The interest of ancestral segregating   haplotypes is multiple: Regional association mapping studies can be performed   in order to detect causative variants related to quantitative animal traits   of interest [13], thus providing greater power than simple SNP-based   genome-wide association analyses when LD is extensive [14, 15, 16, 17].   Furthermore, the study of the frequency distribution of ancestral segregating   haplotypes provides information about population dynamics such as bottlenecks   and adaptation [18]. Ancestral haplotype frequencies are expected to vary due   to perturbations in the population, leading to a potential deficit of some   haplotypes after moderate bottlenecks [19] and/or to unusual high frequency   of specific haplotypes in certain sub-populations due to genetic drift and/or   selection. Selective sweeps resulting from recent intensive selection lead to   extended LD patterns and long highly frequent haplotypes [20, 21, 22, 23],   whereas old selection is expected to lead to shorter haplotypes as a   consequence of recombination breaking the original blocks over the   generations. Moreover, additional genomic characteristics such as   recombination hotspots can also be detected [24, 25], as these genomic   regions show a higher haplotype variation than expected under neutral theory.

分离祖先单倍型的好处是多方面的：可以进行区域关联映射研究，以检测与特定动物量化特征相关的变异[13]，从而在LD（连锁不平衡）广泛存在时比简单的基于单核苷酸多态性的全基因组关联分析提供更大的力量[14，15，16，17]。此外，研究祖先分离单倍型的频率分布提供了有关种群动态的信息，如瓶颈和适应[18]。由于种群的扰动，祖先的单倍型频率预计会发生变化，导致中度瓶颈后某些单倍型的潜在缺失[19]和/或由于遗传漂变和/或选择导致某些亚种群中特定单倍型的异常高频率。由于最近的密集选择所导致的选择清除作用导致较长的连锁不平衡以及长且高频的单倍型[20，21，22，23]，而时间较远的选择作用由于重组破坏了最初的基因块，预计将导致较短的单倍型。此外，还可以检测到其他的基因组特征，如重组热点[24，25]，因为这些基因组区域显示出比中性理论预期的更高的单倍型变异。