Biology subjects

Gomez-Valdes, J.

Publications and source records attributed to Gomez-Valdes, J..

4 recordsLinked to original sources

bioRxiv2025

Ancient genomic insights into Salmonella enterica Paratyphi C in Central Mexico

Salmonella enterica is a widespread pathogen of major global health relevance, with over 2,500 serovars classified into non-typhoidal and typhoidal groups. Within the typhoidal group, S. enterica Paratyphi C causes paratyphoid fever in humans. Ancient DNA from this bacterium has previously been recovered from epidemic-associated burials in Eurasia and Mexico, dating back 6,000 to 300 years. Here, we analyzed dental DNA from seven individuals (radiocarbon dated to 1800-1940 CE) buried at the Temple of the Immaculate Conception in Mexico City, Central Mexico, and identified ancient S. enterica Paratyphi C DNA in a young female with Native American ancestry. Using an in-house targeted enrichment strategy and deep shotgun sequencing, we reconstructed a S. enterica Paratyphi C genome (COYC5) with [~]11X coverage. Phylogenetic and comparative genomic analyses place COYC5 in close association with previously reported S. enterica Paratyphi C genomes associated with the 1545 cocoliztli epidemic in southern Mexico, as well as with European strains. Divergence estimates indicate that the Mexican and European lineages shared a common ancestor approximately 1,400 years before present (yBP), reflecting an ancient evolutionary split predating European colonization of Mexico. In contrast, the divergence between COYC5 and the southern Mexican genomes occurred around 516 yBP, coinciding with the onset of the colonial period. This pattern supports a European introduction of S. enterica Paratyphi C during colonization, followed by its local diversification within Mexico. Despite this regional differentiation, the conserved presence of key virulence loci--such as SPI-7 and an active shufflon system--across COYC5, southern Mexican, and European genomes underscores the enduring pathogenic potential of S. enterica Paratyphi C. The identification of this bacterium in 19th-century Mexico City provides the first genomic evidence of its persistence in urban contexts beyond major epidemic outbreaks, offering new insights into its evolutionary trajectory in Mexico. These findings raise new questions about how the pathogen spread and persisted across different ecological, social, and epidemiological contexts in ancient Mexico and the Americas.

evolutionary biology↗

bioRxiv2021

Disentangling signatures of selection before and after European colonization in Latin Americans

Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. While classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ~4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico and Peru. Our approach replicates previous reports of selection in the HLA region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly-used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.

genomics↗

bioRxiv2020

Prediction Of Eye, Hair And Skin Color In Admixed Populations Of Latin America

We report an evaluation of prediction accuracy for eye, hair and skin pigmentation based on genomic and phenotypic data for over 6,500 admixed Latin Americans (the CANDELA dataset). We examined the impact on prediction accuracy of three main factors: (i) The methods of prediction, including classical statistical methods and machine learning approaches, (ii) The inclusion of non-genetic predictors, continental genetic ancestry and pigmentation SNPs in the prediction models, and (iii) Compared two sets of pigmentation SNPs: the commonly-used HIrisPlex-S set (developed in Europeans) and novel SNP sets we defined here based on genome-wide association results in the CANDELA sample. We find that Random Forest or regression are globally the best performing methods. Although continental genetic ancestry has substantial power for prediction of pigmentation in Latin Americans, the inclusion of pigmentation SNPs increases prediction accuracy considerably, particularly for skin color. For hair and eye color, HIrisPlex-S has a similar performance to the CANDELA-specific prediction SNP sets. However, for skin pigmentation the performance of HIrisPlex-S is markedly lower than the SNP set defined here, including predictions in an independent dataset of Native American data. These results reflect the relatively high variation in hair and eye color among Europeans for whom HIrisPlex-S was developed, whereas their variation in skin pigmentation is comparatively lower. Furthermore, we show that the dataset used in the training of prediction models strongly impacts on the portability of these models across Europeans and Native Americans.

genetics↗

bioRxiv2018

Latin Americans show wide-spread Converso ancestry and the imprint of local Native ancestry on physical appearance

Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the admixture of Native Americans, Europeans and Sub-Saharan Africans1. Using novel haplotype-based methods here we infer the sub-populations involved in admixture for over 6,500 Latin Americans and evaluate the impact of sub-continental ancestry on the physical appearance of these individuals. We find that pre-Columbian Native genetic structure is mirrored in Latin Americans and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that Central Andean ancestry impacts on variation of facial features in Latin Americans, particularly nose morphology, possibly relating to environmental adaptation during the evolution of Native Americans.

genetics↗