Bayesian analyses for the combined data set were performed in a partitioned framework, allowing locus-specific parameter estimation.
One of the key advantages of our approach is that the genotyping assay is dynamic, allowing loci to be added over time as needed to increase power and target additional genomic regions of interest.
The two extreme possibilities are that RIP introduced mutations in the repeat pool only at the time of duplication of NWD1p and NWDp2 or that WD-repeat triggered RIP constantly allows locus specific hypermutation of the repeat arrays.
By comparison, the two-locus model allows loci to differ and be linked.
Also, our results suggest that SNP mapping allows loci to be defined more precisely than STR marker due to the higher marker density (figure 3).
The availability of genotypes of N. furzeri that differ in average lifespan allows loci that control lifespan to be mapped by QTL analysis (Kirschner et al., 2012).
This approach was used in the pied flycatcher and although intron sequences discriminate pseudogenes and nonclassical MHC II B loci from classical class IIB loci, they do not allow locus-specific amplification of the latter [ 48].
Phases (coupling and repulsion) of the marker loci were detected automatically by JoinMap, with the 'CP' option, which allows loci of different phases to be linked on the same chromosome.
Despite the overall similarity between ES and TS, the use of a candidate-based replication timing assay allows loci that are subject to chromatin re-modelling events early in mammalian development to be readily identified.
Among individuals, loci were merged as a single locus if they presented up to three mismatches (n = 3), which allows loci that are fixed differentially among different populations or species (thus represented independently across individuals) to be merged as a single locus (Stacks manual).
There are increasingly more methods to incorporate independent loci in phylogenetic inference, allowing each locus a unique evolutionary history.
