Bayesian inferences suggest that Amazon Yunga Natives diverged from Andeans less than 5000 ybp: implications for South American prehistory

Abstract

Background: Archaeology reports millenary cultural contacts between Peruvian Coast-Andes and the Amazon Yunga, a rainforest transitional region between Andes and Lower Amazonia. To clarify the relationships between cultural and biological evolution of these populations, in particular between Amazon Yungas and Andeans, we used DNA-sequence data, a model-based Bayesian approach and several statistical validations to infer a set of demographic parameters.

Results: We found that the genetic diversity of the Shimaa (an Amazon Yunga population) is a subset of that of Quechuas from Central-Andes. Using the Isolation-with-Migration population genetics model, we inferred that the Shimaa ancestors were a small subgroup that split less than 5300 years ago (after the development of complex societies) from an ancestral Andean population. After the split, the most plausible scenario compatible with our results is that the ancestors of Shimaas moved toward the Peruvian Amazon Yunga and incorporated the culture and language of some of their neighbors, but not a substantial amount of their genes. We validated our results using Approximate Bayesian Computations, posterior predictive tests and the analysis of pseudo-observed datasets.

Conclusions: We presented a case study in which model-based Bayesian approaches, combined with necessary statistical validations, shed light into the prehistoric demographic relationship between Andeans and a population from the Amazon Yunga. Our results offer a testable model for the peopling of this large transitional environmental region between the Andes and the Lower Amazonia. However, studies on larger samples and involving more populations of these regions are necessary to confirm if the predominant Andean biological origin of the Shimaas is the rule, and not the exception.

Figure 1

Isolation with Migration (IM) model. The IM model includes an ancestral population of effective size of N _A individuals that split t generations ago in two populations, one of size sN _A and the other of size (1-s)N _A, where s ∈ [0,1]. Their sizes are allowed to change exponentially to their current effective sizes N ₁ (Quechua) and N ₂ (Shimaa)_. Over t generations, gene flow can occur between the two descendant populations at different rates in both directions (m ₁ and m ₂ ).

Figure 2

Posterior probabilities for the time of divergence between Quechua and Shimaa in its historical context. Posterior probability densities for the time of divergence t (years) between Quechua and Shimaa populations, obtained by MCMC and ABC, in its historical context. The period encompassing the 90% HPD (Highest Posterior Density) interval of the posterior probability of t, estimated by MCMC is highlighted. MCMC plot: Red: three independent runs with migration rate parameters M_i = 10; Blue: three independent runs with migration rate parameters M_i = 0. ABC plot: Gray: model without intra-locus recombination; Black: model with intra-locus recombination. Below are key historical events of Peruvian prehistory in four Peruvian longitudinal regions: Coast, Andes, Amazon Yunga and Amazonia. Pottery and cultivars symbols represent the earliest archaeological record for the region. This chronology is a simplified picture of the Peruvian archaeological history in which we used different dating records for its construction. To account for time uncertainties, we depicted the events in the chronology plot without clearly defined chronological borders. References for the historical events presented are specified in Additional file 2. LH: Late Horizon, LIP: Late Intermediate Period, MH: Middle Horizon, EIP: Early Intermediate Period, EH: Early Horizon, IP: Initial Period. *Controversial geographic region of Arawak origin. Each step in Agriculture and Camelids representations shows an increase in their relative importance.

Figure 3

Posterior probabilities for the parameters N _A , N ₂ , and s. Posterior probability densities obtained by the MCMC method and by the ABC for the parameters N for ancestral effective size (N_A), N Shimaa effective size (N₂), and the s parameter (the proportion of N_A that founded the Quechua (N₁) population. Range of prior probability distributions are in Additional file 1: Table S2. N _i are in number of individuals. MCMC plots: Red: three independent runs with migration rate parameters M_i = 10; Blue: three independent runs with migration rate parameters M_i = 0. ABC plots: Gray: model with no intra-locus recombination; Black: model with intra-locus recombination. Posterior probabilities for N Quechua (N ₁ ), m ₁ and m ₂ did not yield informative densities and are presented in Additional file 1: Figure S3.