Evaluation of the minimum sampling design for population genomic and microsatellite studies. An analysis based on wild maize

Abstract

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

Stabilizing selection on Atlantic cod supergenes through a millennium of extensive exploitation

“…Since SMC++ uses both AFS distributions and linkage between loci to infer past effective population size, the software is well suited for population genomic studies in comparison with other implementations that rely on deep sequencing of fewer individuals. Generally, a minimum of 8 individuals should be used in population studies for estimation of the AFS and genetic diversity derived parameters from high-density genetic markers such as SNP data from resequencing (71,72). Here 19 coastal cod and 22 offshore cod were used to infer past effective population sizes, which should provide sufficient power and precision for the utilized approaches.…”

Species delineation and genetic structure of two Chaerephon species (C. pusillus and C. leucogaster) on Madagascar and the Comoro archipelago

“…This genetic structure could potentially mirror the F ST significance we observed in our study. Although, these values and their level of significance could be biased by the low number of genetic markers and individuals involved in their analyses (e.g., Aguirre‐Liguori et al, 2020; Ruzzante, 1998). The genetic structure observed across Madagascar by Ratrimomanarivo et al (2009) could also result, as suggested by the authors, in a sampling bias (i.e., unsampled areas between genetically differentiated populations).…”

The role of environment, local adaptation, and past climate fluctuation on the amount and distribution of genetic diversity in two subspecies of Mexican wild Zea mays

“…In this sense, neutral molecular markers, such as microsatellites allow for a wide variety of robust analyses (Selkoe and Toonen, 2006; Guichoux et al, 2011; Kalia et al, 2011) including the inference of demographics and migration processes. Microsatellites can be used for many relevant analyses; however, recent studies have highlighted the importance of using a high number of loci (>20) with a comprehensive geographic representation of the species (including numerous populations and individuals) for making reliable conclusions (Aguirre‐Liguori et al, 2020).…”