The Ancestry of Eastern Paraguay: A Typical South American Profile with a Unique Pattern of Admixture

Using uniparental genetic profiles to unravel the complexity of Argentine admixed populations

Latin American countries are distinguished by their highly admixed populations, characterized by a significant preservation of Native American matrilineal ancestry. This contrasts with the paternal lineages, which exhibit different patterns due to pronounced sex-biased mating practices during the colonial period. Uniparental genetic markers have been instrumental in population genetics, facilitating the reconstruction of human settlement histories and serving forensic identification purposes. The primary objective of this study was to investigate the diversity and structure of lineage markers in Argentina and compare them with other admixed populations in South America. For this study, we analyzed Y-STR and mtDNA haplotypes from 5202 unrelated individuals, providing a detailed description of the observed variability in both markers. Additionally, we conducted a genetic distance analysis, incorporating data from bibliographic sources across Argentina and South America. In pairwise comparisons among provinces, higher FST values were found in mtDNA haplotypes than in Y-STR haplotypes. This allows for more provinces to be grouped by similarity when using Y-STR data. These differences were also evident in the multidimensional scaling (MDS) analysis between South American countries. Y-STR haplotypes showed greater similarity to European haplotypes, whereas mtDNA haplotypes exhibited greater dispersion. Thus, the comprehensive compilation of haplotypes in this study, including those integrated from our research and those cited in existing literature, provides an in-depth understanding of the inherent genetic complexities within Argentina.

Application of Targeted Y-Chromosomal Capture Enrichment to Increase the Resolution of Native American Haplogroup Q

Y-chromosomal haplogroups and the Y-SNPs defining them are relevant for the exploration of male lineages, inference of paternal ancestry, and reconstruction of migration pathways, to name a few. Currently, over 300,000 Y-SNPs have been reported, defining 20 main haplogroups. However, ascertainment bias in the investigations has led to some haplogroups being overlooked, which hinders a representative depiction of certain populations and their migration events. For migration pattern analyses of the first settlers of the Americas, the Native American main founding lineage Q-M3 needs to be further investigated to allow clear genetic differentiation of individuals of different ethnogeographic origins. To increase the resolution within this haplogroup, a total of 7.45 Mb of the Y chromosome of 59 admixed South Americans of haplogroup Q was targeted for sequencing using hybridization capture enrichment. Data were combined with 218 publicly available sequences of Central and South Americans of haplogroup Q. After rigorous data processing, variants not meeting the quality criteria were excluded and 4128 reliable Y-SNPs were reported. A total of 2224 Y-SNPs had previously unknown positions in the phylogenetic tree, and 1291 of these are novel. The phylogenetic relationships between the Y-SNPs were established using the software SNPtotree in order to report a redesigned phylogenetic tree containing 300 branches, defined by 3400 Y-SNPs. The new tree introduces 117 previously undescribed branches and is the most comprehensive phylogenetic tree of the Native American haplogroup Q lineages to date. The 214 sequences were assigned to 135 different low- to high-resolution branches, while in the previous phylogenetic tree, only 195 sequences could be sorted into 14 low-resolution branches with the same quality criteria. The improved genetic differentiation of subhaplogroup Q-M3 has a great potential to resolve migration patterns of Native Americans.

Personalized medicine and nutrition in hepatology for preventing chronic liver disease in Mexico

Chronic liver disease is a global health issue. Patients with chronic liver disease require a fresh approach that focuses on the genetic and environmental factors that contribute to disease initiation and progression. Emerging knowledge in the fields of Genomic Medicine and Genomic Nutrition demonstrates differences between countries in terms of genetics and lifestyle risk factors such as diet, physical activity, and mental health in chronic liver disease, which serves as the foundation for the implementation of Personalized Medicine and Nutrition (PerMed-Nut) strategies. Most of the world's populations have descended from various ethnic groupings. Mexico's population has a tripartite ancestral background, consisting of Amerindian, European, and African lineages, which is common across Latin America's regional countries. The purpose of this review is to discuss the genetic and environmental components that could be incorporated into a PerMed-Nut model for metabolic-associated liver disease, viral hepatitis B and C, and hepatocellular carcinoma in Mexico. Additionally, the implementation of the PerMed-Nut approach will require updated medicine and nutrition education curricula. Training and equipping future health professionals and researchers with new clinical and investigative abilities focused on preventing liver illnesses in the field of genomic hepatology globally is a vision that clinicians and nutritionists should be concerned about.

Genetic Diversity Based on Human Y Chromosome Analysis: A Bibliometric Review Between 2014 and 2023

The Y chromosome has gained significant importance in the examination of genetic studies of populations because of its non-recombinant character and its form of uniparental inheritance. This work seeks to offer a comprehensive review of the specialty literature in the field of population genetics, focusing specifically on the analysis of the human Y chromosome using a bibliometric approach and knowledge mapping. This involves establishing worldwide structural networks by identifying the primary research themes, authors, and papers that have had a significant impact on the academic community. The objective is to examine global publications by analyzing citations at both the document and country level. This will involve conducting co-citation analysis for references with a high number of citations, examining bibliographic coupling through journal analysis, analyzing the co-occurrence of keywords, and investigating collaboration between authors from a country perspective. The research papers have been extracted from the Web of Science database. The bibliometric analysis was performed using the Bibliometrix and VOSviewer software tools. The purpose of this article is to serve as a starting point for future research dedicated to the analysis of the diversity of human Y chromosome haplotypes. The objectives of the study were to identify and present the most cited publications and references with the highest number of citations, and to highlight current publications at the national level.

Maternal ancestry and lineages diversity of the Santander population from Colombia

Santander, located in the Andean region of Colombia, is one of the 32 departments of the country. Its population was shaped by intercontinental admixture between autochthonous native Americans, European settlers, and African slaves. To establish forensic databases of haplotype frequencies, the evaluation of population substructure is crucial to capture the genetic diversity in admixed populations. Total control region mitochondrial deoxyribonucleic acid haplotypes were determined for 204 individuals born in the seven provinces across the department. The maternal native heritage is highly preserved in Santander genetic background, with 90% of the haplotypes belonging to haplogroups inside A2, B4, C1, and D. Most native lineages are found broadly across the American continent, while some sub-branches are concentrated in Central America and north South America. Subtle European (6%) and African (4%) input was detected. In pairwise comparisons between provinces, relatively high FST values were found in some cases, although not statistically significant. Nonetheless, when provinces were grouped according to the principal component analysis results, significant differences were detected between groups. The database on mitochondrial deoxyribonucleic acid control region haplotype frequencies established here can be further used for populational and forensic purposes.

Whole Mitochondrial Genome Detection and Analysis of Two- to Four-Generation Maternal Pedigrees Using a New Massively Parallel Sequencing Panel

Mitochondrial DNA (mtDNA) is an effective genetic marker in forensic practice, especially for aged bones and hair shafts. Detection of the whole mitochondrial genome (mtGenome) using traditional Sanger-type sequencing is laborious and time-consuming. Additionally, its ability to distinguish point heteroplasmy (PHP) and length heteroplasmy (LHP) is limited. The application of massively parallel sequencing in mtDNA detection helps researchers to study the mtGenome in-depth. The ForenSeq mtDNA Whole Genome Kit, which contains a total of 245 short amplicons, is one of the multiplex library preparation kits for the mtGenome. We used this system to detect the mtGenome in the blood samples and hair shafts of thirty-three individuals from eight two-generation pedigrees, one three-generation pedigree, and one four-generation pedigree. High-quality sequencing results were obtained. Ten unique mtGenome haplotypes were observed in the mothers from the ten pedigrees. A total of 26 PHPs were observed using the interpretation threshold of 6%. Eleven types of LHPs in six regions were evaluated in detail. When considering homoplasmic variants only, consistent mtGenome haplotypes were observed between the twice-sequenced libraries and between the blood and hair shafts from the same individual and among maternal relatives in the pedigrees. Four inherited PHPs were observed, and the remainder were de novo/disappearing PHPs in the pedigrees. Our results demonstrate the effective capability of the ForenSeq mtDNA Whole Genome Kit to generate the complete mtGenome in blood and hair shafts, as well as the complexity of mtDNA haplotype comparisons between different types of maternal relatives when heteroplasmy is considered.

A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations

Genomics can reveal essential features about the demographic evolution of a population that may not be apparent from historical elements. In recent years, there has been a significant increase in the number of studies applying genomic epidemiological approaches to understand the genetic structure and diversity of human populations in the context of demographic history and for implementing precision medicine. These efforts have traditionally been applied predominantly to populations of European origin. More recently, initiatives in the United States and Africa are including more diverse populations, establishing new horizons for research in human populations with African and/or Native ancestries. Still, even in the most recent projects, the under-representation of genomic data from Latin America and the Caribbean (LAC) is remarkable. In addition, because the region presents the most recent global miscegenation, genomics data from LAC may add relevant information to understand population admixture better. Admixture in LAC started during the colonial period, in the 15th century, with intense miscegenation between European settlers, mainly from Portugal and Spain, with local indigenous and sub-Saharan Africans brought through the slave trade. Since, there are descendants of formerly enslaved and Native American populations in the LAC territory; they are considered vulnerable populations because of their history and current living conditions. In this context, studying LAC Native American and African descendant populations is important for several reasons. First, studying human populations from different origins makes it possible to understand the diversity of the human genome better. Second, it also has an immediate application to these populations, such as empowering communities with the knowledge of their ancestral origins. Furthermore, because knowledge of the population genomic structure is an essential requirement for implementing genomic medicine and precision health practices, population genomics studies may ensure that these communities have access to genomic information for risk assessment, prevention, and the delivery of optimized treatment; thus, helping to reduce inequalities in the Western Hemisphere. Hoping to set the stage for future studies, we review different aspects related to genetic and genomic research in vulnerable populations from LAC countries.