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Molecular-based characterizations of Andean peoples are traditionally conducted in the service of elucidating continental-level evolutionary processes in South America. Consequently, “western” Andean population genetic variation is often represented in relation to “eastern” variation among Amazon and Orinoco River Basin populations. This west-east contrast in patterns of population genetic variation is typically attributed to large-scale phenomena, such as dual founder colonization events and/or differing long-term microevolutionary histories. However, alternative explanations that consider the nature and causes of population genetic diversity within the Andean region remain underexplored.
Here we examine population genetic diversity in the Peruvian Central Andes using mtDNA HVI and Y-chromosome STR data from 17 newly sampled populations combined with published samples. Using this geographically comprehensive data set, we first re-assess the currently accepted pattern of western vs. eastern population genetic structure, which our results ultimately reject: mtDNA population diversities were lower, rather than higher, within Andean versus eastern populations, and only highland Y-chromosomes exhibited significantly higher within-population diversities compared to eastern groups. Multiple populations, including several highland samples, exhibited low genetic diversities for both genetic systems. Second, we explore whether the implementation of Inca state and Spanish colonial policies starting at about A.D. 1400 could have substantially restructured population genetic variation, and consequently constitute a primary explanation for the extant pattern of population diversity in the Peruvian Central Andes. Our results suggest that Peruvian Central Andean population structure cannot be parsimoniously explained as the sole outcome of combined Inca and Spanish policies on the region’s population demography: Highland populations differed from coastal and lowland populations in mtDNA genetic structure only; highland groups also show strong evidence of female-biased gene flow and/or effective sizes relative to other Peruvian ecozones. Taken together, these findings indicate that population genetic structure in the Peruvian Central Andes is considerably more complex than previously reported and that characterizations of, and explanations for, genetic variation may be best pursued within more localized regions and defined time periods.
Cabana, Graciela S.; Lewis, Jr., Cecil M.; Tito, Raúl Y.; Covey, R. Alan; Cáceres, Angela M.; Castillo Pampas, C. Leslie; De La Cruz, Augusto F.; Durand, Diana; Housman, Genevieve; Hulsey, Brannon I.; Iannacone, Gian Carlo; Lopez, Paul W.; Martínez, Rolando; Medina, Ángel; Ortega Dávila, Olimpio; Osorio Pinto, Karla Paloma; Polo Santillán, Susan I.; Rojas Domínguez, Percy; Rubel, Meagan; Smith, Heather F.; Smith, Silvia E.; de Celis, Verónica Rubín; Lizárraga, Beatriz; and Stone, Anne C., "Population Genetic Structure of Traditional Populations in the Peruvian Central Andes and Implications for South American Population History" (2014). Human Biology Open Access Pre-Prints. 56.
Supplemental Appendix S1: 1. Spreadsheet S1: Complete population data for 17 population samples from the Peruvian Central Andes; 2-5. Spreadsheets S1A-S1D: Haplogroups A-D
02_Cabana_Suppl Appendix_S2.xlsx (30 kB)
Supplemental Appendix S2. Y-Chromosome Haplogroup and Haplotype Data in Nine Population Samples from the Peruvian Central Andes