Because the SNPs identified in the today's genomes reflect the combinatory evolutionary processes such as methylated CpG mutation hotspots, high transition rate, selection on functional elements, and error-prone DNA replication and repair, a small effective SNP size suggests the strong influence of one or several genetic factors, especially the CpG effects in vertebrate genomes [ 9, 10].
These animals were sampled from a group of isolated Scottish islands and have a small effective population size [41] and low levels of diversity when assayed using microsatellite markers [12].
So, as expected, it shows a significant amount of overlapping among centered PSFs, and, therefore, a small effective dimensionality of its matrix of stacked, centered at zero, PSFs.
Amanita thiersii is currently undergoing a range expansion in North America (Wolfe, Kuo, et al. 2012), and genetic diversity across its new range is very low, suggesting that the species is experiencing a population bottleneck and has a small effective population size.
In contrast, the two tobacco populations sampled from Southern Brazil and Central NC (US), had a small effective population size.
Generally, these populations have a small effective size, and are composed of a few families with about a hundred descendants.
The conclusion might then be to use HaploMax for animal populations with a small effective size and having evolved over a few generations.
Our hypothesis was that, in these animal populations with a small effective size and having evolved over a few generations, a rough model based on the deterministic evolution of linkage disequilibrium was as accurate as a probabilistic-based model and should therefore be preferred from a computational point of view.
The divergence observed at the mtDNA locus was much higher (11.8%) while the diversity was lower than the nuclear average, in accordance with a higher rate of evolution and a smaller effective population size of the mitochondrial genome.
