Testing for archaic hominin admixture on the X chromosome:: Model likelihoods for the modern human RRM2P4 region from summaries of genealogical topology under the structured coalescent

A 2.4-kb) stretch within the RRM2P4 region of the X chromosome, previously sequenced in a sample of 41 globally distributed humans, displayed both an ancient. time to the most recent. common ancestor (e.g., a TMRCA of similar to 2 million years) and a basal clade composed entire]), of Asian sequences. This pattern was interpreted to reflect a history of introgressive hybridization from archaic hominins (most likely Asian Homo ereclus) into the anatomically modern human genome. Here, we address this hypothesis by resequencing( the 2.4-ki) RRM2P4 region in 131 African and 122 non-African individuals and by extending the length of sequence in a ,inof 16.5 kb encompassing the RRM2P4 pseudogene in a subset of 90 individuals. We find that both the ancient TMRCA and the skew in non-African representation in one of the basal clades are essentially limited to the central 2.4-kb region. We define a new summary statistic called the minimum clade proportion (P-mc), which quantifies the proportion of individuals front a specified geographic region in each of the two basal clades of a binary gene tree, and then employ coalescent simulations to assess the likelihood of the observed central RRM2P4, genealogy Under two alternative views Of human evolutionary history: recent. African replacement (RAR) and archaic admixture (AA). A molecular lar-clock-based TMRCA estimate of 2.33 million years is a statistical outlier Under the RAR model; however, the large variance associated With this estimate makes it difficult to distinguish the predictions of the human origins models tested here. The P-mc summary statistic, which, has inipimproved power with larger samples of chromosomes, yields values that are significant], unlikely under the RAR imodel and fit expectations better under a range of archaic admixture scenarios.