The peopling of the Americas represents the last major expansion of human populations worldwide. As the first humans moved into the continent they were exposed to new environments requiring them to adapt. The subsequent colonization of the continent by Europeans, along with the African slave trade, involved a major admixture process that was accompanied by new selective pressures, most notably exposure to new pathogens. Applying current and novel methods to genome-wide SNP data of Native and admixed Latin Americans, this PhD thesis provides an analysis of the adaptive history in the Americas. I show that prior to the European contact, candidate regions of selection in Native Americans include genes associated with metabolic traits, highlighting a possible adaptation to dietary changes. Using novel and existing methods to detect selection post-admixture, I show that genes related to immune response were probably under selection in admixed Latin Americans. As an example on the evolution of an adaptive trait, I also conduct a Genome Wide Association Study on a sample of over 6,000 Latin Americans for skin, eye and hair pigmentation. I report eighteen independent genome-wide significant signals of association, including five novel variants. One of the novel variants associated to skin pigmentation is common in East Asians and Native Americans, but is almost absent everywhere else in the world. I show that this variant was selected in East Asians after their split from Europeans, and likely carried by the first Americans to the Americas
