Comparing signals of natural selection between three Indigenous North American populations

Abstract

Significance Recent studies have shown that humans have adapted to many different environments around the world. However, few studies have centered on Indigenous groups in the Americas. We present a comparative analysis of genetic adaptations in humans across North America using genome-wide scans for signals of natural selection in three populations inhabiting vastly different environments. We find evidence for adaptation to cold and high latitudes in an Alaskan population, whereas infectious disease was a strong selective pressure in the southeastern United States and central Mexico. Because there are few shared signals of selection between populations, these sweeps likely occurred after population differentiation in the Americas. This study fills an important gap in our knowledge of genetic adaptations in humans. While many studies have highlighted human adaptations to diverse environments worldwide, genomic studies of natural selection in Indigenous populations in the Americas have been absent from this literature until very recently. Since humans first entered the Americas some 20,000 years ago, they have settled in many new environments across the continent. This diversity of environments has placed variable selective pressures on the populations living in each region, but the effects of these pressures have not been extensively studied to date. To help fill this gap, we collected genome-wide data from three Indigenous North American populations from different geographic regions of the continent (Alaska, southeastern United States, and central Mexico). We identified signals of natural selection in each population and compared signals across populations to explore the differences in selective pressures among the three regions sampled. We find evidence of adaptation to cold and high-latitude environments in Alaska, while in the southeastern United States and central Mexico, pathogenic environments seem to have created important selective pressures. This study lays the foundation for additional functional and phenotypic work on possible adaptations to varied environments during the history of population diversification in the Americas.