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Additional file 5: Table S5. The ϕst matrix (lower diagonal) and their statistical probabilities (upper diagonal) among 10 populations, according to Arlequin v3.5.1.2. program, based on control region mtDNA analysis.

Additional file 3: Table S3. Diversity indices for 15 the Y-STR haplotypes among 10 populations studied. n = sample size; K = number of haplotypes; N Y-15 STRs = number of 15 Y-STR polymorphic markers; h = haplotypic diversity; MPD = mean number of pairwise differences; SD = standard deviation.

Additional file 6: Table S6. Diversity indices and neutrality tests for each population using 379 mitochondrial sequences of the control region for the four maternal lineages (A2, B2, C1, D1). n = sample size; K = number of haplotypes; h = haplotypic diversity; S = number of polymorphic sites; π = nucleotide diversity (average over all loci); D = Neutrality Tajima’s D test; Fs = Fu’s Fu test; p = probability.

Additional file 2: Table S2. The RST matrix (lower diagonal) and their statistical probabilities (upper diagonal) among the 10 populations, according to Arlequin v3.5.1.2 program, based on the 15 Y-STR haplotypes.

The present study focuses on the genetic history of the Quechua-Lamistas, inhabitants of the Lamas Province in the San Martin Department, Peru, who speak a peculiar dialect of the Quechua language related to the Ecuadorian Quichua. It has been suggested that different pre-Columbian ethnic groups from the Peruvian Amazonia, like the Motilones or “shaven heads”, assimilated the Quechua language and then formed the current native population of Lamas. However, many Quechua-Lamistas claim to be direct descendants of the Chankas, a famous pre-Columbian indigenous group that escaped from the Inca rule in the Andes. To investigate the Quechua-Lamistas and Chankas’ ancestries, we compared uniparental genetic profiles (17 STRs of Y-chromosome Q-M3 and complete mtDNA control region haplotypes) among autochthonous Amazonian and Andean populations from Peru, Bolivia and Ecuador. The phylogeographic and population genetic analyses indicated that the Quechua-Lamistas ancestry were quite heterogeneous, but closely related to their neighbors who speak Amazonian languages, presenting no direct relationships with populations from the region where the ancient Chankas lived. On the other hand, the genetic profiles of self-identified Chanka descendants living in Andahuaylas (located in the Apurimac Department, Peru, in the Central Andes) were closely related to those living in Huancavelica and the assumed Chanka Confederation area before the Inca expansion. Universidad de San Martín de Porres, Facultad de Medicina Humana, Instituto de Investigación, Centro de Genetica y Biologia Molecular (CGBM)

This study focuses on the genetic history of the Quechua-Lamistas, inhabitants of the Lamas Province in the San Martin Department, Peru, who speak their own distinct variety of the Quechua family of languages. It has been suggested that different pre-Columbian ethnic groups from the Peruvian Amazonia, like the Motilones or "shaven heads", assimilated the Quechua language and then formed the current native population of Lamas. However, many Quechua-Lamistas claim to be direct descendants of the Chankas, a famous pre-Columbian indigenous group that escaped from Inca rule in the Andes. To investigate the Quechua-Lamistas and Chankas' ancestries, we compared uniparental genetic profiles (17 STRs of Q-M3 Y-chromosome and mtDNA complete control region haplotypes) among autochthonous Amazonian and Andean populations from Peru, Bolivia and Ecuador. The phylogeographic and population genetic analyses indicate a fairly heterogeneous ancestry for the Quechua-Lamistas, while they are closely related to their neighbours who speak Amazonian languages, presenting no direct relationships with populations from the region where the ancient Chankas lived. On the other hand, the genetic profiles of self-identified Chanka descendants living in Andahuaylas (located in the Apurimac Department, Peru, in the Central Andes) were closely related to those living in Huancavelica and the assumed Chanka Confederation area before the Inca expansion. This work received funds from the National Geographic Society, the Waitt Family Foundation and IBM from the United States and from FAPEMIG and CNPq from Brazil for laboratory analysis and fieldwork

The Altiplano region of the South American Andes is marked by an inhospitable climate to which the autochthonous human populations adapted and then developed great ancient civilizations, such as the Tiwanaku culture and the Inca Empire. Since pre-Columbian times, different rulers established themselves around the Titicaca and Poopo Lakes. By the time of the arrival of Spaniards, Aymara and Quechua languages were predominant on the Altiplano under the rule of the Incas, although the occurrence of other spoken languages, such as Puquina and Uruquilla, suggests the existence of different ethnic groups in this region. In this study, we focused on the pre-Columbian history of the autochthonous Altiplano populations, particularly the Uros ethnic group, which claims to directly descend from the first settlers of the Andes, and some linguists suggest they might otherwise be related to Arawak speaking groups from the Amazon. Using phylogeographic, population structure and spatial genetic analyses of Y-chromosome and mtDNA data, we inferred the genetic relationships among Uros populations (Los Uros from Peru, Uru-Chipaya and Uru-Poopo from Bolivia), and compared their haplotype profiles with eight Aymara, nine Quechua and two Arawak (Machiguenga and Yanesha) speaking populations from Peru and Bolivia. Our results indicated that Uros populations stand out among the Altiplano populations, while appearing more closely related to the Aymara and Quechua from Lake Titicaca and surrounding regions than to the Amazon Arawaks. Moreover, the Uros populations from Peru and Bolivia are genetically differentiated from each other, indicating a high heterogeneity in this ethnic group. Finally, our results support the distinctive ancestry for the Uros populations of Peru and Bolivia, which are likely derived from ancient Andean lineages that were partially replaced during more recent farming expansion events and the establishment of complex civilizations in the Andes.