Biology subjects

Medina-Munoz, S. G.

Publications and source records attributed to Medina-Munoz, S. G..

4 recordsLinked to original sources

bioRxiv2026

Maize genetic diversity is largely unstructured by human ethnolinguistic diversity in its center of origin

Population structure and environmental features often capture major axes of genetic variation in many species. Yet the impacts of human activity often remain unquantified. For domesticated species that rely on human activity for survival and dispersal, human movements and cultural differences may play key roles patterning genetic diversity. Maize is a staple crop of enormous cultural importance to indigenous peoples of the Americas, but cannot survive or disperse without farmers. Using publicly available genotyping and passport data from almost 2,000 traditional maize varieties, more than 500 whole genome sequences of humans from Mexico, and indigenous linguistic maps, we quantify anthropogenic effects on maize genetic diversity in the Americas. Maize shows very little overall structure, highlighting the effectiveness of indigenous farmers in moving and mixing maize populations. While principal components of maize diversity show meaningful correlations to human genetic diversity, our linear modeling suggests little additional impact of human population structure beyond shared geography. Though differences in maize diversity are often patterned by language locally, we find only weak genome-wide effects at larger spatial scales. Despite the relatively weak global signal of anthropogenic effects, linguistic GWAS, outlier FST analyses, and selection scans identified loci associated with specific languages. Leveraging landscape-level sequencing data, we highlight how anthropogenic factors have shaped patterns of maize genetic diversity across Mesoamerica.

evolutionary biology↗

bioRxiv2025

Rapid turnover and recurrent structural variation at the 17q21.31 locus in modern and ancient human genomes, and primates

The 17q21.31 locus in humans harbors several complex structural haplotypes including a [~]970kb inversion. Different inversion haplotypes have been associated with susceptibility to microdeletions causing Koolen-de Vries syndrome and variation in fecundity and recombination rates. Here, using 210 haplotype-resolved human genome assemblies and pangenome graph-based approaches we characterize 11 distinct structural haplotypes, several of which have not been previously described. Extending our analyses to a set of haplotype-resolved great-ape genomes, we characterize the structure of an independent inversion in chimpanzees which extends an additional 650kb, encompasses 5 additional genes, and is [~]2 million years younger than the human inversion. We further determine that gorillas exhibit an independent duplication of the KANSL1 gene which may predispose them to Koolen-de Vries syndrome causing microdeletions. Using short read sequencing data we characterize 17q21.31 haplotype diversity worldwide in [~]5174 individuals from 107 populations finding increased frequencies of KANSL1 duplication-containing haplotypes in both European and South Asian populations as well as 8 double recombination events between inverted and non-inverted haplotypes ranging in size from 20-180kb. Finally, using 626 ancient Eurasian human genomes we show the frequency of haplotypes containing KANSL1 duplications has increased [~]6-fold over the past 12 thousand years in Europe. Together, our results highlight the dynamics, complexity, and recurrent, independent evolution of a medically relevant locus across humans and great apes.

genomics↗

bioRxiv2023

Demographic Modeling of Admixed Latin American Populations from Whole Genomes

Demographic models of Latin American populations often fail to fully capture their complex evolutionary history, which has been shaped by both recent admixture and deeper-in-time demographic events. To address this gap, we used high-coverage whole genome data from Indigenous American ancestries in present-day Mexico and existing genomes from across Latin America to infer multiple demographic models that capture the impact of different timescales on genetic diversity. Our approach, which combines analyses of allele frequencies and ancestry tract length distributions, represents a significant improvement over current models in predicting patterns of genetic variation in admixed Latin American populations. We jointly modeled the contribution of European, African, East Asian, and Indigenous American ancestries into present-day Latin American populations to capture the historical demographic events that have shaped genetic variation. Our inferred demographic histories are consistent across different genomic regions and annotations, suggesting that our inferences are robust to the potential effects of linked selection. In conjunction with published distributions of fitness effects for new nonsynonymous mutations in humans, we show in large-scale simulations that our models recover important features of both neutral and deleterious variation. By providing a more realistic framework for understanding the evolutionary history of Latin American populations, our models can help address the historical under-representation of admixed groups in genomics research, and can be a valuable resource for future studies of populations with complex admixture and demographic histories.

evolutionary biology↗

bioRxiv2022

Nationwide genomic biobank in Mexico unravels demographic history and complex trait architecture from 6,057 individuals

Latin America continues to be severely underrepresented in genomics research, and fine-scale genetic histories as well as complex trait architectures remain hidden due to the lack of Big Data. To fill this gap, the Mexican Biobank project genotyped 1.8 million markers in 6,057 individuals from 32 states and 898 sampling localities across Mexico with linked complex trait and disease information creating a valuable nationwide genotype-phenotype database. Through a suite of state-of-the-art methods for ancestry deconvolution and inference of identity-by-descent (IBD) segments, we inferred detailed ancestral histories for the last 200 generations in different Mesoamerican regions, unraveling native and colonial/post-colonial demographic dynamics. We observed large variations in runs of homozygosity (ROH) among genomic regions with different ancestral origins reflecting their demographic histories, which also affect the distribution of rare deleterious variants across Mexico. We analyzed a range of biomedical complex traits and identified significant genetic and environmental factors explaining their variation, such as ROH found to be significant predictors for trait variation in BMI and triglycerides.

genomics↗