Detecting evolutionary strata on the human X chromosome: Markov Segmentation and Clustering Analysis

In mammalian sex chromosomes, a stratum is formed on the X chromosome following the cessation of X-Y recombination. In the absence of homologous recombination, the non-recombining regions accumulate DNA elements, such as, transposable or repetitive elements, and sequences with shifts in GC content and thus the sequence composition of each strata diverges from the regions on the X that still undergo X-Y recombination. To delineate the stratum boundaries, we developed a multi-pronged strategy that applies a recursive segmentation and an agglomerative clustering algorithm within the framework of statistical hypothesis testing to identify compositionally distinct regions on the X chromosome.