Preprint online right before the holidays! Excited to share the first piece of work from the Zhang Lab, led by my absolutely stellar postdoc Michelle Kim! In this work, we ask how admixture, selection and demography shape complex trait genetics and GWAS performance www.biorxiv.org/content/10.6...

Determining the driving factors shaping genetic architecture of complex traits in recently admixed populations

Understanding the genetic architecture of complex traits in admixed populations remains challenging due to heterogeneous genetic backgrounds and demographic histories. Mischaracterizing admixture can ...

biorxiv.org

Work from my amazing undergrad @leyan-wang.bsky.social is just preprinted! TL;DR: If you worry that ARG methods might fail on unphased data due to phasing errors, you may not need to. Check it out & consider reposting to support a great young scientist!

Leyan Wang@leyan-wang.bsky.social · 8mo ago

We are excited to share our recent work on the surprising robustness of Ancestral Recombination Graph (ARG) inference tools to computational phasing errors, now available on BioRxiv: biorxiv.org/content/10.1.... This work is co-advised by @yundeng.bsky.social and Rasmus Nielsen. 1/7

Excited to share work from my postdoc with @docedge.bsky.social and collaborators Matt Pennell and @jgschraiber.bsky.social, newly out over the weekend: www.biorxiv.org/content/10.1... (1/6)

Observational epidemiological studies can mitigate genetic confounding with the genetic relatedness matrix

Observational studies are commonly used in psychology and epidemiology to identify risk factors correlated with health outcomes. However, these studies are vulnerable to confounding when shared geneti...

biorxiv.org

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

Nature Reviews Cancer@natrevcancer.nature.com · 10mo ago

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. 📖 ⬇️

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. 📖 ⬇️

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

Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fish

A combination of mapping approaches identifies interacting genes that lead to incompatibility and melanoma in natural hybrid fish.

science.org

Nature Reviews Cancer@natrevcancer.nature.com · 11mo ago

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/...

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 ...

science.org

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...

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.mx

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...

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

academic.oup.com

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)

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...

arxiv.org

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.

Mashaal Sohail@mashaals.bsky.social · last yr.

Our new work is now out in AJHG "Natural selection acting on complex traits hampers the predictive accuracy of polygenic scores in ancient samples." Great collaboration with @delvecchyo.bsky.social and Emilia Huerta-Sanchez, led by Valeria Añorve-Garibay.

📣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

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 ...

cell.com

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/ 🪅🚨

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

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

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...

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...

biorxiv.org

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

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.

meetings.cshl.edu

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.

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...

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

biorxiv.org

Happy to see @Alanizarr, Sebastián Iturbe and Abad Guzmán from our group presenting their work during the poster session. #SMBE2024

During dinner a lot of people were asking: "Where is the after party?". It is tomorrow at 9am. We have a great set of talks on new approaches to estimate demography and natural selection. Symposium organized with @valenomics #smbe2024

"Community Engagement Experiences of the Afromexico Genomics Project" by @paleogenomics .

Our group will have a strong presence at #SMBE2024 . Two students will be giving talks and another three students will be presenting posters.

The abstract book is available online along with the scientific program and the travel guide to #smbe2024 #smbe24 https://smbe2024.org/ . Happy to see the community in Puerto Vallarta, Mexico soon.

Don't forget to register for #SMBE2024 https://smbe2024.org/ today in order to be part of the scientific program if you were accepted to give a poster or oral presentation.

We had a strong presence in the "Días Académicos" event held the last couple of days @LIIGH_UNAM . We had poster presentations by Sebastián Iturbe and Abad Guzmán. @AlanIzarr and @PsyduckResearch gave talks.

Our perspective piece "The Promise of Inferring the Past Using the Ancestral Recombination Graph (ARG)" is out. Work with Débora YC Brandt, Christian D Huber , Charleston WK Chiang: academic.oup.com/gbe/article/...

The Promise of Inferring the Past Using the Ancestral Recombination Graph

Abstract. The ancestral recombination graph (ARG) is a structure that represents the history of coalescent and recombination events connecting a set of sequence

academic.oup.com

Our perspective piece "The Promise of Inferring the Past Using the Ancestral Recombination Graph (ARG)" is out. Work with @deboraycb, @christiandhuber and @CharlestonCWKC : https://academic.oup.com/gbe/article/16/2/evae005/7577593

We, Alan Izarraras Gomez and I, wrote a 'News and Views' on the latest Nakatsuka et al. (2023) paper discovering an ancient migration (around 5,200 years old) from Northwest Mexico to California that likely spread a language family in California: www.nature.com/articles/d41... rdcu.be/drLBe