The Americas, with their relatively recent history of population diffusion and collapse after European contact, represent an ideal case-study for testing the genetic footprints left by demographic changes. Native American mtDNA genomes have been successfully employed to reconstruct the timing and magnitude of the initial population expansion into the continent. However, previous studies were based on collections of individual lineages and were missing actual population samples. This limited perspective lacked the resolution to explore regional population spread and diversification. Furthermore, the recent collapse was not adequately tested in populations with different prehistories and in different regions.
In this study we focus on Meso- and South America to explore 1) the diversification of populations who crossed the Isthmus of Panama into South America and 2) the traces of a recent demographic collapse in various sets of population mitogenomes. Our dataset comprises 320 full mtDNA genomes from 13 populations from Mesoamerica and from different ecogeographic regions of South America: the Andes, Amazonia and the Gran Chaco. A Bayesian approach is employed to reconstruct population demographies and to test different scenarios of expansion and collapse. Our results suggest different prehistories for the populations studied, irrespective of their geographic location. Similarities between Mesoamerican and Andean populations indicate a possible connection on the Pacific coast, which is tested with spatially-informed simulations. Coalescent simulations support the recent collapse in most of our populations, helping us to understand the impact of recent events on population mitogenomes.
Populations in the Americas experienced different demographic trajectories and strong diversification, which possibly drove the high cultural and linguistic diversity reported today. Including mtDNA genomes from modern populations along with ancient samples promises to shed light into the past of the Americas and into the demographic dynamics behind population divergence.