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Average continental ancestry of Bolivians analyzed using a panel of 46 AIMs. These values are obtained from the STRUCTURE analysis and the optimal value K = 4. doi:10.1371/journal.pone.0058980.g004
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Only a few genetic studies have been carried out to date in Bolivia. However, some of the most important (pre)historical enclaves of South America were located in these territories. Thus, the (sub)-Andean region of Bolivia was part of the Inca Empire, the largest state in Pre-Columbian America. We have genotyped the first hypervariable region (HVS-...
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Context 1
... evaluating the differentiation between departments, it was again observed that comparisons of other departments with Santa Cruz were the ones that displayed the highest F ST values ( Figure S3). The influence of this department is also indirectly observed when studying F ST values between the main ecological regions, indicating that the comparisons between Llanos and the other two areas showed the largest values ( Figure S4). ...
Context 2
... of ancestry was carried out using STRUCTURE. Figure 4 summarizes the average continental ancestries observed in Bolivians under different grouping schemes, while Figure 5 shows the STRUCTURE bar-plots. The analysis showed that, on average, 71% of the component in the total Bolivian sample is Native American, followed by 25% of European ancestry. ...
Context 3
... analysis showed that, on average, 71% of the component in the total Bolivian sample is Native American, followed by 25% of European ancestry. When examining the ancestry by departments, La Paz was the region that showed the highest Native American ancestry (79%) ( Figure 4 and Figure 5), and, therefore, the lowest European component (19%). On the other side is the department of Santa Cruz, with 57% of Native American ancestry and 39% European. ...
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... Phillips et al. assessed 32 STRs for bio-geographical ancestry assignment by combining Promega Fusion and Qiagen HDplex kits, effectively distinguishing individuals across five superpopulations in the CEPH panel [59]. Another advantage brought by additional polymorphic markers lies in the improved predictive efficiency and mitigated biases that commonly waned in small-scale panels [67]. Our PCA and STRUCTURE results demonstrated that the combination of 20 CODIS and 88 non-CODIS markers effectively captured the population structure from a global perspective, providing insights into the intricate admixture patterns among diverse populations (Figs. 3 and 4). ...
The worldwide implementation of short tandem repeats (STR) profiles in forensic genetics necessitated establishing and expanding the CODIS core loci set to facilitated efficient data management and exchange. Currently, the mainstay CODIS STRs are adopted in most general-purpose forensic kits. However, relying solely on these loci failed to yield satisfactory results for challenging tasks, such as bio-geographical ancestry inference, complex DNA mixture profile interpretation, and distant kinship analysis. In this context, non-CODIS STRs are potent supplements to enhance the systematic discriminating power, particularly when combined with the high-throughput next-generation sequencing (NGS) technique. Nevertheless, comprehensive evaluation on non-CODIS STRs in diverse populations was scarce, hindering their further application in routine caseworks. To address this gap, we investigated genetic variations of 178 historically available non-CODIS STRs from ethnolinguistically different worldwide populations and studied their characteristics and forensic potentials via high-coverage whole genome sequencing (WGS) data. Initially, we delineated the genomic properties of these non-CODIS markers through sequence searching, repeat structure scanning, and manual inspection. Subsequent population genetics analysis suggested that these non-CODIS STRs had comparable polymorphism levels and forensic efficacy to CODIS STRs. Furthermore, we constructed a theoretical next-generation sequencing (NGS) panel comprising 108 STRs (20 CODIS STRs and 88 non-CODIS STRs), and evaluated its performance in inferring bio-geographical ancestry origins, deconvoluting complex DNA mixtures, and differentiating distant kinships using real and simulated datasets. Our findings demonstrated that incorporating supplementary non-CODIS STRs enabled the extrapolation of multidimensional information from a single STR profile, thereby facilitating the analysis of challenging forensic tasks. In conclusion, this study presents an extensive genomic landscape of forensic non-CODIS STRs among global populations, and emphasized the imperative inclusion of additional polymorphic non-CODIS STRs in future NGS-based forensic systems.
... The research suggests an approximate origin dating back to 5200 years ago, with some within-clade variations. Geographically, this lineage appears to be primarily concentrated in Bolivia and its adjacent regions with a limited distribution [98][99][100]. ...
This article presents a comprehensive genetic study focused on pre-Hispanic individuals who inhabited the Aburrá Valley in Antioquia, Colombia, between the tenth and seventeenth centuries AD. Employing a genetic approach, the study analyzed maternal lineages using DNA samples obtained from skeletal remains. The results illuminate a remarkable degree of biological diversity within these populations and provide insights into their genetic connections with other ancient and indigenous groups across the American continent. The findings strongly support the widely accepted hypothesis that the migration of the first American settlers occurred through Beringia, a land bridge connecting Siberia to North America during the last Ice Age. Subsequently, these early settlers journeyed southward, crossing the North American ice cap. Of particular note, the study unveils the presence of ancestral lineages from Asian populations, which played a pivotal role in populating the Americas. The implications of these results extend beyond delineating migratory routes and settlement patterns of ancient populations. They also enrich our understanding of the genetic diversity inherent in indigenous populations of the region. By revealing the genetic heritage of pre-Hispanic individuals from the Aburrá Valley, this study offers valuable insights into the history of human migration and settlement in the Americas. Furthermore, it enhances our comprehension of the intricate genetic tapestry that characterizes indigenous communities in the area.
... Tal es el caso de los haplotipos B2o y B2v.El haplotipo B2o fue identificado en un individuo de la comunidad de El Altar, representando el 1,15% de la muestra. El origen de este sublinaje se remonta aproximadamente a unos 2.600 años A.P. en Bolivia(Taboada-Echalar et al., 2013). Ha sido encontrado en San Martín de Pangoa en Perú(Fuselli et al., 2003), Bolivia(Taboada-Echalar et al., 2013), grupos Tobas argentinos (A.Sala et al., 2019) y en la provincia de Jujuy en Argentina(Cardoso et al., 2013). ...
... El origen de este sublinaje se remonta aproximadamente a unos 2.600 años A.P. en Bolivia(Taboada-Echalar et al., 2013). Ha sido encontrado en San Martín de Pangoa en Perú(Fuselli et al., 2003), Bolivia(Taboada-Echalar et al., 2013), grupos Tobas argentinos (A.Sala et al., 2019) y en la provincia de Jujuy en Argentina(Cardoso et al., 2013). En una tesis reciente también se identificaron individuos con este sublinaje en la ciudad de San Carlos en Chile(Castillo Torres, 2021) El sublinaje B2v se encontró en dos individuos de la comunidad de Rinconada de Punitaqui, representando el 2,3% de la muestra. ...
Las poblaciones agropastoriles de la región de Coquimbo se destacan, dentro de otras
poblaciones mestizas campesinas del país, debido a un modo de vida particular basado en
la trashumancia de cabras. Se ha propuesto que el origen de estas poblaciones se sitúa en
la época colonial, a partir de poblaciones mestizas que se establecen en espacios
marginales de los distintos valles de la región. Sin embargo, la conformación de estas
poblaciones mestizas no es clara, al recibir esta zona constantes migraciones de indígenas
encomenderos, mulatos, europeos y al establecerse la extinción normativa de los pueblos
locales, en un intento de establecer valores nacionales durante la época de la República. A
través del análisis de la región hipervariable del ADN mitocondrial, se busca esclarecer el
origen materno de estas comunidades, a través de la exploración de las relaciones
filogeográficas de estas comunidades con otras poblaciones nativas y mestizas de Chile y
Argentina. Siendo la hipótesis de trabajo que el origen genético mitocondrial de las
poblaciones agropastoras de la región de Coquimbo se encuentra en poblaciones nativas
de la zona. Dentro de los resultados, se registraron patrones haplotípicos atípicos en
comparación a otras poblaciones indígenas y mestizas del país, así como también la
presencia de haplogrupos raros para el cono sur, un posible nuevo sublinaje, y un relativo
aislamiento genético respecto a las poblaciones de comparación. Se evidencia también una
similitud genética de estas comunidades a pueblos indígenas y mestizos del Noroeste de
argentina, como las poblaciones Kolla argentinas y el pueblo de Calingasta, las que pueden
ser producto de los patrones de movilidad que tienen las comunidades agropastoras. Estos
resultados permiten sugerir que el escenario más probable es que el componente femenino
de estas comunidades esté mayormente conformado por poblaciones nativas.
... The A2ab subhaplogroup has been identified in contemporary Native American populations residing in the United States [47]. Similarly, the A2ad1 and A2af1b1b subhaplogroups have been detected in present-day population groups with indigenous ancestry in Panamá, and Ciudad de Colón and Costa Rica, respectively [46]. ...
The analysis of mitochondrial DNA (mtDNA) hypervariable region (HVR) sequence data from ancient human remains provides valuable insights into the genetic structure and population dynamics of ancient populations. mtDNA is particularly useful in studying ancient populations, because it is maternally inherited and has a higher mutation rate compared to nuclear DNA. To determine the genetic structure of three Colombian pre-Hispanic populations and compare them with current populations, we determined the haplotypes from human bone remains by sequencing several mitochondrial DNA segments. A wide variety of mitochondrial polymorphisms were obtained from 33 samples. Our results support a high population heterogeneity among pre-Hispanic populations in Colombia.
... These results are in line with the expected for Andean populations where European admixture was essentially mediated by men [6,12]. In fact, a much higher proportion of autosomal (biparental) European ancestry (58%) was reported for the North East Andean populations (including those from Santander and Norte Santander departments) [5], supporting sex biassed intermarriages between European men and native women, typical from South American postcolonial populations [41,49,50]. The low contribution of African ancestry is explained by the low number of Africans that arrived in the department during the Atlantic slave trade. ...
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.
... We note that Cui et al. 2013 named this haplotype A2ah; however, this haplotype is now recognized as A2aq, 39 while A2ah refers to a different haplotype that is common in South America. 40 We used HaploGrep2 41 to confirm that TYYS's mitochondrial haplotype is indeed A2aq. Using the radiocarbon-dated ages from the ancient samples for divergence time calibration, the age of the most recent common ancestor of these four A2aq whole mitogenomes (TYYS, Ancient 160a, Tsimshian 069, and Nisga'a B009) was estimated to be $9,056 years BP (95% Highest Posterior Density: 5,535, 13,286 years BP). ...
Many specifics of the population histories of the Indigenous peoples of North America remain contentious owing to a dearth of physical evidence. Only few ancient human genomes have been recovered from the Pacific Northwest Coast, a region increasingly supported as a coastal migration route for the initial peopling of the Americas. Here, we report paleogenomic data from the remains of a ∼3,000-year-old female individual from Southeast Alaska, named Tatóok yík yées sháawat (TYYS). Our results demonstrate at least 3,000 years of matrilineal genetic continuity in Southeast Alaska, and that TYYS is most closely related to ancient and present-day northern Pacific Northwest Coast Indigenous Americans. We find no evidence of Paleo-Inuit (represented by Saqqaq) ancestry in present-day or ancient Pacific Northwest peoples. Instead, our analyses suggest the Saqqaq genome harbors Northern Native American ancestry. This study sheds further light on the human population history of the northern Pacific Northwest Coast.
... Furthermore, a close look at the LAC countries also reveals the different distribution of ancestry proportions in subpopulations and regions, as observed in Cuba (Fortes-Lima et al., 2018), Garifuna population in Honduras (Herrera-Paz et al., 2010), Mexico (Rubi-Castellanos et al., 2009;Silva-Zolezzi et al., 2009), Venezuela (Moura et al., 2015), Colombia (Godinho et al., 2008;Ibarra et al., 2014;Mogollón Olivares et al., 2020;Chande et al., 2021), Bolivia Taboada-Echalar et al., 2013), Paraguay (Simão et al., 2021), Argentina (Godinho et al., 2008), Chile (Eyheramendy et al., 2015) and Brazil (Kehdy et al., 2015;Moura et al., 2015;Mychaleckyj et al., 2017;Secolin et al., 2019;. Also, as observed in several studies, the admixture events were sex biased and occurred between European males and Native American and/or sub-Saharan African females in Cuba (Mendizabal et al., 2008), Jamaica (Deason et al., 2012), Dominican Republic (D'Atanasio et al., 2020), Nicaragua (Nuñez et al., 2010), Belize (Monsalve and Hagelberg, 1997), El Salvador (Lovo-Gómez et al., 2007;Casals et al., 2022), Panama (Migliore et al., 2021), Costa Rica (Carvajal-Carmona et al., 2003), Mexico (Green et al., 2000), Ecuador (González-Andrade et al., 2007), Colombia (Carvajal-Carmona et al., 2003), Brazil (Pena et al., 2011), Uruguay (Sans et al., 2002), and Argentina (Dipierri et al., 1998). ...
... The Amerindian populations in Nicaragua (8.9%) and Costa Rica (2.4%) showed a high degree of paternal genetic differentiation, even though they share geographic proximity (Melton et al., 2013). In South America, Bolivia stands out 17 , as this country has predominant Native American features: 62.2% of the population self-identifies as Native American (Figure 1), and only 0.5%-12% of people have European ancestry (Galanter et al., 2012;Watkins et al., 2012;Taboada-Echalar et al., 2013). In Ecuador, which harbors 7% of Native Americans, a study showed that Mestizos had predominant Native American (Kichwas) (71.2%) ancestry compared with European contribution (Poulsen et al., 2011). ...
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.
... The ML method confirmed the statistical consistency and accuracy of the evolutionary relationship of our strain (Fig. 1). These findings were also true for evolutionary distance-based NJ (Fig. S2) and character-based MP (Fig. S3) trees (Taboada-Echalar et al. 2013). Therefore, these phylogenetic analyses confirmed that the strain CtC72 T could be classified as a new species within the genus Actinomyces. ...
An obligately anaerobic, rod-shaped, Gram-stain-positive, non-spore-forming, non-motile bacterial strain; designated as CtC72T was isolated from the rumen of cattle. The 16S rRNA gene sequence similarity of less than 98.65% revealed the strain as a member of the genus Actinomyces, nearest to but distinct from Actinomyces qiguomingii DSM 106201T, Actinomyces ruminicola DSM 27982T, Actinomyces procaprae JCM 33484T, Actinomyces succiniciruminis TISTR 2317, Actinomyces glycerinitolerans TISTR 2318. The low values of digital DNA-DNA hybridization (< 70%) and average nucleotide identity (< 95%) further highlighted the distinctive nature of strain CtC72T from its closest relatives. The strain CtC72T could grow at temperatures between 30 and 50 °C (optimum 40 °C), pH between 6.0 and 9.0 (optimum 7.5–8.0), and NaCl between 0 and 1.5% (optimum 0%). The strain hydrolysed cellulose and xylan and utilised a range of mono-, di-, and oligo-saccharides as a source of carbon and energy. Glucose fermentation resulted in acetic acid and formic acid as major metabolic products, while propionic acid, lactic acid, and ethanol as minor products along with CO2 production. The DNA G + C content of strain CtC72T was 68.40 (mol%, Tm) and 68.05 (%, digital). Major cellular fatty acids (> 10%) were C16:0, C18:1 ω9c, and C18:1 ω9c DMA. Based on these data, we propose that strain CtC72T be classified as a novel species, Actinomyces ruminis sp. nov., under the genus Actinomyces. The type strain is CtC72T (= KCTC 15726T = JCM 32641T = MCC 3500T).
... Most American populations are characterized by miscegenation between three predominant ethnic groups, namely Native Americans, Europeans, and Africans, in varying proportions depending on the country (Adhikari et al., 2016;Moura et al., 2015;Reich et al., 2012;Risch et al., 2009;Salzano & Sans, 2014;Santangelo et al., 2017;Taboada-Echalar et al., 2013;Wang et al., 2008;Willerslev & Meltzer, 2021;Xavier et al., 2015). These admixture events can be divided into two periods whose duration differs greatly. ...
Background:
The population of the American countries is genetically heterogeneous, whose genesis result from of recent admixture events. In this process, the transoceanic European component displaced the original inhabitants of the continent.
Aim:
To investigate whether socially differentiated cohorts exhibit underlying ancestry components within an urban admixed population, two cohorts of individuals inhabiting Argentina were studied. One cohort included genetically unrelated individuals involved in voluntary paternity testing while the other included sexual or blood-crime suspects.
Materials & methods:
We analyzed over 2500 unrelated individuals: four Native American maternal lineage mtDNA markers in 1024 samples, five Y chromosome haplogroups in 658 male samples, 24 autosomal ancestry informative markers (AIMs) in 205 samples, and 15 autosomal short tandem repeats (STRs) in 1557 samples; countrywide and divided by regions.
Results:
While our results confirm a tricontinental ethnic contribution to both cohorts, their proportions showed statistically significant differences, with a higher proportion of Native American ancestry in the cohort linked to violent crimes compared to those in paternity testing. This hallmark was observed with all the marker sets used and at various levels of analysis.
Discussion:
Since paternity tests are costly, socio-economic differences might help to interpret our observations. The effect of discrimination against descendants of Native American minorities, and exposure to violent social environments, might link marginal groups to criminality.
Conclusion:
Our findings underscore the relevance of proper social management since only by improving living conditions, reducing discrimination, promoting education, and providing job opportunities will it be possible to attain equality in a heterogeneous society. Genetic markers proved to be highly informative in unveiling unexpected social differences.
... De las secuencias del haplogrupo A2 (Fig. 3), el único caso asignable a un subhaplogrupo anteriormente definido fue el de la secuencia (1), de Trinidad , que pertenece a A2ah, con un tronco común con la secuencia (2), de Perú y con dos secuencias (3, 4) de las provincias bolivianas de Santa Cruz y El Beni respectivamente (Taboada-Echalar et al., 2013). FIGURA 3. Localización geográfica de las secuencias que presentaron similitud con los mitogenomas uruguayos secuenciados, incluyéndose los nuevos subhaplogrupos y D1+15519C+16187A. ...
Recently, several studies on the Uruguayan population have shown that it is formed
by unequal contributions from Europeans, Africans, Native Americans, and others. The
native component is larger when maternal contribution is analyzed, but its ethnic/
geographic origin remains unclear, as it is also unclear how and when these groups
arrived. To contribute to the knowledge about prehistoric and historic peopling of the
territory and its relations with other populations, 32 complete mitochondrial genomes
(mitogenomes) were obtained by next generation sequencing. They belong to present
inhabitants of the country, whose hypervariable regions were previously analyzed and
whose identified haplogroups belonged to one of the four main haplogroups of Native
American origin. Seven new subhaplogroups (A2be, A2bf, B2an, C1d1h, C1b30, C1b31
and D1x) were determined, another was redenominated (C1d1d - present C1d1g), and
the criteria to assign B2b6 and D1g5 were reviewed. The age of the new subhaplogroups was estimated between 4.554 and 11.985 years, while the age of C1d1g was
estimated in 20.736 years. Some sequences could be related to different ethnic groups,
or to several geographic regions such as Amazonia, Chaco, Pampa or Andes. The new
subhaplogroup assignations, together with their geographic distribution and chronology, are discussed in relation to the general panorama of South America.
