Likelihood Estimation of Arabidopsis Population Parameters with MAPGD

Background

MAPGD (Ackerman, 2016; Ackerman et al., 2022) is a series of related programs that estimate allele frequency, heterozygosity, Hardy-Weinberg disequilibrium, linkage disequilibrium, and identity-by-descent coefficients from population genomic data using a statistically rigorous maximum likelihood approach. The MAPGD software was primarily designed for analysis of planktonic crustacean Daphnia populations (Lynch et al., 2017; Maruki et al., 2019; Ye et al., 2019). It is most useful for the analysis of low coverage population genomic data or pooled data, where many individuals are used to prepare a single sample (Lynch et al., 2014). Since its release, MAPGD has been widely used in population genomic studies of various organisms, including the nematode Caenorhabditis elegans (Adams et al., 2022), stickleback fish (Jeffries et al., 2022), and human gut microbiota (Shoemaker, 2022). A benchmark study showed that MAPGD could outperform other single nucleotide polymorphism (SNP) callers and has great potential in different applications (Guirao-Rico and González, 2021). Here, we demonstrate the usage of MAPGD in the analysis of a publicly available Arabidopsis population dataset (The 1001 Genomes Consortium, 2016). We show that MAPGD could be used for plant population genomic studies.