S. Lorena Ament

Figure showing the experimental overview as a graphic. Remaining alt text taken from the figure caption in the paper: (A) we sampled flies from six wild orchard populations ranging from Homestead, FL, to Lancaster, MA, and established isofemale lines in the laboratory. (B) We returned to a focal orchard in Media, PA, at early- and late-season timepoints and collected flies to capture evolutionary patterns following winter and summer conditions. (C) We then seeded outdoor mesocosms (N = 9) with an outbred population originating from early-season collections in Media, PA, and sampled flies at the end of summer (mid-season) and fall (late-season) to determine if seasonal patterns are recapitulated in experimental populations controlled for migration, drift, and cryptic population structure. (D) Across each wild or experimental context, we sampled flies, established lines in the lab, completed common garden treatment to remove environmental effects, and scored females for abdominal pigmentation. We also conducted pooled DNA sequencing on additional flies sampled from each population to map genomic patterns for candidate pigmentation SNPs.

How predictably does complex trait adaptation proceed over space and time in wild populations?
doi.org/10.1093/evle...

Now in @evolletters.bsky.social by @skylerberardi.bsky.social, @paulrschmidt.bsky.social et al.

📷: Dr. Rush Dhillon

@charleston.bsky.social and colleagues introduce the ancestry-specific expected genetic relationship matrix (as-eGRM), an analysis framework that estimates the relatedness within ancestry components between admixed individuals, in the @ajhgnews.bsky.social latest article: bit.ly/3U5p0aI #ASHG

A pangenomics-enabled platform for the high-throughput discovery of antifungal resistance factors in crop pathogens https://www.biorxiv.org/content/10.1101/2025.07.18.665620v1

The auditorium is slowly filling up for the opening session and our inaugural keynote speech...

#SMBE2025

Our description of the transcriptomic changes during sexual development in #Podospora anserina is out in @genomics.peercommunityin.org ! peercommunityjournal.org/articles/10....
@i2bcparissaclay.bsky.social @univparissaclay.bsky.social

New preprint: we advertise DAFNEE, a database of academia-friendly eco-evo-archaeo journals. 1/6
#AcademicPublishing #ecoevo #archaeology #EthicalPublishing #SocietyJournals #DiamondOpenAccess
doi.org/10.32942/X24...

This work was done in both Stockholm and Bordeaux Universities as part of my Vetenskapsrådet postdoc mobility grant. I am grateful to my co-authors and to everybody who supported me along the way! Yay!!

woody and buzz lightyear from toy story are standing next to each other and saying `` everywhere ! '' ALT: woody and buzz lightyear from toy story are standing next to each other and saying `` everywhere ! ''

So in conclusion, het-d and het-e independently evolved the capacity of recognizing het-c, even in the presence of interparalog repeat exchange! This little story is relevant for NLRs in general, as ~13% of all fungal NLRs and a lot of bacterial NLRs have HIC repeats! end/n

#Bacteria #immunity

For the repeat domain, we extracted >1100 individual repeats and performed a PCA of their nucleotide sequences. Indeed, het-d and het-e are not that similar, but we discovered that het-e seems to be exchanging repeats with another gene! 8/n

Are het-d and het-e capable of recognizing het-c because of shared ancestry? No! It turns out they are not that closely related, judging by phylogenies along the gene for a bunch of NLRs in Podospora. 7/n

We sequenced a panel of strains with known alleles, which can now be used to assign a phenotype to wild-type strains. With this information in hand, we determined that reactive alleles fold into two beta-propellers that likely embrace their cognate ligand HET-C like a clam. 6/n
#AlphaFold

Of course, these HIC repeats are hard to sequence. We showed that assemblies of Illumina reads often recover broken or incorrect (!) allele reconstructions. But #PacBio and #Nanopore data get them just fine. 5/n
#genomics

het-d/e have "high internal conservation" (HIC): their C-term domain is made out of nearly identical WD40 repeats. Only a few sites are different and evolve under diversifying selection. Concerted evolution (or something) homogenizes the repeats and leads to loss, gain, and shuffling of repeats. 4/n

In the model fungus #Podospora anserina, the het-d
and het-e NLRs are highly polymorphic genes, whose products recognize different alleles of another gene, het-c. If two confronting strains have incompatible het-e/d and het-c alleles, a rejection reaction occurs. 3/n

NOD-like receptors (NLRs) are intracellular proteins that play key roles in the innate immune system of plants and animals. But in fungi we know the function of only a few cases: they all work in heterokaryon incompatibility (rejection between different strains during vegetative fusion). 2/n

Reconstructing NOD-like receptor alleles with high internal conservation in Podospora anserina using long-read sequencing NOD-like receptors (NLRs) are intracellular immune receptors that detect pathogen-associated cues and trigger defence mechanisms, including regulated cell death. In filamentous fungi, some NLRs mediat...

Happy to see this out! "Reconstructing NOD-like receptor alleles with high internal conservation in #Podospora anserina using long-read sequencing", now in ‪@microbiologysociety.org‬! 🧬

Keep reading for a simple explanation 🧵 1/n
#Fungi #Allorecognition
www.microbiologyresearch.org/content/jour...

Selection for altruistic defense in structured populations We model natural selection for or against an anti-parasite (or anti-predator) defense allele in a host (or prey) population that is structured into ma…

Can genetic drift generate enough variation between subpopulations to allow for the evolution of defence against predators or parasites via multi-level selection? In www.sciencedirect.com/science/arti... we have explored this for a structured population model.

URGENT: FlyBase has lost practically all its funding overnight; even user fees are tied up in denied grant funding. 🤬🤯

Any lab using @flybase.bsky.social please donate using the link in post below.

This incredible community, on whose backs our #Drosophila labs depend, can't be left out to dry.

Do you like potatoes? Don't miss our most recent work on tetraploid potato genome!
@nature.com
#potato #genomics #history #evolution

Sketch, capture and layout phylogenies www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/husonlab/phy...

Illustration depicting the ways in which fungi can exchange genetic material with each other. Starship mediated HGT is confirmed experimentally in this preprint.

We did it! We caught Starship #transposons moving between #fungal species in the lab, including between species separated by ~100my. We think Starships are a mediator of HGT in fungi, akin to conjugative elements in bacteria. Check out the preprint. www.biorxiv.org/content/10.1...

Awww 🥰

Getting massive FOMO from all the #ECFG17 posts. It looks fun!

Women are credited less in science than men - Nature The difference between the number of men and women listed as authors on scientific papers and inventors on patents is at least partly attributable to unacknowledged contributions by women scientists.

On #InternationalDayofWomenandGirlsinScience let me remind you that we are NOWHERE NEAR parity. A few examples.

1. Women are credited less in science than men.
www.nature.com/articles/s41...

Sweeps in space: leveraging geographic data to identify beneficial alleles in Anopheles gambiae As organisms adapt to environmental changes, natural selection modifies the frequency of non-neutral alleles. For beneficial mutations, the outcome of this process may be a selective sweep, in which a...

New preprint! We find a novel signal of positive selection in georeferenced genotype data, then use this signal to identify in-progress selective sweeps in the malaria vector Anopheles gambiae:

www.biorxiv.org/content/10.1...

The chance of the broccoli-headed fascists reaching NIH and destroying online NCBI tools and datasets we rely on isn't 0%, so it's worth making a list of the mirrors/alts offered by EMBL-EBI, etc that many of us (including me) are unaware of.
#bioinformatics #genomics #biology #evosky #molevol

One Health: EU agencies unite to tackle azole fungicide resistance in Aspergillus fungi | European Medicines Agency (EMA) The extensive use of azole fungicides (azoles), particularly in some agricultural and horticultural practices, can increase the risk of Aspergillus fungi developing resistance to essential antifungal ...

Widespread use of azole fungicides in agriculture may reduce the effectiveness of antifungal treatments for patients with aspergillosis. EMA highlights that nearly all 120,000 tonnes of azoles sold in the EU were used as pesticides, potentially contributing to #AMR

www.ema.europa.eu/en/news/one-...

A meme with 4 panels showing a lichen with a cartoonish face drawn on it. The text says: “A lichen sits in a community. Is the community made of lichen? Or is the lichen made of community? It screams, for it does not know”.

Our study on #lichen #symbiosis is out in @currentbiology.bsky.social! How can multiple microbes create a large, 3D, and structurally complex organism? To answer this question, we used #metagenomics, #metatranscriptomics, and a bit of protein structure modeling 🧵1/7
🧬 🖥️ 🧪 🦠 🧫 #SymbioSky

Thanks! I wrote an issue in the repo, let's see what they say...

Sorry to bother you again. I tried to transform my pod5 files into fast5 with the pod5 python package but I lost the raw signal information (i might be doing something wrong...). Do you happen to know how to go from pod5 to fast5 safely?