Biology subjects

Quinto-Cortes, C. D.

Publications and source records attributed to Quinto-Cortes, C. D..

3 recordsLinked to original sources

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↗

bioRxiv2021

Admixture dynamics in colonial Mexico and the genetic legacy of the Manila Galleon

Mexico has considerable population substructure due to pre-Columbian diversity and subsequent variation in admixture levels from trans-oceanic migrations, primarily from Europe and Africa, but also, to a lesser extent, from Asia. Detailed analyses exploring sub-continental structure remain limited and post-Columbian demographic dynamics within Mexico have not been inferred with genomic data. We analyze the distribution of ancestry tracts to infer the timing and number of pulses of admixture in ten regions across Mexico, observing older admixture timings in the first colonial cities and more recent timings moving outward into southern and southeastern Mexico. We characterize the specific origin of the heterogeneous Native American ancestry in Mexico: a widespread western-central Native Mesoamerican component in northern Aridoamerican states and a central-eastern Nahua contribution in Guerrero (southern Mexico) and Veracruz to its north. Yucatan shows lowland Mayan ancestry, while Sonora exhibits a unique northwestern native Mexican ancestry matching no sampled reference, each consistent with localized indigenous cultures. Finally, in Acapulco, Guerrero a notable proportion of East Asian ancestry was observed, an understudied heritage in Mexico. We identified the source of this ancestry within Southeast Asia--specifically western Indonesian and non-Negrito Filipino--and dated its arrival to approximately thirteen generations ago (1620 CE). This points to a genetic legacy from the 17th century Manila Galleon trade between the colonial Spanish Philippines and the Pacific port of Acapulco in Spanish Mexico. Although this piece of the colonial Spanish trade route from China to Europe appears in historical records, it has been largely ignored as a source of genetic ancestry in Mexico, neglected due to slavery, assimilation as "Indios" and incomplete historical records.

genetics↗

bioRxiv2021

Efficient ancestry and mutation simulation with msprime 1.0

Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this necessity, a large number of specialised simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and tskit library. We summarise msprimes many features, and show that its performance is excellent, often many times faster and more memory efficient than specialised alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.

genetics↗