Rather than PCR-based locus isolation via homologous primers, during which loci may be missed due to primer mismatching, we used magnetic bead-based DNA hybridization of universal probes (Figure 1A).
While the above approach succeeded to create a single cell line expressing GLuc from the endogenous Pmp22 locus, isolation of additional clones was hampered by low efficiency recombination using this reporter insertion strategy.
Here, our finding provided a novel approach for duplicated loci isolation that avoids the likelihood of errors from PCR amplification [ 30].
Premise of the study: We have optimized a version of a microsatellite loci isolation protocol for first-generation sequencing (FGS) technologies.
Here, we report microsatellite loci isolation, characterization, and cross-amplification for O. ophiuroides Louzada & Wand., a species endemic to the Chapada Diamantina section of the Espinhaço Range in the state of Bahia, Brazil (Louzada and Wanderley, 2008).
We ignore back mutations and consider the dynamics of the two alleles at this locus in isolation; i.e., there is no interaction with other alleles elsewhere in the genome.
The predicted coding effect of each variant allele landing in a codon was made by a script that considered each locus in isolation and examined the reference codon versus the alternate codon induced by the variant allele as interpreted by the standard universal genetic code, and codons with multiple loci were generally excluded from downstream analyses.
These loci, also called isolation loci, can act on a variety of phenotypic and physiological traits to ensure pre-zygotic and/or post-zygotic isolation.
We used Mantel tests to detect whether patterns of population differentiation at MHC and microsatellite loci showed isolation by distance.
For instance, a snapshot taken after 10 000 generations of introgression shows that while the step has completely vanished at freely recombining neutral loci, neutral loci in partial linkage with reproductive isolation loci have retained the signal of differentiation between populations due to their reduced effective migration rate (Fig. 3B).
Simulations have demonstrated that selection against specific hybrid genotypes (i.e., locus-specific reproductive isolation), whether arising from single locus (underdominance) or multilocus (Dobzhansky-Muller) incompatibilities, affects α and β, but the effect of selection on α is often more pronounced, particularly if dispersal from parental populations is limited [ 20, 52].
