eliminate AMR bacteria and block plasmid transmission in the chicken gut microbiome

Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky

www.biorxiv.org/content/10.1...
Plasmid dependent phage eliminate pathogenic bacteria and antibiotic resistance plasmids from the chicken gut microbiome
Conjugative plasmids are a key reservoir of antimicrobial resistance (AMR) in commensal and pathogenic bacteria within the gut microbiome. Plasmid-dependent phage (PDPs) are a promising therapeutic op...
www.biorxiv.org
October 27, 2025 at 8:19 AM
Reposted by Afra Salazar
yagmurerten.bsky.social
Applications for the MEME programme (www.evobio.eu
) are now open! MEME is a research- and mobility-oriented master’s in evolutionary biology (& I’m a proud alumna!), jointly run by the Unis of Groningen, Uppsala, Montpellier, and LMU Munich, with Harvard and Lausanne as partners. Spread the word!
October 23, 2025 at 12:15 PM
Reposted by Afra Salazar
sanmillan.bsky.social
New paper with my (amazing) friend and mentor @jrpenades.bsky.social
Really looking forward to see what plasmid aficionados think of this one!!
With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others
www.cell.com/cell-reports...
Non-conjugative plasmids limit their mobility to persist in nature
Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...
www.cell.com
October 22, 2025 at 1:12 PM