A message from this study is that Y chromosome diversity within an already settled territory can indeed be wiped out. Introduction of new pathogens or a technological differential between colonists and natives, are just two possible ways to achieve this.
Many technological innovations (e.g. farming, Bronze, Iron) originated in a very small part of the Old World and spread far and wide. I would not be very surprised if this coincided with a massive replacement of Y chromosomes. The legacy of the earlier inhabitants may, of course, endure, via mtDNA, or autosomal DNA.
BMC Evol Biol. 2008 Jul 21;8(1):213. [Epub ahead of print]
Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba.
Mendizabal I, Sandoval K, Berniell-Lee G, Calafell F, Salas A, Martinez-Fuentes A, Comas D.
ABSTRACT: BACKGROUND: Before the arrival of Europeans to Cuba, the island was inhabited by two Native American groups, the Tainos and the Ciboneys. Most of the present archaeological, linguistic and ancient DNA evidence indicates a South American origin for these populations. In colonial times, Cuban Native American people were replaced by European settlers and slaves from Africa. It is still unknown however, to what extent their genetic pool intermingled with and was 'diluted' by the arrival of newcomers. In order to investigate the demographic processes that gave rise to the current Cuban population, we analyzed the hypervariable region I (HVS-I) and five single nucleotide polymorphisms (SNPs) in the mitochondrial DNA (mtDNA) coding region in 245 individuals, and 40 Y-chromosome SNPs in 132 male individuals. RESULTS: The Native American contribution to present-day Cubans accounted for 33% of the maternal lineages, whereas Africa and Eurasia contributed 45% and 22% of the lineages, respectively. This Native American substrate in Cuba cannot be traced back to a single origin within the American continent, as previously suggested by ancient DNA analyses. Strikingly, no Native American lineages were found for the Y-chromosome, for which the Eurasian and African contributions were around 80% and 20%, respectively. CONCLUSIONS: While the ancestral Native American substrate is still appreciable in the maternal lineages, the extensive process of population admixture in Cuba has left no trace of the paternal Native American lineages, mirroring the strong sexual bias in the admixture processes taking place during colonial times.