Of the regions identified in both datasets, a selective sweep on BTA13 was detected in Holstein using the BovineSNP50 data and was also discovered in Wagyu using the AFFXB1P data.
It should, however, be kept in mind that iHS in itself might not be a very good metric for testing selective sweeps in a dataset which is known to contain many CPS SNPs of moderate allele frequencies because, unless on a single haplotype, these SNPs will have a tendency to disrupt long haplotype blocks.
This new metric may be of use to researchers trying to identify selective sweeps to datasets that are influenced by ascertainment bias.
This dataset consists of an extensive list of selective sweeps related to chicken domestication, based on resequencing of populations of RJF and a number of domesticated breeds.
In addition, we performed another sweep scan using patterns of LD with this dataset.
Extended regions of homozygosity, indicative of selective sweeps, were identified in a genome-wide scan dataset of 25 Boxers from the United Kingdom genotyped at ~20,000 single-nucleotide polymorphisms (SNPs).
The authors also stated that the future work should focus on performing parameter sweeps for GE and SVM parameters for different dataset to discover the true potential of GESVM.
For each simulated replicate dataset, we calculated the log-likelihood ratio in favor of an adaptive sweep using the CLRT, producing a null distribution from which to estimate the P-value of the observed log-likelihood ratio.
When the analysis was performed over all genes, LRTs indicated that the bottleneck (M2) and selective sweep (M3) models both showed a significantly better fit with the dataset than the constant-size (M1) model.
We carried out a genome-wide scan of signatures of positive selection using the 1000 Genomes Phase I dataset, in order to identify pigmentation genes showing putative signatures of selective sweeps in East Asia.
