Diego Ortega-Del Vecchyo

Alessandro and I discussed a paper analyzing a deleterious genetic interaction that causes melanoma in swordtail fishes.

In this #Journal Club, @delvecchyo.bsky.social &Co discuss a study that mapped the genetic basis of hybrid incompatibility in swordtail fish, revealing #melanoma-causing gene interactions that reduce survival in natural hybrid populations.

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Alessandro and I discussed this great paper www.science.org/doi/10.1126/... that investigates a deleterious genetic interaction that causes melanoma.

The MUC19 gene: An evolutionary history of recurrent introgression and natural selection We study the gene MUC19, for which some modern humans carry a Denisovan-like haplotype. MUC19 is a mucin, a glycoprotein that forms gels with various biological functions. We find diagnostic variants ...

Our paper on the evolution of MUC19 in humans, Neanderthals, and Denisovans is finally out today in Science!

This has been a six-year effort by 13 authors to weave together 3 separate but related evolutionary stories around this one gene (more on thread 🧵).

www.science.org/doi/10.1126/...

La selección natural complica las predicciones genéticas - Gaceta UNAM Hacen menos confiables los análisis de características físicas en humanos antiguos, afirma artículo publicado en la revista científica The American Journal of Human Genetics, en el cual participa un g...

Gaceta UNAM cubrió nuestra investigación sobre el impacto de la selección natural en la predicción genética de rasgos complejos en individuos del pasado:

www.gaceta.unam.mx/la-seleccion...

Trying something with huitlacoche (such as quesadilla of huitlacoche) is a good and interesting choice. Other good things to try are guacamole as well as "Chile relleno de queso".

I just saw this message!

Going to one branch of the "El Cardenal" restaurants is a good choice. They have good salads and omelettes. They also have some dishes made with avocado, huitlacoche (corn fungus which is delicious), Poblano (pepper) and cheese.

k-mer-based diversity scales with population size proxies more than nucleotide diversity in a meta-analysis of 98 plant species Abstract. A key prediction of neutral theory is that the level of genetic diversity in a population should scale with population size. However, as was note

Hey, Miles' @milesroberts.bsky.social beautiful paper showing that sequence diversity missed by standard methods contributes to Lewontin's paradox is officially published in @evolletters.bsky.social. academic.oup.com/evlett/advan...

Not Just $N_e$ $N_e$-more: New Applications for SMC from Ecology to Phylogenies Genomes contain the mutational footprint of an organism's evolutionary history, shaped by diverse forces including ecological factors, selective pressures, and life history traits. The sequentially Ma...

Our review of recent Sequentially Markovian Coalescent methods is up on arXiv: arxiv.org/abs/2506.00692 (based on last year's @official-smbe.bsky.social symposium)

Happy to have worked on this project with @mashaals.bsky.social , Emilia Huerta-Sanchez and Valeria Añorve-Garibay. We analyzed how stabilizing and directional selection cause problems to predict traits in ancient samples.

Natural selection acting on complex traits hampers the predictive accuracy of polygenic scores in ancient samples Using polygenic scores, we find that two types of natural selection, stabilizing selection and directional selection, can decrease the prediction accuracy of complex traits in ancient individuals. We ...

📣Online now!
📄Natural selection acting on complex traits hampers the predictive accuracy of polygenic scores in ancient samples
🧑‍🤝‍🧑 @delvecchyo.bsky.social @mashaals.bsky.social & co

We continue with the #human genetic variation and ancient #genomics session! Our next speaker is @delvecchyo.bsky.social, who is telling us about how to use geographical and temporal information to infer the action of natural #selection @liigh-unam.bsky.social #LIIGH10anniversary

The next talk is by PhD student Alan Izarraras from @delvecchyo.bsky.social's group, and he is telling us about how to infer the distribution of fitness effects using local genealogies @liigh-unam.bsky.social #LIIGH10anniversary

🚨🪅 Registration is NOW OPEN for our Symposium on Ancient Pathogen Genomics! 🦠🧬 Join us on April 12-13 2025 in Juriquilla, Mexico. Featuring top speakers & great science in a beautiful venue! Plz RT !
liigh.unam.mx/apg/ 🪅🚨

Digging up the recent past: how effective are genomic tools at deciphering our genetic ancestry? Researchers evaluate the accuracy of common statistical methods to identify recent genetic ancestry in GENETICS.

genestogenomes.org/digging-up-t...

Phantom epistasis through the lens of genealogies Phantom epistasis arises when, in the course of testing for gene-by-gene interactions, the omission of a causal variant (with a purely additive effect on the phenotype) causes the spurious inference o...

New preprint (with @linoafferreira.bsky.social) where we explore the idea of using genealogies (in the form of ancestral recombination graphs, ARGs) to tell apart real GxG interaction signals between nearby variants from false positives www.biorxiv.org/content/10.1...

Hi, I recommend checking out some of the papers and software we cite in our paper. Best of luck!

Probabilistic Modeling in Genomics Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

Don't forget to submit your abstract for "Probabilistic Modeling in Genomics 2025". Deadline: January 10th, 2025. meetings.cshl.edu/meetings.asp...

Ese meme es mi filosofía moral.

Spending more time here sounds great!

Thanks, Rebekah! Happy that our paths crossed as some of the last postdocs from Monty.

I have received tenure! I got here thanks to the support from my students, colleagues, mentors and home institution ( @liigh-unam.bsky.social ). I plan to continue doing research on Theoretical Population Genetics and developing methods to understand how Evolution has shaped our past.

Natural selection can provoke substantial biases in predicting complex traits from ancient genomes using polygenic scores, so it’s crucial to consider its impact when predicting complex traits! 7/7

In addition, our simulations showed that both types of selection can hamper polygenic scores accuracy for traits like height and BMI, despite having complete genotype data and perfect effect size estimates. 6/7

This leads to a reduction in ancient polygenic scores accuracy for the first, and a reduction that depends on the allele effects for the later. 5/7

We found that while stabilizing selection accelerates the loss of high-effect alleles, directional selection leads to the loss of alleles that drive phenotypes away from the optimal value. 4/7

We observed that each type of selection creates a different pattern for the alleles that are lost and conserved through time between ancient and modern individuals. 3/7

Using forward in time simulations, we modeled a single additive trait evolving under neutrality, stabilizing selection and directional selection. We examined how each of these evolutionary dynamics affects ancient polygenic scores accuracy. 2/7

Thread by Valeria Añorve-Garibay reproduced here:

We used a simulation-based approach to explore how natural selection acting on complex traits impacts the predictive accuracy of polygenic scores when applied to ancient samples. 1/7

Natural selection acting on complex traits hampers the predictive accuracy of polygenic scores in ancient samples bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Our preprint analyzing the impact of stabilizing and directional selection on the prediction of complex traits in ancient samples is out. Work spearheaded by
Valeria Añorve-Garibay in collaboration with Mashaal Sohail and Emilia Huerta-Sánchez. Thread below:

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