Getting back to the ever-present time issue; the inferences on this paper are, of course, based on assumption about Y-STR diversity accumulation that I have criticized elsewhere and I will not repeat.
But, isn't it strange that the authors claim a Paleolithic gene pool, while, at the same time, discovering a sharp divide? Common sense dictates that genetic distinctions across a long time span would be blurred, and there would be no sharp divide.
Sharp divides are created by recent population movements and are maintained by insurmountable geographical barriers (e.g., the Sahara or the Pacific) that persist for a long-time.
Molecular Biology and Evolution, doi:10.1093/molbev/msq063
Major East-West Division Underlies Y Chromosome Stratification Across Indonesia
Tatiana M. Karafet et al.
The early history of Island Southeast Asia is often characterized as the story of two major population dispersals: the initial Paleolithic colonization of Sahul 45 thousand years ago and the much later Neolithic expansion of Austronesian-speaking farmers 4,000 years ago. Here, in the largest survey of Indonesian Y chromosomes to date, we present evidence for multiple genetic strata that likely arose through a series of distinct migratory processes. We genotype an extensive battery of Y chromosome markers, including 85 SNPs/indels and 12 Y-STRs, in a sample of 1,917 men from 32 communities located across Indonesia. We find that the paternal gene pool is sharply subdivided between western and eastern locations, with a boundary running between the islands of Bali and Flores. Analysis of molecular variance reveals one of the highest levels of between-group variance yet reported for human Y chromosome data (e.g., ?ST = 0.47). Eastern Y chromosome haplogroups are closely related to Melanesian lineages (i.e., within the C, M and S subclades) and likely reflect the initial wave of colonization of the region, while the majority of western Y chromosomes (i.e., O-M119*, O-P203, and O-M95*) are related to haplogroups that may have entered Indonesia during the Paleolithic from mainland Asia. In addition, two novel markers (P201, P203) provide significantly enhanced phylogenetic resolution of two key haplogroups (O-M122, O-M119) that are often associated with the Austronesian expansion. This more refined picture leads us to put forward a four-phase colonization model in which Paleolithic migrations of hunter-gatherers shape the primary structure of current Indonesian Y chromosome diversity, and Neolithic incursions make only a minor impact on the paternal gene pool, despite the large cultural impact of the Austronesian expansion.