The A lineages you're talking about are hundreds of thousands of years old, older than all the language families. There is no link whatsoever between Nilotic languages and Khoisan languages. I don't even know what your argument is anymore. Were there an ancient people who lived in southern Somalia prior to the arrival of Cushitic people? Maybe? Were they Khoisan speakers? Definitely not.
Khoikhoi and San are both very much the product of ancient Southern Africa, but they are a distinct people with their own history, they are not ancient humans frozen in time. The treatment of these tribes as some weird relic out of time is very strange.
The thing you have to keep in mind is that during the ice age, Somalia was uninhabitable. It was a brutal true desert until 10,000 years ago. 10,000 years ago the climate shifted and Somalia became grasslands much wetter than today, which is when Cushitic migration from the north moved down and colonized the newly habitable land, so there is a VERY GOOD PROBABILITY that the ancestors of Somalis were the very first humans to colonize Somalia.
James,
The Khoe are part of a recent (2kya) migration from the north that carries even Neanderthal DNA.
https://mg.co.za/article/2016-02-04-the-origins-of-the-khoisan-disprove-notions-of-race
"About 140 000 years ago human populations from East or Central Africa moved southwards and “colonise” western southern Africa. The probable nearest living relatives of these source populations are:
This migration gave rise to the present-day
San hunter-gatherers.
Much more recently – about 2 000 years ago – there was a second movement of “colonists” from the north into southwestern Africa. They gave rise to the pastoral
Khoikhoi people.
This second group of “settlers” carried within its genome bits of Eurasian-sourced – and even some
Neanderthal – DNA derived from European humans who had returned to Africa about 3 000 years ago.
Subsequent to this second colonisation, there was intermixing between the Khoikhoi and San. This gave rise to their close anatomical similarities despite the fact that they retained their marked cultural and linguistic differences.
Much more recently – about 1 700 years ago – there was a third major north-to-south migration. This time it was the Bantu-speaking, black Africans into south-eastern Africa. Those “settlers” that eventually became the Xhosa peoples moved westwards and encountered the Khoikhoi, whom they drove further west and intermixed with genetically."
Also, you didn't read this:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC384897/#RF25
"In conclusion, the present study underscores the complexity and substructure of the Ethiopian Y-chromosome gene pool. First, the presence of different Y-chromosome haplotypes belonging to African-specific Group I in all groups of Ethiopians and in the Khoisan (at frequencies of ∼13% and 44%, respectively) confirms that these populations share an ancestral paternity, as was previously suggested by the 49a,f data (Passarino et al.
1998), and it indicates that Group I was part of the proto-African Y-chromosome gene pool. The virtual absence of this clade in the other African ethnic groups suggests that they could derive from a more recent ancestral population that went through a long period of differentiation before expansion. In addition, Group II, the next closest to the NRY genealogy root and typically an African group, is shared by Ethiopians and the Khoisan but to a lesser degree. In the case of Group II, the split responsible for the differences observed between Ethiopian and Khoisan haplotypes is also old. Second, most of the Ethiopian Y chromosomes, the rest of the Khoisan Y chromosomes, and the majority of the Senegalese Y chromosomes belong to Group III, which is also mainly African but whose precursor is believed to be involved in the first migration out of Africa (Underhill et al.
2001). Third, the remainder of the Ethiopian Y chromosomes (Groups VI, VIII, and IX) may be explained by back migrations from Asia."