Massive parallel sequencing (MPS) is revolutionizing the field of molecular ecology by allowing us to understand better the evolutionary history of populations and species, and to detect genomic regions that could be under selection. However, the economic and computational resources needed generate a tradeoff between the amount of loci that can be obtained and the number of populations or individuals that can be sequenced. In this work, we analyzed and compared two simulated genomic datasets fitting a hierarchical structure, two extensive empirical genomic datasets, and a dataset comprising microsatellite information. For all datasets, we generated different subsampling designs by changing the number of loci, individuals, populations, and individuals per population to test for deviations in classic population genetics parameters (H S , F IS , F ST). For the empirical datasets we also analyzed the effect of sampling design on landscape genetic tests (isolation by distance and environment, central abundance hypothesis). We also tested the effect of sampling a different number of populations in the detection of outlier SNPs. We found that the microsatellite dataset is very sensitive to the number of individuals sampled when obtaining summary statistics. F IS was particularly sensitive to a low sampling of individuals in the simulated, genomic, and microsatellite datasets. For the empirical and simulated genomic datasets, we found that as long as many populations are sampled, few individuals and loci are needed. For the empirical datasets, we found that increasing the number of populations sampled was important in obtaining precise landscape genetic estimates. Finally, we corroborated that outlier tests are sensitive to the number of populations sampled. We conclude by proposing different sampling designs depending on the objectives.

14Massive parallel sequencing is revolutionizing the field of molecular ecology by allowing to 15 understand better the evolutionary history of populations and species, and to detect genomic 16 regions that could be under selection. However, the needed economic and computational 17 resources generate a tradeoff between the amount of loci that can be obtained and the number 18 of populations or individuals that can be sequenced. In this work, we analyzed and compared 19 two extensive genomic and one large microsatellite datasets consisting of empirical data. We 20 generated different subsampling designs by changing the number of loci, individuals, 21 populations and individuals per population to test for deviations in classic population genetics 22 parameters (HS, FIS, FST) and landscape genetic tests (isolation by distance and environment, 23 central abundance hypothesis). We also tested the effect of sampling different number of 24 2 populations in the detection of outlier SNPs. We found that the microsatellite dataset is very 25 sensitive to the number of individuals sampled when obtaining summary statistics. FIS was 26 particularly sensitive to a low sampling of individuals in the genomic and microsatellite 27 datasets. For the genomic datasets, we found that as long as many populations are sampled, 28 few individuals and loci are needed. For all datasets we found that increasing the number of 29 population sampled is important to obtain precise landscape genetic estimates. Finally, we 30 corroborated that outlier tests are sensitive to the number of populations sampled. We 31 conclude by proposing different sampling designs depending on the objectives. 32 33