Evolutionary Responses to a Constructed Niche: Ancient Mesoamericans as a Model of Gene-Culture Coevolution

Hünemeier, Tábita; Amorim, Carlos Eduardo Guerra; Azevedo, Soledad; Contini, Veronica; Acuña-Alonzo, Víctor; Rothhammer, Francisco; Dugoujon, Jean-Michel; Mazières, Stephane; Barrantes, Ramiro; Villarreal-Molina, María Teresa; Paixão-Côrtes, Vanessa Rodrigues; Salzano, Francisco M.; Canizales-Quinteros, Samuel; Ruiz-Linares, Andres; Bortolini, Maria Cátira

To detect loci under selection, we used a method that contrasted the observed population differentiation (F ST ) with that generated for a null simulated distribution under a hierarchical island model using a coalescent approach. In this model, demes exchange more migrants within groups than between groups to generate the joint distribution of genetic diversity within and between populations [38] . Thus, a p value can be estimated from the joint distribution for the population heterozygosity (H e ) and F ST using a kernel density estimation procedure [30] . The analysis was performed using Arlequin 3.5.1 in consideration of 126 Native Americans whose results for the ABCA1*230 locus were known. Data from 20 other autosomal SNPs (rs6559725, rs11140096, rs4877767, rs4014024, rs11140109, rs7872891, rs7850633, rs17086298, rs10746709, rs5014093, rs10868019, rs11140116, rs3860938, rs3860941, rs4097644, rs9942844, rs12551103, rs7863524, rs4877785, and rs70439590) from these same individuals were compiled from a major SNP panel (Table S2 ). These 20 additional SNPs were selected based on their location (chromosome 9: from position 85252250 to 85317359) inside the putative neutral region, defined by Schroeder and colleagues [39] , which comprises ,76,000 bp around the D9S1120 locus. Using this database (Table S2 and Figure S1 ), we were able to evaluate whether the joint distribution of the observed H e and F ST for the ABCA1*230 Caution is needed regarding the classification of these modes of subsistence, since they are not stable over time and may not be unique. However, the two categories adopted here (agriculturalist and hunter-gatherer/forager) represent general pre- American hunter-gatherer/foragers. In addition, we simulated 100,000 neutral genealogies for a region containing two distinct sets of 20 biallelic markers under demographic scenarios mimicking the settlement of the Americas [32, 40] . To accomplish these simulations, we used the msABC software [41] , a modification of ms software [42] (2) three demes that corresponded to the sampled subdivisions (Mesoamerican agriculturalists, Andean agriculturalists, South American hunter-gatherers/foragers); (3) a single ancestral population that existed from 6,350 to 18,000 YBP [32, 40] ; and (4) different exponential growth rates to include the possibility of an ancestral population of 70 to 830 individuals (i.e., constant population size [40] ).