In looking at the following diagram...
For those with inadequate screen size, view the above image in full with: here
...it is apparent that at the least, U5 and U6 diverge into respective branches independent from that of the rest of U macro-haplogroup. Similar observation has been made about U1, which too, seems to have an independent branch from the rest of the U haplogroup. In other words, these three—either U1, U5 or U6—don't appear to have an ancestral clade within the main haplogroup U branch which is defined by the nucleotide transition at 1811 or vice versa. This is how it goes, courtesy of Maca-Meyer et al. 2003:
U6 is defined by two motifs represented by positions in the coding and HVR respectively: 3348 and 16172.
U5 is defined by the transitions at: 3197, 9477, 13617 and 16270.
And the rest of the U haplgroup [sans U1], defined by the mutation designated by position: 1811.
Maca-Meyer et al. add that:
U presents the following mutations with respect to rCRS: 73, 263, 311i, 750, 1438, 2706, 4769, 7028, 8860, 11467, 11719, 12308, 12372, 14766 and 15326. - Maca-Meyer et al. 2003
N macrohaplogroup is removed from the root of L3 by about 5 mutations, we are told. This is relevant, in that U haplogroup is often posited as having split from R, which derives from Haplogroup N. Speaking of haplogroup U splitting from R, we are told that this is the case via three mutations represented by: 11467, 12308 and 12372
Hence, the family association has been made between U6 [as is for U1 & U5] and the rest of the U haplogroup, primarily thanks to sharing of the above mentioned transition trio; if it weren't for these basic transitions, U6 would have likely just been considered as just another separate sub-branch of haplogroup R. Perhaps, if a clade was located—sharing the same transition trio but devoid of any known downstream coding or HVR mutations in either U6, U1 or U5 and the rest of haplogroup U, it could provide us with a possible candidate as the proto-U ancestor that gave rise to the divergent U branches in question. However, to date, no such lineage has come to light.
In their publication "The mtDNA Legacy of the Levantine Early Upper Palaeolithic in Africa" - 2006, Anna Olivieri et al.'s argument, like that of Gonzalez et al., depends on the idea that U6 entered Africa in a parallel dispersal with M1, which the present author has demonstrated elsewhere to be a weak hypothesis [see: Mitochondrial DNA M1 haplogroup: A Response To Ana M. Gonzalez et al. 2007]. M1 basal coding markers emerge from that of an African background, and the "missing-link" lineage of the M Macrohaplogroup was found in a sub-Saharan sample [specifically in a Senegalese sample].
Thus, the re-examination point:
— U6 with respect to U5 , or U6 with respect to U1, and U6 with respect to the rest of haplogroup U, doesn't share defining motifs, outside of the basic transitions, particularly at the aforementioned position trio.
— In relation to the above, U6 doesn't have a common recent ancestor that is a U5 sub-lineage or vice versa, U6 doesn't have a common recent ancestor that is a U1 sub-lineage or vice versa, nor does U6 have a common recent ancestor that is a U*(xU1, U5) sub-lineage or vice versa.
...brings us to the question of:
Could U6 then be a standalone clade, in that, short of the aforementioned basic mutations by which the U-designated lineages diverge from macro-haplogroup R — particularly at 11467, 12308 and 12372, it is essentially mutually-independent of the other U-designated lineages?
The relationship of U6 with other U haplogroups is only inferred from non-U subclade-specific basal markers.
U6 is a branch on its own, independent from other U groups, and proto-U6 has not been located to date.
Time will tell, as to whether much more improved resolution of mtDNA will bear out the possible candidate of the elusive proto-U6 ancestor, but until then, it would appear that the proto-U6 bearing population was quite small in size, such that proto-U6 itself would eventually be overwhelmed and essentially be erased by expansion of descendant U6 carriers and possibly, incursions from other populations. It is uncertain whether a proto-U6 ancestor would have been the very same ancestor that begot U1, U5 and U*(xU6,U1,U5) respectively elsewhere, or whether it would have been a single step or a few steps genetic-neighbor to those which begot the latter U groups, but it appears that the latter respective ancestors too were modestly represented 'population-wise', such that they too would have been overwhelmed by subsequent demographic expansions that gave rise to descendant populations and incoming groups from elsewhere. Whatever may be said about a proto-U6 ancestor's origin, one thing is clear: U6 itself is an autochthonous African marker, which would eventually spill over to parts of Europe, particularly those hugging the Mediterranean sea, and parts of "southwest Asia". It too, like M1 (clickable), has been implicated in the expansion of proto-Afrasan (aka proto-Afro-Asiatic) and/or Afrasan speakers outside of mainland Africa.
— Maca-Meyer et al. 2003, Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography.