Genetic ancestry of families of putative Inka descent

Abstract

This study focuses on the descendants of the royal Inka family. The Inkas ruled Tawantinsuyu, the largest pre-Columbian empire in South America, which extended from southern Colombia to central Chile. The origin of the royal Inkas is currently unknown. While the mummies of the Inka rulers could have been informative, most were destroyed by Spaniards and the few remaining disappeared without a trace. Moreover, no genetic studies have been conducted on present-day descendants of the Inka rulers. In the present study, we analysed uniparental DNA markers in 18 individuals predominantly from the districts of San Sebastian and San Jerónimo in Cusco (Peru), who belong to 12 families of putative patrilineal descent of Inka rulers, according to documented registries. We used single-nucleotide polymorphisms and short tandem repeat (STR) markers of the Y chromosome (Y-STRs), as well as mitochondrial DNA D-loop sequences, to investigate the paternal and maternal descent of the 18 alleged Inka descendants. Two Q-M3* Y-STR clusters descending from different male founders were identified. The first cluster, named AWKI-1, was associated with five families (eight individuals). By contrast, the second cluster, named AWKI-2, was represented by a single individual; AWKI-2 was part of the Q-Z19483 sub-lineage that was likely associated with a recent male expansion in the Andes, which probably occurred during the Late Intermediate Period (1000-1450 AD), overlapping the Inka period. Concerning the maternal descent, different mtDNA lineages associated with each family were identified, suggesting a high maternal gene flow among Andean populations, probably due to changes in the last 1000 years.

Keywords: Inkas; MtDNA; Panakas; Y chromosome; Y-SNPs; Y-STRs.

Fig. 1

Map showing the reference locations of samples investigated in this study. Dashed lines that cross from Pasto to Peru, Bolivia and Argentina indicate a part of the ‘backbone’ of Qhapaq Ñan (Great Inka Road). Dashed and dotted lines show the geographical extension of the Wari and Tiwanaku Empires

Fig. 2

Median-joining network for Q-M3* Y-STR haplotypes among selected individuals (n = 282) from different populations. Different population groups (Ayllu/Language/Location) are indicated using distinct colours. Haplotypes composed of alleles on 15 Y-STRs are represented with circles; the size of the circle is proportional to the number of individuals, and the branch length is proportional to STR mutation steps (one-step unit between haplotypes in the AWKI-1 clan). The AWKI-1 and AWKI-2 clusters are identified as Q-M3 and Q-Z19483 lineages, respectively. Population groups: Chima, Avayni, Aucaylli, Sucso and Tumipampa are ayllus from San Sebastian and San Jerónimo; Peruvian Quechuas (Quechua_PE); Bolivian Quechuas (Quechua_BO); Ecuadorian Quechuas (Quechua_EC); and Argentinian Mapuche (Mapuche). Sample codes are listed in Supplemental Table 3a

Fig. 3

Median-joining network for A2, B2, C1 and D1 control region mtDNA haplotypes among selected individuals (n = 193) from different populations. Different population groups (Group/Language/Location) are indicated using distinct colours. The mtDNA haplotypes are indicated with circles; the size of the circle is proportional to the number of individuals, and the branch length is proportional to the number of nucleotide changes. Population groups: the Panakas comprised individuals from all five ayllus of the San Sebastian and San Jerónimo districts; Peruvian Quechuas (Quechua_PE); Bolivian Quechuas (Quechua_BO); Ecuadorian Quechuas (Quechua_EC); Urus from Chipaya, Bolivia (Uru_Chp); Lima and Piura, Peru (LI-PI); SGO samples were from Santiago del Estero, Argentina (Pauro et al. 2013); Colla samples were from Jujuy, Argentina (Álvarez-Iglesias et al. 2007); SSN1–SSN5, Tiw (Tiwanaku), Ica, Llullaillaco and L–W–C–Y (Lima–Wari–Chancay–Ychsma) samples were from Llamas et al. (2016); and Lauricocha sample was from Huanuco (Fehren-Schmitz et al. 2015). Amazonia comprised samples from several Amazonian ethnic groups, including Andoas and Jivaro (Peru), Arawak, Tupi-Guarani, Cayubaba, Itonama and Movima (Bolivia) and Je and Puinavean (Brazil)