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The study was carried out with 1168 individuals from the sites of Puna de Jujuy, San Pedro de Atacama, Calama, Pisagua and 29 craniometric variables. Discriminant Analysis methods were used for the evaluation of differences between sites and sexes and the reclassification of individuals in another site than the original one. | Journal of Anthropology and Archaeology December 2017, Vol. 5, No. 2, pp. 56-73 ISSN 2334-2420 (Print) 2334-2439 (Online) Copyright © The Author(s). All Rights Reserved. Published by American Research Institute for Policy Development DOI: 10.15640/jaa.v5n2a5 URL: https://doi.org/10.15640/jaa.v5n2a5 South Central Andean Area. Social Interaction, Relationship and Genetic Divergence in the Atacama Desert José A. Cocilovo12, Héctor H. Varela1 & Silvia G. Valdano1 Abstract Social relations and their impact on genetic divergence are analyzed between localities in a key path linking the Argentine Northwest with the Northern Arid of Chile. The study was carried out with 1168 individuals from the sites of Puna de Jujuy, San Pedro de Atacama, Calama, Pisagua and 29 craniometric variables. Discriminant Analysis methods were used for the evaluation of differences between sites and sexes and the reclassification of individuals in another site than the original one. The Fst statistic was calculated to determine the genetic structure and the kinship relationships within and between populations. The Fst value between localities is Fst=0.0825 ± 0.0030. Considering the sexes by site, the observed genotypic variance (Fst=0.1195 ± 0.0037) increased by 45%, compared to the expected variance. The Puna de Jujuy sample showed a greater contribution of outside the region variability, including both sexes, in relation to the remaining sites. The migratory effect between localities depended mainly on the circulation of men and by a smaller proportion, the women. Migration rates estimated between localities vary between 1.8 and 2.8 individuals per generation. Evidence of extinction of kinship by distance between localities is presented. There is also evidence of patterns of matrilocal residence. Keywords: exchange, social relations, integration and genetic divergence. 1. Introduction Archaeological research revealed the occupation of the Central South Andean Area (CSAA) from 1300012000 BC .