Native Americans experienced a strong population bottleneck coincident with European contact

Abstract

The genetic and demographic impact of European contact with Native Americans has remained unclear despite recent interest. Whereas archeological and historical records indicate that European contact resulted in widespread mortality from various sources, genetic studies have found little evidence of a recent contraction in Native American population size. In this study we use a large dataset including both ancient and contemporary mitochondrial DNA to construct a high-resolution portrait of the Holocene and late Pleistocene population size of indigenous Americans. Our reconstruction suggests that Native Americans suffered a significant, although transient, contraction in population size some 500 y before the present, during which female effective size was reduced by ∼50%. These results support analyses of historical records indicating that European colonization induced widespread mortality among indigenous Americans.

Fig. 1.

Extended Bayesian skyline plot of female effective population size scaled by generation time (g), with archaeological sites and historical events as shown. Colored regions indicate Bayesian credibility intervals.

Fig. 2.

Extended Bayesian skyline plot constructed without calibrating information from ancient sequences. Darker colors indicate regions of reduced certainty.

Fig. 3.

Density of ratios of population size during the bottleneck (500 ypb for calibrated analysis, 2.5 × 10⁻⁵ subs. per site for uncalibrated analysis) to size before bottleneck (4000 ypb for calibrated analysis, 1.5 × 10⁻⁴ subs. per site for uncalibrated analysis). Shaded regions indicate 95% highest posterior density (HPD) intervals.

Fig. 4.

Majority-rule consensus tree constructed from genealogies sampled by the Markov chain. Gray bars indicate one SD in node height. Red lineages are ancient samples from North America; blue lineages are ancient samples from South America.