I wouldn't be very surprised if many of the markers supposedly signifying recent gene flow Africa and Eurasia were actually quite old in Eurasia. The trouble is that reports of such gene flow were often based on simply observing that marker "X" occurs at a higher frequency in Africa than in Eurasia, so a common sense explanation is that it reflects limited recent gene flow between the continents. But, it is now known that common sense is not always the best guide, as e.g., ancient Europeans had mtDNA haplogroup M (in the past considered evidence of Asian admixture), Y-chromosome haplogroup C (ditto), and now U6.
The same should also apply to the Middle East where there has been admixture with Africans since the Islamic period at least. The existence of such admixture does not mean that every single lineage that occurs at low frequency in the Middle East and high frequency in Africa is diagnostic of this later period of admixture. Some of them could well be relics of old Middle Eastern populations. Who knows what people inhabited the presently inhospitable landscape of the Saharan-Arabian desert zone? The living populations can certainly make no claim to being the first ones there, but the genetic heritage of those earlier occupants may still persist in them in traces.
Similarly for the New World; in that case, there is a better case that European-looking lineages are indeed due to the colonization of the Americas over the last five centuries. However, that does not mean that all of them are, and we should be mindful of the possibility of pre-Columbian contact between the Old and New worlds.
Scientific Reports 6, Article number: 25501 (2016)
The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa
M. Hervella et al.
After the dispersal of modern humans (Homo sapiens) Out of Africa, hominins with a similar morphology to that of present-day humans initiated the gradual demographic expansion into Eurasia. The mitogenome (33-fold coverage) of the Peştera Muierii 1 individual (PM1) from Romania (35 ky cal BP) we present in this article corresponds fully to Homo sapiens, whilst exhibiting a mosaic of morphological features related to both modern humans and Neandertals. We have identified the PM1 mitogenome as a basal haplogroup U6*, not previously found in any ancient or present-day humans. The derived U6 haplotypes are predominantly found in present-day North-Western African populations. Concomitantly, those found in Europe have been attributed to recent gene-flow from North Africa. The presence of the basal haplogroup U6* in South East Europe (Romania) at 35 ky BP confirms a Eurasian origin of the U6 mitochondrial lineage. Consequently, we propose that the PM1 lineage is an offshoot to South East Europe that can be traced to the Early Upper Paleolithic back migration from Western Asia to North Africa, during which the U6 lineage diversified, until the emergence of the present-day U6 African lineages.