Native American Contributions Research Articles

Genetic landscape of Gullah African Americans.

ObjectivesGullah African Americans are descendants of formerly enslaved Africans living in the Sea Islands along the coast of the southeastern U.S., from North Carolina to Florida. Their relatively high numbers and geographic isolation were conducive to the development and preservation of a unique culture that retains deep African features. Although historical evidence supports a West‐Central African ancestry for the Gullah, linguistic and cultural evidence of a connection to Sierra Leone has led to the suggestion of this country/region as their ancestral home. This study sought to elucidate the genetic structure and ancestry of the Gullah.Materials and MethodsWe leveraged whole‐genome genotype data from Gullah, African Americans from Jackson, Mississippi, African populations from Sierra Leone, and population reference panels from Africa and Europe to infer population structure, ancestry proportions, and global estimates of admixture.ResultsRelative to non‐Gullah African Americans from the Southeast US, the Gullah exhibited higher mean African ancestry, lower European admixture, a similarly small Native American contribution, and increased male‐biased European admixture. A slightly tighter bottleneck in the Gullah 13 generations ago suggests a largely shared demographic history with non‐Gullah African Americans. Despite a slightly higher relatedness to populations from Sierra Leone, our data demonstrate that the Gullah are genetically related to many West African populations.DiscussionThis study confirms that subtle differences in African American population structure exist at finer regional levels. Such observations can help to inform medical genetics research in African Americans, and guide the interpretation of genetic data used by African Americans seeking to explore ancestral identities.

Population structure and relatedness estimates in a Mexican sample.

Population stratification (PS) is a confounding factor in genome-wide association studies (GWASs) and also an interesting process itself. Latin American populations have mixed genetic ancestry, which may account for PS. We have analyzed the relatedness, by means of the identity-by-descent (IBD) estimations, in a sample of 1805 individuals and 1.006.703 autosomal mutations from a case-control study of colorectal cancer in Mexico. When using the recommended protocol for quality control assessment, 402 should have been removed due to relatedness. Our purpose was to analyze this value in the context of an admixed population. For that aim, we reanalyzed the sample using two software designed for admixed populations, obtaining estimates of 110 and 70 related individuals to remove. The results showed that the first estimation of relatedness was an effect of the higher Native American contribution in part of the data samples, being a confounding factor for IBD estimations. We conclude in the importance of considering PS and genetic ancestry in order to avoid spurious results, not only in GWAS but also in relatedness analysis.

Study of 17 X-STRs in Native American and Mestizo populations of Central America for forensic and population purposes.

In the present work, an extensive analysis of the X-chromosomal pool of Native American and Mestizo groups of Central America (Guatemala, El Salvador, Nicaragua, and Panama) has been carried out. Allele and haplotype frequency databases, as well as other forensic parameters for these populations, are presented. The admixture analysis supports the tri-hybrid composition in terms of ancestry in the Mestizo populations, with a predominant Native American contribution (54-69%), followed by European (19-28%) and African contributions (12-19%). Pairwise FST genetic distances highlight the genetic proximity between the northernmost Central American populations, especially among admixed populations. The unique and complex nature of this area, where populations from different origins intercrossed, as well as the informativity of X-STR data, highpoint the great interest of this genetic study. Furthermore, the X-chromosome databases for Central American populations here provided will be not only useful for forensic and population purposes not only in the target countries but also in the host countries.

Genetic structure of Mataco-Guaycur\xfa speakers from Argentina and the extent of their genetic admixture with neighbouring urban populations

Argentina hosts more than 30 Native American groups, who are widely distributed throughout the country. Mataco-Guaycurú speakers settled in the ecoregion of Gran Chaco and represent 26.7% of the extant aboriginal population of the country. To further investigate the genetic attributes of these speakers, we focused our attention on four aboriginal groups, namely, Wichí, Toba, Pilagá and Mocoví, belonging to the Mataco-Guaycurú linguistic group. Our main goal was to evaluate the interrelationships among the groups and the relationships of these groups with admixed urban populations and to assess correspondences between molecular analysis and historical information. A total of 890 samples (282 Native Americans and 608 inhabitants of admixed urban areas) were analysed. Genetic information was gathered from 15 autosomal STRs, 17 Y-STRs, entire mtDNA control region sequences, 24 AIM-SNPs and 46 AIM-DIPs. Native American signatures were detected in 97.9% of mtDNA lineages, 89.1% of Y-haplotypes and 90.3% to 96.9% of autosomal markers. Wichí exhibited the genetic composition with the largest Native American contribution among the groups and a weak signal of gene flow. This work provides extended genetic information of potential interest in the fields of molecular anthropology and forensic genetics.

Genetic characterization of 32 X-InDels in a population sample from São Paulo State (Brazil).

X-chromosomal markers can be useful in some forensic cases, where the analysis of the autosomal markers is not conclusive. In this study, a population sample of 500 unrelated individuals born in São Paulo State was characterized for 32 X-InDel markers. No deviations from the Hardy-Weinberg equilibrium were detected, except for MID1361. The 32 X-InDels showed an accumulated power of discrimination of 0.9999999999993 in females and 0.99999993 in males and an exclusion chance of 0.999996 in trios and 0.99995 in duos. São Paulo showed lower genetic distances to the Colombian admixed and European populations than to Native American, Asian, or African populations. Ancestry analysis revealed 41.8% European, 31.6% African, and 26.6% Native American contributions. Segregation analysis was performed in 101 trios, and the mutation rate was estimated to be low.

Genetic Admixture Analysis in the Population of Tacuarembó-Uruguay Using Alu Insertions.

Tacuarembó is a department located in northeastern Uruguay, whose population is the result of several migration waves from Europe and Near East, as well as Africans and Afro-descents mostly from Brazil; these waves settled with the territory's various Native ethnic groups (Charrúa, Minuán, and Guaraní). In the past, this population has been the focus of genetic studies showing this trihybrid origin, with greater contributions of Natives and Africans than in other Uruguayan regions. In this study we analyzed eight Alu insertions (A25, ACE, APOA1, B65, D1, F13B, PV92, TPA25) to provide valuable information for ancestrality and genetic differentiation and to compare with both previous studies on the Tacuarembó population and Alu frequencies in other Uruguayan populations. The European contribution to Alu and classical markers was almost equal to that of a previous study using 22 classical markers (63% vs. 65%), while African contribution was higher (30% vs. 15%), and Native American contribution shows an important difference in Alu: 7% versus 20%. We found no significant differences in genetic differentiation between Tacuarembó and Montevideo but significant differences between Tacuarembó and Basque descendants from Trinidad. Our results support previous findings obtained with classical markers that demonstrate the trihybrid composition of the Tacuarembó population, correlated with historical records. Thus, Alu insertions provide interesting information in light of the admixture process in the Uruguayan population.

A systematic scoping review of the genetic ancestry of the Brazilian population.

The genetic background of the Brazilian population is mainly characterized by three parental populations: European, African, and Native American. The aim of this study was to overview the genetic ancestry estimates for different Brazilian geographic regions and analyze factors involved in these estimates. In this systematic scoping review were included 51 studies, comprehending 81 populations of 19 states from five regions of Brazil. To reduce the potential of bias from studies with different sampling methods, we calculated the mean genetic ancestry weighted by the number of individuals. The weighted mean proportions of European, African, and Native American ancestries were 68.1%, 19.6%, and 11.6%, respectively. At the regional level, the highest European contribution occurred in the South, while the highest African and Native American contributions occurred in the Northeastern and Northern regions, respectively. Among states in the Northeast region, Bahia and Ceará showed significant differences, suggesting distinct demographic histories. This review contributes for a broader understanding of the Brazilian ancestry and indicates that the ancestry estimates are influenced by the type of molecular marker and the sampling method.

Ancestry estimates in afrodescendant population from San Basilio de Palenque, Colombia

San Basilio de Palenque is located in Colombia, and was founded by escaped slaves mainly from Cartagena in the sixteenth century. For its history, traditions, ethnicities, culture and language, San Basilio de Palenque has been declared as Intangible Cultural Heritage of Humanity by UNESCO. Insertion/deletion polymorphisms (InDels) have considerable potential in the field of identification and ancestry assessment, since they combine desirable characteristics as genetic markers as simplicity of analysis through PCR and capillary electrophoresis. In the present work a sample from San Basilio de Palenque population (n=187) was characterized using 46 autosomalAIM-indels. A database was built for genotypic and allelic frequencies, and used to assess the genetic ancestry of this peculiar group. As expected for an Afrodescendant population, the most representative ancestry estimate was African with 81.2%, followed by 10.6% European, and 8.2% Native American contributions. The results obtained were compared with previous estimates for a sub region of the Department of Bolivar, called Montes de Maria, which also include San Basilio de Palenque. In the pre-Hispanic era, this region was populated by Zenú indigenous, who mixed with the Spanish settlers. The African ancestry in San Basilio is four times higher than in Bolivar. Interestingly, the second component in San Basilio is European while in Bolivar it is Native American. Our findings can be useful to investigate the genetic structure of Bolivar department and show the importance of considering the heterogeneity that exists when selecting reference populations for forensic applications.

Genetics and genomic medicine in Cuba.

Genetics and genomic medicine in Cuba.

Native American Contributions to a Christian Theology of Space

Native Christian theologians frequently contribute to a theology of space through their writings on other theological subjects. Native American traditionalism is structured spatially; mythology, rituals and ethics are entirely focused on the tribe's surroundings and the individual's responsibility in living within his or her own place. Thus, Native Christians continue this thought by expressing and exploring the Christian faith through spatial constructs. In discussing the Kingdom of God, they speak of the implications of where the Kingdom resides rather than focusing on when it will be consummated. Additionally, they write on the Christian's responsibility in preserving harmony throughout creation and debate about how this spatial harmony is achieved. In liberation theology, they claim societies can only be liberated by re-establishing their relationship to their surrounding environment; in this way, creation is the basis for liberation. They also discuss the locational implications of eschatology, analysing what it means for every place within the cosmos to be renewed and how Christians should then live within these same places presently. Finally, a brief survey of other issues within theologies of space is presented, and consideration is given to the potential contributions Native Christian theologians could make to these issues as well.

Assessing the suitability of different sets of InDels in ancestry estimation

Ancestry informative markers (AIMs) are useful to estimate individual and population ancestries, providing important information to forensic investigations. Several AIM sets were described and evaluated by comparison with data from GWAS. Taking into account that an efficient set of AIMs shall provide identical results between full brothers and GWAS are not easily performed, we aimed to see if the accuracy of the ancestry estimates are correlated to differences obtained in siblings. Pairs of siblings from Brazil were genotyped for 83 InDels; and values of African, European and Native American contributions were compared using diverse sets of markers. The comparison of the ancestry in siblings was only meaningful for markers with high inter-populations variation. The lowest average differences between brothers were obtained for the complete set of 83 InDels, even including markers with low inter-populations variation.

Genetic determinants for gestational diabetes mellitus and related metabolic traits in Mexican women.

Epidemiological and physiological similarities among Gestational Diabetes Mellitus (GDM) and Type 2 Diabetes (T2D) suggest that both diseases, share a common genetic background. T2D risk variants have been associated to GDM susceptibility. However, the genetic architecture of GDM is not yet completely understood. We analyzed 176 SNPs for 115 loci previously associated to T2D, GDM and body mass index (BMI), as well as a set of 118 Ancestry Informative Markers (AIMs), in 750 pregnant Mexican women. Association with GDM was found for two of the most frequently replicated T2D loci: a TCF7L2 haplotype (CTTC: rs7901695, rs4506565, rs7903146, rs12243326; P=2.16x10-06; OR=2.95) and a KCNQ1 haplotype (TTT: rs2237892, rs163184, rs2237897; P=1.98x10-05; OR=0.55). In addition, we found two loci associated to glycemic traits: CENTD2 (60’ OGTT glycemia: rs1552224, P=0.03727) and MTNR1B (HOMA B: rs1387153, P=0.05358). Remarkably, a major susceptibility SLC16A11 locus for T2D in Mexicans was not shown to play a role in GDM risk. The fact that two of the main T2D associated loci also contribute to the risk of developing GDM in Mexicans, confirm that both diseases share a common genetic background. However, lack of association with a Native American contribution T2D risk haplotype, SLC16A11, suggests that other genetic mechanisms may be in play for GDM.

Cuba: exploring the history of admixture and the genetic basis of pigmentation using autosomal and uniparental markers.

We carried out an admixture analysis of a sample comprising 1,019 individuals from all the provinces of Cuba. We used a panel of 128 autosomal Ancestry Informative Markers (AIMs) to estimate the admixture proportions. We also characterized a number of haplogroup diagnostic markers in the mtDNA and Y-chromosome in order to evaluate admixture using uniparental markers. Finally, we analyzed the association of 16 single nucleotide polymorphisms (SNPs) with quantitative estimates of skin pigmentation. In the total sample, the average European, African and Native American contributions as estimated from autosomal AIMs were 72%, 20% and 8%, respectively. The Eastern provinces of Cuba showed relatively higher African and Native American contributions than the Western provinces. In particular, the highest proportion of African ancestry was observed in the provinces of Guantánamo (40%) and Santiago de Cuba (39%), and the highest proportion of Native American ancestry in Granma (15%), Holguín (12%) and Las Tunas (12%). We found evidence of substantial population stratification in the current Cuban population, emphasizing the need to control for the effects of population stratification in association studies including individuals from Cuba. The results of the analyses of uniparental markers were concordant with those observed in the autosomes. These geographic patterns in admixture proportions are fully consistent with historical and archaeological information. Additionally, we identified a sex-biased pattern in the process of gene flow, with a substantially higher European contribution from the paternal side, and higher Native American and African contributions from the maternal side. This sex-biased contribution was particularly evident for Native American ancestry. Finally, we observed that SNPs located in the genes SLC24A5 and SLC45A2 are strongly associated with melanin levels in the sample.

“Travels of an American Indian into the Hinterlands of Soviet Russia”: Rethinking Indigenous Modernity and the Popular Front in the Work of Archie Phinney and D’Arcy McNickle

After returning from a five-year journey to the Soviet Union in the late 1930s, Nez Perce anthropologist Archie Phinney urged formally educated Indians to go “beyond old tribal horizons toward a racial identity” to link Native struggles for self-determination with racial struggles for justice in the United States and abroad. Pan-Indian, cosmopolitan, and self-reflexively modern, Phinney represented a crucial link between Native American intellectuals in the 1930s and 1940s and other radical intellectuals of color. While Phinney was perhaps the most prominent Native American to openly support the Soviet Union, a small but nonetheless visible presence of Native Americans in socialist organizations created unemployed councils on reservations, agitated for extended federal aide to Native communities, fought against the deportation of Mexican Americans in San Francisco, and even ran for the US Senate on the Communist Party ticket. These social movements suggests ways we can reread the first modern Native American novel, D’Arcy McNickle’s The Surrounded , in context of the 1930s transnational movements, deploying theories of minority self-determination to suggest an indigenous nationalism in conversation with third-world liberation movements around the world. Together, these sources shed light on how Native American contributions helped shape the “radical modernity” of the Popular Front era, as well as how Native American intellectuals deployed ideas of modernity to fashion new forms of indigenous sovereignty.

Questioning the "melting pot": analysis of Alu inserts in three population samples from Uruguay.

The way that immigrants integrate into recipient societies has been discussed for decades, mainly from the perspective of the social sciences. Uruguay, as other American countries, received diffferent waves of European immigrants, although the details of the process of assimilation, when it did occur, are unclear. In this study we used genetic markers to understand the process experienced by the Basques, one of the major migration waves that populated Uruguay, and their relation to other immigrants, as well as to Native American and African descendants. For this purpose, we analyzed the allele frequencies of 10 ALU loci (A25, ACE, APOA1, B65, D1, F13B, PV92, TPA25, HS2.43, and HS4.65) in three samples from Uruguay (two of Basque descendants, one of non-Basque descendants) from two locations: Montevideo and Trinidad. No departure from Hardy-Weinberg expectations was observed, with the exceptions of the APOA1 and D1 loci in the non-Basque descendants' samples. Our data show that the major genetic contribution in the three samples comes from Europe (78-88%), with minor African (10-15%) and Native American (0-10%) contributions. Genetic distances reveal that Basque descendants from Trinidad cluster with Europeans, whereas both Montevideo samples cluster together and are separate from other populations, showing two diffferent types of integration, related to the general characteristics of each regional population.

Questioning the “Melting Pot”: Analysis of Alu Inserts in Three Population Samples from Uruguay

Questioning the “Melting Pot”:Analysis of Alu Inserts in Three Population Samples from Uruguay Pedro C. Hidalgo, Patricia Mut, Elizabeth Ackermann, Gonzalo Figueiro, and Monica Sans abstract The way that immigrants integrate into recipient societies has been discussed for decades, mainly from the perspective of the social sciences. Uruguay, as other American countries, received different waves of European immigrants, although the details of the process of assimilation, when it did occur, are unclear. In this study we used genetic markers to understand the process experienced by the Basques, one of the major migration waves that populated Uruguay, and their relation to other immigrants, as well as to Native American and African descendants. For this purpose, we analyzed the allele frequencies of 10 ALU loci (A25, ACE, APOA1, B65, D1, F13B, PV92, TPA25, HS2.43, and HS4.65) in three samples from Uruguay (two of Basque descendants, one of non-Basque descendants) from two locations: Montevideo and Trinidad. No departure from Hardy-Weinberg expectations was observed, with the exceptions of the APOA1 and D1 loci in the non-Basque descendants’ samples. Our data show that the major genetic contribution in the three samples comes from Europe (78–88%), with minor African (10–15%) and Native American (0–10%) contributions. Genetic distances reveal that Basque descendants from Trinidad cluster with Europeans, whereas both Montevideo samples cluster together and are separate from other populations, showing two different types of integration, related to the general characteristics of each regional population. key words Admixture, Gene Diversity, Population structure, Alu Insertion Polymorphisms According to the 2011 national census, Uruguay has a population of 3,286,314 inhabitants, 1,319,108 of them living in the capital city, Montevideo (INE 2012). The present population is the consequence of various processes, several of them shared with other Latin American countries. However, some differences make the Uruguayan population unique, such as the variety of European source populations and the lack of Native American–descendant and African-descendant communities. In general terms, it is possible to recognize several origins for European migratory waves, most of them occurring during the nineteenth and twentieth centuries, that originate with the Iberians (mostly from the Canary Islands but also several Basque locations and Portugal) that occupied the region during colonial times (Pi Hugarte and Vidart 1969). The first wave of immigrants (1825–1842) came during the early times of Uruguayan independence and includes 40,000–45,000 individuals, mostly French Basques. More Basques came in a second wave (1842–1876), in this case mainly from Spain (Barrán and Nahum 1990; Marenales Rossi and Luzuriaga 1990). [End Page 83] These two “foundational” waves were composed mostly of males (81.8% vs. 18.2% females). A third, “forced” wave occurred during the Spanish Civil War (1936–1939) and also included several Basques (Arocena and Aguiar 2007). It should be emphasized that during the nineteenth century, migrants to Uruguay were mostly of Spanish, Portuguese, and Italian origin, whereas during the twentieth century origins diversified, adding several thousands of Armenians; Jews from Western Europe, Central Europe, and the Middle East; Russians; Swiss; and others (Vidart and Pi Hugarte 1969). In 1908 the proportion of foreigners in the population was approximately 18%, decreasing to 8% in 1963 and to a present-day minimum of 3% (INE 2012). The process of assimilation, when it did occur, is unclear, and the coexistence in a common social space, shared by the immigrants and other ethnic groups (Africans, Natives, and their descendants), does not necessary imply a “melting pot,” a model inspired in by Israel Zangwill’s 1907 play about immigrants in the United States of America in which immigrants quickly amalgamated with the receiver population. This model is opposed to “cultural pluralism,” in which ethnic groups retained some individuality. According to Yinger (1985), the process of assimilation includes four threads: structural, cultural, psychological, and biological (amalgamation). Amalgamation, which results in the gene pools being indistinguishable, depends on the characteristics of both the migrants and the recipients, and various barriers that can restrain the process (linguistic, religious, or “racial”) have been observed. However, in general terms, coexistence of different groups does not occur under conditions of equality. Nowadays in Uruguay, Native American...

Lest We Remember: Civil War Memory and Commemoration among the Five Tribes

Lest We RememberCivil War Memory and Commemoration among the Five Tribes Jeff Fortney (bio) On Main Street in Norman, Oklahoma, nestled between a Bank of America and a Hobby Lobby, stands an unmistakable yet unanticipated object: a statue of a Civil War soldier. Most Americans remember the Civil War as a conflict that was fought between Northern and Southern states predominantly in the eastern theater over issues of slavery and to some limited extent states’ rights. Therefore, the question emerges: Who and what does this statue commemorate in what was formerly Indian Territory?1 As with other parts of the western theater, the Civil War in Indian Territory is frequently overlooked. Although this venue of the war is often forgotten, the Civil War enveloped Indian Territory, disrupted lives, and broke apart families just as it did in Georgia, Virginia, and other battleground states. Conservative estimates suggest that over 3,530 Native Americans fought in the Federal Indians’ Brigade, including 1,019 who were killed. Over 7,000 Indians joined the service of the Union army in an official capacity. This figure excludes a significant number of Natives who donned the rebel gray and fought for the Confederacy. Brutal home-front conditions of poverty, street fighting, and total war cut the Cherokee population in half, while diseases in refugee camps spread rapidly, decimating the Creek population. The war made more than one-third of the Cherokee women into widows and turned over 25 percent of children into orphans. The vast majority of noncombatant Natives were displaced from their homes. Some were forced to march across the Oklahoma plains in winter to seek refuge in Kansas. Native property was destroyed, while human property fled to Northern territories for freedom.2 [End Page 525] In keeping with the overall theme of this issue, this study addresses the ways in which Natives practiced self-silence in regard to public Civil War commemoration. Notwithstanding the incredible impact on Indian Territory and Indian lives, Oklahoma Indians themselves did not typically commemorate the Civil War. Therefore, Native American contribution to the Civil War was largely skewed in the American historical narrative as well as in public memorialization. A large concentration of statues, monuments, and other commemorative signifiers in the North and South excludes not only white and black soldiers who fought in the West but also the significant number of Indians who fought, resisted, and supported their own unique causes during the Civil War. For example, the aforementioned soldier’s statue in Norman, Oklahoma, is intended to commemorate a white soldier, an ancestor of those who erected it, rather than a Native American who actually fought in the area. This monument is not atypical. This seems peculiar, considering that one must traverse “World War I Memorial Highway” and pass tributes to twentieth-century Chickasaw and Choctaw war accomplishments in order to arrive at a pantribal powwow celebrating war veterans. In light of this peculiarity, this study examines why Natives who made critical sacrifices during the war sought to bury the past. It asserts that while the North won the military conflict, the South came out the victor during the subsequent Reconstruction era. As the two sides reconciled, they made concessions that allowed the South to venerate its past heritage and transplant it onto Oklahoma Natives. Native peoples, on the other hand, lost during both the war and the Reconstruction periods, regardless of which side they supported. Thus, the only true monuments in Indian Territory during Reconstruction became the scorched grounds in place of homes, weeds and sprouts instead of corn rows, and memories of federal abandonment and betrayal instead of fulfilled promises. As Indian Territory became allotted and the white population overtook the Native population, Northern and Southern Americans’ visions of the war supplanted Native Civil War and Reconstruction recollections. In actuality this meant that white settlers attempted to assimilate the Native story into their own narratives via public commemorative endeavors. Even today, as monuments of white Union soldiers and plaques from United Daughters of the Confederacy (udc) chapters dot the Oklahoma landscape, Native people generally choose not to include Civil War loyalty or Southern “lost cause” mythology as part of their collective memory. [End Page...

Estimates of interethnic admixture in the Brazilian population using a panel of 24 X‐linked insertion/deletion markers

In this study, we aimed to identify ancestry informative haplotypes and make interethnic admixture estimates using X-chromosome markers. A significant sample (461 individuals) of European, African, and Native American populations was analyzed, and four linkage groups were identified. The data obtained were used to describe the ancestral contribution of populations from four different geographical regions of Brazil (745 individuals). The global interethnic admixture estimates of the four mixed populations under investigation were calculated applying all the 24 insertion/deletion (INDEL) markers. In the North region, a larger Native Americans ancestry was observed (42%). The Northeast and Southeast regions had smaller Native American contribution (27% in both of them). In the South region, there was a large European contribution (46%). The estimates obtained are compatible with expectations for a colonization model with biased admixture between European men (one X chromosome) and Native American and African women (two X chromosomes), so the 24 X-INDEL panel described here can be a useful to make admixture interethnic estimates in Brazilian populations.

Prehistoric life: evolution and the fossil record

Prehistoric life: evolution and the fossil record

Reconstructing the population history of Nicaragua by means of mtDNA, Y‐chromosome STRs, and autosomal STR markers

Before the arrival of the Spaniards in Nicaragua, diverse Native American groups inhabited the territory. In colonial times, Native Nicaraguan populations interacted with Europeans and slaves from Africa. To ascertain the extent of this genetic admixture and provide genetic evidence about the origin of the Nicaraguan ancestors, we analyzed the mitochondrial control region (HVSI and HVSII), 17 Y chromosome STRs, and 15 autosomal STRs in 165 Mestizo individuals from Nicaragua. To carry out interpopulation comparisons, HVSI sequences from 29 American populations were compiled from the literature. The results reveal a close relationship between Oto-manguean, Uto-Aztecan, Mayan groups from Mexico, and a Chibchan group to Nicaraguan lineages. The Native American contribution to present-day Nicaraguan Mestizos accounts for most of the maternal lineages, whereas the majority of Nicaraguan Y chromosome haplogroups can be traced back to a West Eurasian origin. Pairwise Fst distances based on Y-STRs between Nicaragua and European, African and Native American populations show that Nicaragua is much closer to Europeans than the other populations. Additionally, admixture proportions based on autosomal STRs indicate a predominantly Spanish contribution. Our study reveals that the Nicaraguan Mestizo population harbors a high proportion of European male and Native American female substrate. Finally, the amount of African ancestry is also interesting, probably because of the contribution of Spanish conquerors with North African genetic traces or that of West African slaves.