Biology subjects

Anorve-Garibay, V.

Publications and source records attributed to Anorve-Garibay, V..

3 recordsLinked to original sources

bioRxiv2026

Joint ancestry inference reveals the landscape of archaic introgression in admixed populations

Studying the evolutionary history of archaic segments in recently admixed individuals requires inferring both continental and archaic ancestry in admixed genomes. Here, we present TRACTINATOR, the first deep-learning method for simultaneous inference of continental and archaic ancestry in admixed human genomes. The model combines SNP sequences, population allele-frequency information, and S* statistics to improve both inference tasks. By learning relationships between haplotypes and population allele frequencies, TRACTINATOR can generalize across genomic regions and even across different genomic datasets. We train our model using both real and synthetic data, and show that augmenting with synthetic data improves accuracy for both continental and archaic ancestry inference. Finally, we apply TRACTINATOR to admixed Latin American populations from the 1,000 Genomes Project, revealing how archaic ancestry is distributed within chromosomal segments of African, European and Indigenous American ancestry in Latin American individuals. For candidates of adaptive introgression, we also infer whether the archaic haplotype was introduced via European or Indigenous American ancestors.

bioinformatics↗

bioRxiv2024

Natural selection acting on complex traits hampers the predictive accuracy of polygenic scores in ancient samples

The prediction of phenotypes from ancient humans has gained interest due to its potential to investigate the evolution of complex traits. These predictions are commonly performed using polygenic scores computed with DNA information from ancient humans along with genome-wide association studies (GWAS) data from present-day humans. However, numerous evolutionary processes could impact the prediction of phenotypes from ancient humans based on polygenic scores. In this work we investigate how natural selection impacts phenotypic predictions on ancient individuals using polygenic scores. We use simulations of an additive trait to analyze how natural selection impacts phenotypic predictions with polygenic scores. We simulate a trait evolving under neutrality, stabilizing selection and directional selection. We find that stabilizing and directional selection have contrasting effects on ancient phenotypic predictions. Stabilizing selection accelerates the loss of large-effect alleles contributing to trait variation. Conversely, directional selection accelerates the loss of small and large-effect alleles that drive individuals farther away from the optimal phenotypic value. These effects result in specific shared genetic variation patterns between ancient and modern populations which hamper the accuracy of polygenic scores to predict phenotypes. Furthermore, we conducted simulations that include realistic strengths of stabilizing selection and heritability estimates to show how natural selection could impact the predictive accuracy of ancient polygenic scores for two widely studied traits: height and body mass index. We emphasize the importance of considering how natural selection can decrease the reliability of ancient polygenic scores to perform phenotypic predictions on an ancient population.

evolutionary biology↗

bioRxiv2023

The MUC19 gene in Denisovans, Neanderthals, and Modern Humans: 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 for the Denisovan-like MUC19 haplotype at high frequencies in admixed Latin American individuals, and at highest frequency in 23 ancient Indigenous American individuals, all predating population admixture with Europeans and Africans. We find that the Denisovan-like MUC19 haplotype is under positive selection and carries a higher copy number of a 30 base-pair variable number tandem repeat, and that copy numbers of this repeat are exceedingly high in American populations. Finally, some Neanderthals carry the Denisovan-like MUC19 haplotype, and that it was likely introgressed into human populations through Neanderthal introgression rather than Denisovan introgression. One-Sentence SummaryModern humans and Neanderthals carry a Denisovan variant of the MUC19 gene, which is under positive selection in populations of Indigenous American ancestry.

evolutionary biology↗