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González-Pérez E, Esteban E, Via M, Gayà-Vidal M, Athanasiadis G, Dugoujon JM, Luna F, Mesa MS, Fuster V, Kandil M, Harich N, Bissar-Tadmouri N, Saetta A, Moral P. Population relationships in the Mediterranean revealed by autosomal genetic data (Alu and Alu/STR compound systems). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 141:430-9. [PMID: 19918993 DOI: 10.1002/ajpa.21161] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The variation of 18 Alu polymorphisms and 3 linked STRs was determined in 1,831 individuals from 15 Mediterranean populations to analyze the relationships between human groups in this geographical region and provide a complementary perspective to information from studies based on uniparental markers. Patterns of population diversity revealed by the two kinds of markers examined were different from one another, likely in relation to their different mutation rates. Therefore, while the Alu biallelic variation underlies general heterogeneity throughout the whole Mediterranean region, the combined use of Alu and STR points to a considerable genetic differentiation between the two Mediterranean shores, presumably strengthened by a considerable sub-Saharan African genetic contribution in North Africa (around 13% calculated from Alu markers). Gene flow analysis confirms the permeability of the Sahara to human passage along with the existence of trans-Mediterranean interchanges. Two specific Alu/STR combinations-CD4 110(-) and DM 107(-)-detected in all North African samples, the Iberian Peninsula, Greece, Turkey, and some Mediterranean islands suggest an ancient genetic background of current Mediterranean peoples.
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Affiliation(s)
- Emili González-Pérez
- Secció d'Antropologia, Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
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Gayà-Vidal M, Dugoujon JM, Esteban E, Athanasiadis G, Rodríguez A, Villena M, Vasquez R, Moral P. Autosomal and X chromosome Alu insertions in Bolivian Aymaras and Quechuas: two languages and one genetic pool. Am J Hum Biol 2010; 22:154-62. [PMID: 19593738 DOI: 10.1002/ajhb.20967] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Thirty-two polymorphic Alu insertions (18 autosomal and 14 from the X chromosome) were studied in 192 individuals from two Amerindian populations of the Bolivian Altiplano (Aymara and Quechua speakers: the two main Andean linguistic groups), to provide relevant information about their genetic relationships and demographic processes. The main objective was to determine from genetic data whether the expansion of the Quechua language into Bolivia could be associated with demographic (Inca migration of Quechua-speakers from Peru into Bolivia) or cultural (language imposition by the Inca Empire) processes. Allele frequencies were used to assess the genetic relationships between these two linguistic groups. Our results indicated that the two Bolivian samples showed a high genetic similarity for both sets of markers and were clearly differentiated from the two Peruvian Quechua samples available in the literature. Additionally, our data were compared with the available literature to determine the genetic and linguistic structure, and East-West differentiation in South America. The close genetic relationship between the two Bolivian samples and their differentiation from the Quechua-speakers from Peru suggests that the Quechua language expansion in Bolivia took place without any important demographic contribution. Moreover, no clear geographical or linguistic structure was found for the Alu variation among South Amerindians.
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Affiliation(s)
- Magdalena Gayà-Vidal
- Unitat d'Antropologia, Biologia Animal, Universitat de Barcelona, Barcelona, Spain
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Bourgeois S, Yotova V, Wang S, Bourtoumieu S, Moreau C, Michalski R, Moisan JP, Hill K, Hurtado AM, Ruiz-Linares A, Labuda D. X-chromosome lineages and the settlement of the Americas. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 140:417-28. [PMID: 19425105 DOI: 10.1002/ajpa.21084] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Most genetic studies on the origins of Native Americans have examined data from mtDNA and Y-chromosome DNA. To complement these studies and to broaden our understanding of the origin of Native American populations, we present an analysis of 1,873 X-chromosomes representing Native American (n = 438) and other continental populations (n = 1,435). We genotyped 36 polymorphic sites, forming an informative haplotype within an 8-kb DNA segment spanning exon 44 of the dystrophin gene. The data reveal continuity from a common Eurasian ancestry between Europeans, Siberians, and Native Americans. However, the loss of two haplotypes frequent in Eurasia (18.8 and 7%) and the rise in frequency of a third haplotype rare elsewhere, indicate a major population bottleneck in the peopling of the Americas. Although genetic drift appears to have played a greater role in the genetic differentiation of Native Americans than in the latitudinally distributed Eurasians, we also observe a signal of a differentiated ancestry of southern and northern populations that cannot be simply explained by the serial southward dilution of genetic diversity. It is possible that the distribution of X-chromosome lineages reflects the genetic structure of the population of Beringia, itself issued from founder effects and a source of subsequent southern colonization(s).
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Affiliation(s)
- Stephane Bourgeois
- Centre de Recherche de l'Hôpital Sainte-Justine, Montréal, QC H3T 1C5, Canada
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Ibarra-Rivera L, Mirabal S, Regueiro MM, Herrera RJ. Delineating genetic relationships among the Maya. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2008; 135:329-47. [DOI: 10.1002/ajpa.20746] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Xing J, Witherspoon DJ, Ray DA, Batzer MA, Jorde LB. Mobile DNA elements in primate and human evolution. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2008; Suppl 45:2-19. [PMID: 18046749 DOI: 10.1002/ajpa.20722] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Roughly 50% of the primate genome consists of mobile, repetitive DNA sequences such as Alu and LINE1 elements. The causes and evolutionary consequences of mobile element insertion, which have received considerable attention during the past decade, are reviewed in this article. Because of their unique mutational mechanisms, these elements are highly useful for answering phylogenetic questions. We demonstrate how they have been used to help resolve a number of questions in primate phylogeny, including the human-chimpanzee-gorilla trichotomy and New World primate phylogeny. Alu and LINE1 element insertion polymorphisms have also been analyzed in human populations to test hypotheses about human evolution and population affinities and to address forensic issues. Finally, these elements have had impacts on the genome itself. We review how they have influenced fundamental ongoing processes like nonhomologous recombination, genomic deletion, and X chromosome inactivation.
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Affiliation(s)
- Jinchuan Xing
- Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
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Resano M, Esteban E, González-Pérez E, Vía M, Athanasiadis G, Avena S, Goicoechea A, Bartomioli M, Fernández V, Cabrera A, Dejean C, Carnese F, Moral P. How many populations set foot through the Patagonian door? Genetic composition of the current population of Bahía Blanca (Argentina) based on data from 19 Alu polymorphisms. Am J Hum Biol 2008; 19:827-35. [PMID: 17876811 DOI: 10.1002/ajhb.20648] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The city of Bahía Blanca occupies a strategic place in Argentina south of the Pampean region in the north-east corner of the Patagonia. Since 1828, this city has been the historical and political border between Amerindian lands in the south, and the lands of European colonists. Nowadays, Bahía Blanca is an urban population mainly composed by descendents of immigrants from Spain and other European countries with apparently low admixture with Amerindians. In view of the unexpectedly high Amerindian admixture levels (about 46.7%) suggested by mtDNA data, and protein markers (19.5%), we analyzed a set of 19 Alu polymorphisms (18 autosomal, 1 of Chromosome Y) in a well-documented genealogical sample from Bahía Blanca. The genotyped sample was made up of 119 unrelated healthy individuals whose birth place and grandparent origins were fully documented. According to available genealogical records, the total sample has been subdivided into two groups: Bahía Blanca Original (64 individuals with all 4 gandparents born in Argentina) and Bahía Blanca Mix (55 individuals with one to three grandparents born out of Argentina). Allele frequencies and gene diversity values in Bahía Blanca fit well into the European ranges. Population relationships have been tested for 8 Alu markers, whose variation has been described in several Amerindian and European samples. Reynolds genetic distances underline the significant genetic similarity of Bahía Blanca to Europeans (mean distance 0.044) and their differentiation from Amerindians (0.146). Interestingly enough, when the general sample is divided, Bahía Blanca Original appears slightly closer to Amerindians (0.127) in contrast to Bahía Blanca Mix (0.161). Furthermore, the genetic relationships depicted through a principal components analysis emphasize the relative similarity of Bahía Blanca Original to Amerindians. A thorough knowledge of the sample origins has allowed us to make a subtle distinction of the genetic composition of Bahía Blanca.
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Affiliation(s)
- M Resano
- Unitat d'Antropologia, Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
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Battilana J, Cardoso-Silva L, Barrantes R, Hill K, Hurtado AM, Salzano FM, Bonatto SL. Molecular variability of the 16p13.3 region in Amerindians and its anthropological significance. Ann Hum Genet 2007; 71:64-76. [PMID: 17227477 DOI: 10.1111/j.1469-1809.2006.00296.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A total of 1558 base pairs in the 16p13.3 region were investigated in 98 individuals of Mongolian, Northern Arctic and Amerindian affiliation, and the results compared with those obtained in a previous worldwide study of the same genomic region. Fifty-five polymorphic sites could be classified into thirty-five haplotypes from the total data. A median joining network based on the haplotypes revealed two distinct clusters: one with low diversity, with haplotypes found in all five geographic-ethnic categories; while the other, with the most divergent haplotypes, was composed mainly of Africans and a few Amerindians. Almost all neutrality parameters yielded significantly negative values. Demographic simulations with the exclusively Amerindian dataset rejected all scenarios, including a bottleneck beginning more than 12,000 years ago. The demographic scenarios tested considering population growth were similar among the Amerindian and worldwide or Eurasian data sets. The results suggest that Amerindians are a representative sample of Eurasian populations, preserving the signal of demographic growth from the out of Africa exodus and, together with data from uniparental markers, support a scenario of a bottleneck of moderate intensity during the peopling of the New World.
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Affiliation(s)
- J Battilana
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, 91501-970 Porto Alegre, RS, Brazil
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Neves WA, Hubbe M, Correal G. Human skeletal remains from Sabana de Bogotá, Colombia: A case of Paleoamerican morphology late survival in South America? AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2007; 133:1080-98. [PMID: 17554759 DOI: 10.1002/ajpa.20637] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Human skeletal remains of the first Americans are scarce, especially in North America. In South America the situation is less dramatic. Two important archaeological regions have generated important collections that allow the analysis of the cranial morphological variation of the Early Americans: Lagoa Santa, Brazil, and Sabana de Bogotá, Colombia. Human crania from the former region have been studied by one of us (WAN) and collaborators, showing that the cranial morphology of the first South Americans was very different from that prevailing today in East Asia and among Native Americans. These results have allowed for proposing that the New World may have been colonized by two different biological populations in the final Pleistocene/early Holocene. In this study, 74 human skulls dated between 11.0 and 3.0 kyr, recovered in seven different sites of Sabana de Bogotá, Colombia, were compared with the world cranial variation by different multivariate techniques: Principal Components Analysis, Multidimensional Scaling, and Cluster of Mahalanobis distance matrices. The Colombian skeletal remains were divided in two chronological subgroups: Paleocolombians (11.0-6.0 kyr) and Archaic Colombians (5.0-3.0 kyr). Both quantitative techniques generated convergent results: the Paleocolombians show remarkable similarities with Lagoa Santa and with modern Australo-Melanesians. Archaic Colombians exhibited the same morphological patterns and associations. These findings support our long-held proposition that the early American settlement may have involved two very distinct biological populations coming from Asia. On the other hand, they suggest the possibility of late survivals of the Paleoamerican pattern not restricted to isolated or marginal areas, as previously thought.
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Affiliation(s)
- Walter A Neves
- Laboratório de Estudos Evolutivos Humanos, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, C.P. 11461, 05422.970 São Paulo, Brazil.
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Herrera RJ, Rojas DP, Terreros MC. Polymorphic Alu insertions among Mayan populations. J Hum Genet 2006; 52:129-142. [PMID: 17151812 DOI: 10.1007/s10038-006-0089-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Accepted: 11/03/2006] [Indexed: 10/23/2022]
Abstract
The Mayan homeland within Mesoamerica spans five countries: Belize, El Salvador, Guatemala, Honduras and Mexico. There are indications that the people we call the Maya migrated from the north to the highlands of Guatemala as early as 4000 B.C. Their existence was village-based and agricultural. The culture of these Preclassic Mayans owes much to the earlier Olmec civilization, which flourished in the southern portion of North America. In this study, four different Mayan groups were examined to assess their genetic variability. Ten polymorphic Alu insertion (PAI) loci were employed to ascertain the genetic affinities among these Mayan groups. North American, African, European and Asian populations were also examined as reference populations. Our results suggest that the Mayan groups examined in this study are not genetically homogeneous.
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Affiliation(s)
- R J Herrera
- Department of Biological Sciences, Florida International University, University Park Campus, Miami, FL, 33199, USA.
| | - D P Rojas
- Department of Biological Sciences, Florida International University, University Park Campus, Miami, FL, 33199, USA
| | - M C Terreros
- Department of Biological Sciences, Florida International University, University Park Campus, Miami, FL, 33199, USA
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Battilana J, Fagundes NJR, Heller AH, Goldani A, Freitas LB, Tarazona-Santos E, Munkhbat B, Munkhtuvshin N, Krylov M, Benevolenskaia L, Arnett FC, Batzer MA, Deininger PL, Salzano FM, Bonatto SL. Alu insertion polymorphisms in Native Americans and related Asian populations. Ann Hum Biol 2006; 33:142-60. [PMID: 16684689 DOI: 10.1080/03014460500487347] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
BACKGROUND Alu insertions provide useful markers for the study of inter-population affinities and historical processes, but data on these systems are not numerous in Native Americans and related populations. AIM The study aimed to answer the following questions: (a) do the population relationships found agree with ethnic, historical and geographical data? and (b) what can heterozygote levels and associated results inform us about the events that led to the colonization of the New World? SUBJECTS AND METHODS Twelve Alu insertion polymorphisms were studied in 330 individuals belonging to South American Native, Siberian and Mongolian populations. These data were integrated with those from 526 persons, to ascertain the relationships between Asian, Northern Arctic and Amerindian populations. RESULTS A decreasing trend concerning heterozygosities and amount of gene flow was observed in the three sets, in the order indicated above. Most results indicated the validity of these subdivisions. However, no clear structure could be observed within South American Natives, indicating the importance of dispersive (genetic drift, founder effects) factors in their differentiation. CONCLUSIONS The answers to the questions are: (a) yes; and (b) an initial moderate bottleneck, intensified by more recent historical events (isolation and inbreeding), can explain the current Amerindian pattern of diversity.
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Affiliation(s)
- Jaqueline Battilana
- Centro de Biologia Genômica e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Faculdade de Biociências, Porto Alegre, RS, Brazil
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Abstract
The present review considered: (a) the factors that conditioned the early transition from non-life to life; (b) genome structure and complexity in prokaryotes, eukaryotes, and organelles; (c) comparative human chromosome genomics; and (d) the Brazilian contribution to some of these studies. Understanding the dialectical conflict between freedom and organization is fundamental to give meaning to the patterns and processes of organic evolution.
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Affiliation(s)
- Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, 91501-970 Porto Alegre, RS, Brazil.
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