Characterizing the ecological niche of insertion sequences within prokaryotic genomes academic.oup.com/ismej/advanc... #jcampubs

Characterizing the ecological niche of insertion sequences within prokaryotic genomes

Abstract. Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious

academic.oup.com

A step forward in discovering Buchnera's key to the aphid's heart, published today! Thanks to Jerry Maeda and other authors--a great team -- and to the helpful reviewers #SymbioSky doi: doi.org/10.1038/s415...

A secreted endosymbiont protein essential for colonizing host cells - Nature

SyeA was present in the Buchnera ancestor, is secreted into the host cytoplasm, is homologous to secreted effectors of bacterial pathogens and is essential for Buchnera transmission.

doi.org

Scott Gilbert made a useful critique of our preprint, which we have replied to: doi.org/10.32942/X2W...

Gavin Douglas@gmdouglas.bsky.social · 3mo ago

"The holobiont is not a useful model for most host-microbiome interactions". A new preprint (a perspective piece) from myself and Andrew Inkpen: doi.org/10.32942/X2W.... Feedback welcome!

Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them academic.oup.com/gbe/article/...

A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them

Abstract. Many long-standing questions in population genomics can now be addressed through comparative analyses and by leveraging the vast amount of genomi

academic.oup.com

Amy Angert and I are recruiting 2 temporary field technicians to assist with demographic surveys across the range of scarlet monkeyflower in California and Oregon. Perfect for recent graduates who are considering applying for grad school. Apply here: jobs.ncsu.edu/postings/231.... Please share!

We are actively searching for a postdoc to join the lab! Details provided here - johrilab.org/join Please share. I will be at PEQG and will be happy to chat if you're interested!

New paper about zero-shot predictions of mutational effects. There's a lot of misunderstanding about what such predictions can and cannot do. In brief, they're good at identifying deleterious mutations but bad at predicting fitness improvements. 1/ www.biorxiv.org/content/10.6...

Overestimating zero-shot fitness prediction: Broad benchmarks mask local failures and practical limitations

Deep learning models have emerged as promising tools for navigating mutational landscapes in protein engineering. These models can be used to predict mutation fitness without the need for task-specifi...

biorxiv.org

Our preprint, where we infer the fitness effects of new mutations in regulatory regions of the D. melanogaster genome. We find an abundance of weakly deleterious effects - www.biorxiv.org/content/10.6... Led by @adaigle.bsky.social .

Very happy to announce a big new paper from the lab, led by grad students @smishra677.bsky.social and Laia Pomar-Pallarès (in collaboration with @roblanfear.bsky.social). We introduce a new way to study introgression, with accompanying software (DAFT) 1/n 🧵 www.biorxiv.org/content/10.6...

Andy Kern, who doesn't (really) have an account here, would like to share his group's new tool for speeding up pop gen summary stat calculations using GPUs. Check it out here: www.biorxiv.org/content/10.6... And see his thread over at the other place: x.com/pastramimach...

I’m excited to share a new paper out today led by Dr. Younghwan Kwak. Cool story on symbiont genomic variation within individual hosts. (And, also, just an impressive display of -omics skill). academic.oup.com/mbe/advance-...

Intrahost mutational dynamics parallel long-term genome evolution in endosymbionts

Abstract. Obligate endosymbionts of insects undergo extreme genome evolution, marked by accelerated molecular evolution, severe base-pair compositional bia

academic.oup.com

If you would like the government to know what you think about their proposal to put federal science funding, communication, and travel under strict political control, you can tell them in the public comment section here: www.regulations.gov/commenton/OM...

elizabethginexi.bsky.social@elizabethginexi.bsky.social · 2mo ago

Summary of Key Changes in OMB’s Proposed Federal Financial Assistance Rule. Russell Vought is going destroy American Science. elizabethginexi.substack.com/p/summary-of...

Check out this exciting new paper in @currentbiology.bsky.social from my friend and collaborator @stephaniesimone.bsky.social’s lab on the genomics of novel rhizobium endosymbiosis www.cell.com/current-biol...

The evolutionary genomics of novel endosymbiosis in wild rhizobia bacteria

Resolving early steps in how hosts and microbes unite in novel endosymbiosis is critical for understanding key evolutionary innovations and ecosystem functions. Montoya et al. reveal how mobile geneti...

cell.com

#ERGAReads | How Did Evolution Halve Genome Size During an Oceanic Island Colonization? 🏝️ 🧬 🕷️ academic.oup.com/mbe/article/... #genomes #evolution #islandevolution #biology @molbioevol.bsky.social @ub.edu @jrozasub.bsky.social

How Did Evolution Halve Genome Size During an Oceanic Island Colonization?

Abstract. Red devil spiders of the genus Dysdera colonized the Canary Islands and underwent an extraordinary diversification. Notably, their genomes are ne

academic.oup.com

Check out this very nice piece by @gmdouglas.bsky.social and S. Andrew Inkpen. ecoevorxiv.org/repository/v...

A very important preprint to check out: The holobiont is not a useful model for most host-microbiome interactions By Gavin M Douglas an S. Andrew Inkpen ecoevorxiv.org/repository/v...

Very excited to share our new paper out in Nature. Congrats to Xiaoqian (Annie) Yu and all the coauthors. www.nature.com/articles/s41...

IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...

IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models

Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih

academic.oup.com

Super excited to share our lab's work led by PhD student Margot Ruffieux on domestication of Saccharomyces cerevisiae, with a focus on sourdough and baking associated yeast! 🍞

Please circulate: I will have a postdoc opening soon, ideally with a start date sometime this summer or fall. If you're interested in empirical population genetics, computational methods development, and/or evolutionary modeling via simulation, don't hesitate to reach out. For more info on the lab:

Diversity-generating retroelements for programmable targeted hypermutagenesis - @dbikard.bsky.social @institutpasteur.bsky.social go.nature.com/3OG2nKN

Diversity-generating retroelements for programmable targeted hypermutagenesis - Nature Biotechnology

Diversity-generating retroelements are engineered for directed evolution in E.coli.

go.nature.com

Machine learning models by the Bernheim and Laub labs vastly expand the predicted space of bacterial immunity, demonstrating that we are still at the beginning of our exploration 🔎 Congrats @mdmlab.bsky.social and @pdeweirdt.bsky.social et al!

Nature@nature.com · 4mo ago

Bacteria have been fighting off viruses using a huge arsenal of molecular weaponry that scientists did not know about — until now. Researchers have identified proteins that could lead to virus-fighting drugs and technologies. go.nature.com/4dqQnXI

I am excited to share our latest paper, Uniform bacterial genetic diversity along the gut, now out in Nature Communications! www.nature.com/articles/s41.... (1/n)

Horizontal gene transfer is often depicted as a process distributing pre-existing functions to novel genetic backgrounds. Yet HGT can also increase the rate of functional innovation after transfer. Here's a brief review on the topic: ecoevorxiv.org/repository/v... #evosky #microsky

New preprint where @lbobay.bsky.social and I were motivated by the fact that non-synonymous substitutions are commonly analyzed in molecular evolution studies, but the similarity of the amino acids being substituted is an understudied area. doi.org/10.64898/202...

New paper showing that much of the apparent success of protein language models in predicting mutational effects is a mirage: These models mostly memorize sites. 1/ www.biorxiv.org/content/10.6...

➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔 🧵👇

If you are interested in investigating horizontal gene transfer by phages and virus-like particles using computational approaches, this postdoc position in the Callahan Lab could be for you jobs.ncsu.edu/postings/226...

I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.

@carolinamicro.bsky.social Huang & @lbobay.bsky.social investigated genomic rearrangements across 121 microbial species, showing that rearrangements occur at a variable pace across bacteria and archaea, pointing to different selective constraints. 🔗 doi.org/10.1093/gbe/evag002 #genome #evolution

Prevalence and Evolutionary Implications of Genome Rearrangements in Bacteria

Abstract. The genetic material of bacteria and archaea is organized into various structures and setups, attesting that genome architecture is dynamic in th

doi.org