Ancient DNA perspectives on American colonization and population history

Abstract

Ancient DNA (aDNA) analyses have proven to be important tools in understanding human population dispersals, settlement patterns, interactions between prehistoric populations, and the development of regional population histories. Here, we review the published results of sixty-three human populations from throughout the Americas and compare the levels of diversity and geographic patterns of variation in the ancient samples with contemporary genetic variation in the Americas in order to investigate the evolution of the Native American gene pool over time. Our analysis of mitochondrial haplogroup frequencies and prehistoric population genetic diversity presents a complex evolutionary picture. Although the broad genetic structure of American prehistoric populations appears to have been established relatively early, we nevertheless identify examples of genetic discontinuity over time in select regions. We discuss the implications this finding may have for our interpretation of the genetic evidence for the initial colonization of the Americas and its subsequent population history.

Contradictions and Concordances in American Colonization Models

“…The coastal distribution of D4h3 was seen as consistent with coastal refugia models of migration during the LGM. It is worth noting that the results of these two aDNA studies provided evidence for the presence of three of the five major Native American haplogroups early in prehistory and are therefore consistent with the inference of Raff et al (2011) that mtDNA diversity was present and geographically structured early in the colonization process. Smith et al (2005) assayed mtDNA variation in all of the oldest human remains available for study (e.g., most samples over 7,500 years in age) and found that all of the major mtDNA haplogroups were present except for haplogroup X, confirming the range of mitochondrial diversity early in American populations.…”

“…In this regard, the result of Fix's colonization simulation based on mtDNA data (2003) is not concordant with the simulations of colonization based on archeological data (Anderson and Gillam 2000;Surovell 2000). It is useful to recall that there is evidence that the striking geographic structure in mtDNA haplogroup frequencies in the Americas was established several thousand years before present (O'Rourke et al 2000;Raff et al 2011), shortening even more the temporal span over which such differentiation must have developed if it is constrained by the terminal LGM; presumably further weakening the argument for a single, late colonizing population as the primary source for later Native American populations (Volodko et al 2008).…”

“…If the Native American gene pool differentiated during an isolated pause in Beringia, we must expect that all of the founding mtDNA haplotypes were present at polymorphic frequencies in this source population. Yet only haplotypes associated with haplogroups A and D are present in this core area today, and as far as ancient DNA data can speak to the issue, it has been so for a very long time (Raff et al 2011). What demographic scenario can account for the absence of the majority of founding haplotypes in the core area of the proposed source population?…”

“…A decade ago, O'Rourke et al (2000) examined the few population-based aDNA studies conducted in the Americas to that time (n=6) and found that (1) the strong geographic structure apparent in modern populations appeared to be present in the ancient populations studied as well and (2) the diversity observed in the ancient samples was essentially equivalent to the modern populations, at least as measured by nucleotide diversity. More recently, Raff et al (2011) reexamined this issue by examining over 60 aDNA studies conducted throughout the Americas, the majority based on hypervariable segment (HVSI) sequence data. They note that the signal of geographic structure is still strongly evident in the expanded ancient sample, indicating that the geographic structure that characterizes Native American populations was established several thousands of years ago, based on the antiquity of samples studied genetically.…”

Genetic analysis of paleo-colombians from Nemocón, Cundinamarca provides insights on the early peopling of northwestern South America

“…A small number of aDNA results from the Americas would postpone the time of settlement by several thousands of years. The oldest samples studied (≥8 14 C ka BP), ostensibly the most informative for studies of the peopling of the continent, usually come from single individuals, while more recent ancient samples are suitable for the regional prehistory (Raff, et al 2011;Pickrell & Reich 2014;Llamas, et al 2016). Several findings of human remains from the Savannah of Bogotá (Figure 1a,1b) and from Boyacá (eastern Cordillera, Colombia) along with other relevant findings from elsewhere in the Americas (Pleistocene/ Holocene) are cited in Table 1.…”