There is a divergence in the frequencies of mobile genetic elements in the three Plasmodium species investigated.
We analyzed the number of reads for conserved miRNAs and found it has large divergence in the expression frequency among these miRNAs.
As population structure is typically assessed by estimating divergence in the allele frequencies at neutral genetic markers (i.e., microsatellite loci), this class of genetic markers is routinely used to delineate both ESUs (Small et al. 1998) and MUs (Palsbøll et al. 2006).
The most significant divergence in allele frequencies in the Andean horse is found in the TENM2 gene, a member of the teneurin family of type II tramsmembrane glycoproteins (p = 7.9 × 10 14, Figure 3).
For example, polymorphisms that exhibit the greatest divergence in allele frequency among populations (FST outliers) may represent loci subject to divergent selection (Lewontin and Krakauer 1973; Beaumont and Nichols 1996).
Second, the genome-wide significance threshold of the present study is quite stringent, requiring high divergence in allele frequency between populations.
To prevent the substantial divergence in allele frequencies from population stratification, we replicated the association in the other unrelated 1087 samples of 563 cases and 524 control subjects.
Results are presented for a significance level of 5% over a range of F ST, encompassing no divergence in allele frequencies between the case-control source population and the external cohorts (F ST = 0), through to the level of differentiation expected between European and African populations.
We first develop a simple statistical model based on classical population genetic methods to analyze whole genome divergence in allele frequency.
The first method examines genotypic data at multiple low-resolution loci, such as chromosomal morphs, allozymes, microsatellites, amplified fragment length polymorphisms (AFLPs) or single nucleotide polymorphisms (SNPs), for heterogeneity of divergence in allele frequency.
