Evaluation of the Minimum Sampling Design for Population Genomic and Microsatellite Studies: An Analysis Based on Wild Maize

Frontiers in Genetics
Jonas A Aguirre-LiguoriLuis Enrique Eguiarte

Abstract

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 ob...Continue Reading

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Jul 11, 2019·Proceedings. Biological Sciences·Jonás A Aguirre-LiguoriLuis E Eguiarte

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Citations

Mar 16, 2021·Evolutionary Anthropology·Darice WestphalAndrea L Baden
Sep 15, 2021·Proceedings of the National Academy of Sciences of the United States of America·Vinay SagarUma Ramakrishnan
Nov 5, 2021·PloS One·Scott D FosterCampbell Davies

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Methods Mentioned

BETA
Genotyping
PCA

Software Mentioned

strataG package of
fastsimcoal
WorldClim
gplots
ecodist
hierfstat
Bayescan
BEDASSLE
R custom scripts
Bayenv

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