Peter Andolfatto
@pandolfatto.bsky.social
Evolution/Ecology meets Genetics @ Columbia University. We use a variety of organisms (🪰🦋🐸🪲) and approaches (mol evo and pop gen, mol bio, experimental evo, genetic engineering) to better understand constraints on adaptation.
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
1/n Check out our new paper, spearheaded by @fborne.bsky.social, just out in PLoS Genetics doi.org/10.1371/jour....
Epistasis among clustered lineage-specific amino acid substitutions in the Drosophila Trio protein
Author summary Proteins fold into three-dimensional structures that are essential for their function. Because these structures depend on interactions among amino acids, the fitness effect of a mutatio...
doi.org
🎉 Please join us in welcoming @pandolfatto.bsky.social, Elspeth Bruford, Kazuo Emoto, Toshie Kai, @harmitmalik.bsky.social, Yansong Miao, and Allyson O’Donnell to the editorial board of #GENETICS! 🔗Read more: buff.ly/0Rbgrzy
Happy to highlight new findings by Vanesa Getseva and Lin Poyraz about the sources of variation in germline mutation rates among humans: www.biorxiv.org/content/10.6... Joint work with Anastasia Stolyarova and @ipsitaagarwal.bsky.social. 1/n
A sibling study of variation in parental mutation rates
People are born with variable numbers of de novo germline mutations (DNMs), depending primarily on the ages of their parents. To explore additional causes, we developed an approach to call DNMs from nucleotide differences between siblings in genomic regions inherited identical by descent from both parents. Applying it to whole genome sequences from 28,985 sibling pairs of diverse genetic ancestries present in the UK Biobank and All of Us datasets, as well as 2,330 trios, we identified >800K autosomal DNMs and characterized mutation phenotypes in 27,645 sets of parents. We found subtle shifts in the mutation spectrum but no differences in total DNM rates among genetic ancestry groups, or between smokers and non-smokers. Testing for associations between parental mutation phenotypes and their burden of loss-of-function and deleterious missense variants in a set of 180 DNA repair and maintenance genes, we discovered that disruptions in REV1 and LIG1 increase germline mutation rates, and thus that rare mutator alleles segregate in population cohorts. ### Competing Interest Statement The authors have declared no competing interest. NIH, R35 GM083098
biorxiv.org
Closely related species often exhibit distinct morphologies. Kenta Tomihara @pinharanda.bsky.social Takashi Kiuchi @pandolfatto.bsky.social &co uncover the #genetic basis of caudal horn size differences between the #SilkMoth and its wild relative @plosbiology.org 🧪 #evolution plos.io/4b3kwdR
Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social, @natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
What sets the mutation rate of a cell type in an animal species?
Germline mutation rates per generation are strikingly similar across animals, despite vast differences in life histories. Analogously, in at least one somatic cell type, mutation rates at the end of l...
biorxiv.org
Join your local protest on April 19th. Spread the word.
NYC, it’s time to take to the streets again. We’re joining over 40 cosponsors to protest authoritarianism, and march for a planet where we place people over profit. 📅 Saturday, April 19 ⏰ 12pm 📍 Bryant Park We’ll see you in the streets.
1. For the past thirty years I've had the best job in the world. I've had the opportunity to follow my curiosity; explore the workings of nature and society; mentor students and junior colleagues in the same process; and teach generations of students about it all.
📢 Institut Jacques Monod Seminar 📅 February 14th 📍 Institut Jacques Monod Next Friday, @pandolfatto.bsky.social , will give the IJM Seminar "The evolution of toxin-resistant Na+,K+-ATPases: new insights from frogs and fireflies" ➡️ https://buff.ly/40wHF1R
“The distribution of highly deleterious variants across human ancestry groups”. Preprint with Anastasia Stolyarova and @gcbias.bsky.social: www.biorxiv.org/content/10.1...
The distribution of highly deleterious variants across human ancestry groups
A major focus of human genetics is to map severe disease mutations. Increasingly that goal is understood as requiring huge numbers of people to be sequenced from every broadly-defined genetic ancestry...
biorxiv.org
Although it feels bizarre to be posting about research with what has been going on in the US this week, I want to highlight new work from graduate student @nemovrobles.bsky.social whose first-first author paper on mitonuclear incompatibilities in swordtails just posted on bioRxiv. shorturl.at/gC71V
Admixture mapping reveals evidence for multiple mitonuclear incompatibilities in swordtail fish hybrids
How barriers to gene flow arise between closely related species is one of the oldest questions in evolutionary biology. Classic models in evolutionary biology predict that negative epistatic interacti...
shorturl.at
"We describe a #mtDNA variant that confers protection against variety of pathogens in #Drosophila. This protection was at least partially caused by enhanced cell-mediated innate #immunity, including higher numbers of immune cells prior to and during infection." journals.plos.org/plosgenetics...
A naturally occurring mitochondrial genome variant confers broad protection from infection in Drosophila
Author summary The strength of immune response and the disease symptoms vary among individuals even when exposed to the same pathogen. Much of this variation is due to the genes directly involved in a...
journals.plos.org
www.linkedin.com/posts/curren...
Current Biology by Cell Press on LinkedIn: Carotenoid color ornaments play important roles in social signaling and…
Carotenoid color ornaments play important roles in social signaling and species recognition. Hooper et al. show that bill-color variation in long-tailed…
linkedin.com
This year I always had my camera and a small photo box to hand when I was gardening. My children are always finding caterpillars outside, and I wanted to document that a bit this year. With the exception of the garden tiger moth (Arctia caja), they all came from my garden.
Want to perform HIGH EFFICIENCY Homology Directed Repair in Drosophila spp? Try Atalanta plasmids. About 10X higher efficiency than other methods! Tag or delete genes, invert chromosome regions, make scarless site-specific modifications. All with easy cloning. This paper is proudly bioRxiv only!
📣 Two ERC-funded positions are available in the lab! If you are interested in exploring the mechanisms underlying mutation, we’d love to hear from you. PhD: shorturl.at/Oc04N Postdoc: shorturl.at/1ShHB RPs and shares would be greatly appreciated! 🧪🧬🖥️ #ScienceJobs #PostdocJobs
Just posting this to #popgen Here's a link to my notes on population & quantitative genetics: github.com/cooplab/popg... Hoping to extend it more after the winter holidays, as I'm just finishing up teaching the undergrad version of class.
Releases · cooplab/popgen-notes
Population genetics notes. Contribute to cooplab/popgen-notes development by creating an account on GitHub.
github.com
Please share widely: The 2025 Speciation Gordon Research Conference (March 2-7 2025) is now open for registration to anyone. If you wish to attend, apply here: www.grc.org/speciation-c... Attendees can present posters, and there are a couple open talk slots to be filled from poster abstracts.
2025 Speciation Conference GRC
The 2025 Gordon Research Conference on Speciation will be held in Ventura, California. Apply today to reserve your spot.
grc.org
A really nice News and Views about our paper by @tollkuhn.bsky.social 🙏🏽 www.nature.com/articles/d41...
Parental-care puzzle in mice solved by thinking outside the brain
Both parents of oldfield mice care for offspring, whereas in deer mice, mothers usually care for pups. The discovery of a type of adrenal-gland cell that is present in oldfield mice but not in deer mi...
nature.com
Andres Bendesky@bendeskylab.com · 2y agoExcited to share our newest paper, in which we report our discovery that monogamous oldfield mice have very recently evolved a novel cell type in their adrenal glands that promotes parental care Work led by the fabulous Natalie Niepoth and @jennymerritt.bsky.social 🧵 rdcu.be/dH1Kn
How do animals know when it’s their turn to communicate during a conversation? In our latest preprint, we study the behavior and neurobiology of aggressive visual turn-taking of Siamese fighting (betta) fish to find out. Work lead by Claire Everett 🧵 1/8 www.biorxiv.org/content/10.1...
Nice write up in Science Magazine about our ivory lncRNA color patterning preprints! Way to go @hwkmthcrspr.bsky.social, @lucalivraghi.bsky.social, and Tian Shen! www.science.org/content/arti...
Surprise RNAs solve mystery of how butterfly wings get their colorful patterns
Understudied means of regulating genes likely widespread in butterflies—and perhaps other animals
science.org
Excited to share a new pre-print from our lab that demonstrates surprisingly repeatable genome evolution in replicated Xiphophorus hybrid populations! Led by former postdoc Quinn Langdon with substantial contributions from Jeff Groh from @gcbias.bsky.social's lab: www.biorxiv.org/content/10.1...
Zach Baker's paper modeling the rapid evolution of PRDM9 is now out in eLife: elifesciences.org/articles/83769
This is me trying out Blusky! I am interested in #viruses #genomes #Drosophila #evolution and #popgen. Here is a pretty picture of some flies from the UK, as an attention-grabber (visit obbard.bio.ed.ac.uk/photos.html for more!)
