It is fairly straight-forward:
- Mesolithic/Neolithic Egyptians mixed with Mesolithic/Neolithic Sudanese
- Group 1 has no real modern equivalent but the closest are modern day Copts & Bedouins
- Group 2 also has no real equivalents today but the closest are modern day Dinka & Gumuz
- This mixture forms the earliest Cushites in Sudan and Southern Egypt around the Neolithic
- A segment of these people (Proto-Agaw-East-South) eventually go down into the Horn
- There they acquire varying degrees of Mota (native Ethio HG) related admixture
- Eventually around 1000 BCE or so people from Yemen come with Proto-Ethiosemitic
- Early group leave a strong genetic imprint in the northern highlands and a linguistic legacy
- Later internal migrations occur in the Horn so everyone has some of the ancient Yemeni
And that's the ancestral history of modern Somalis in a nutshell. Y-DNA E-V32 and T-L208 come from the ancient North-African ancestors as do likely all the mtDNA N&M lineages while the trace amounts of A-M13 and nearly all the L(xM&N) lineages come from the native East African ancestors while a few L lineages do seem to come from native Ethio HGs. Then the trace amounts of J1 is likely all from the Jazeera in some way or another.
I'd wager like 80%+ of Somalis' ancestry comes from "Group 1 & 2" whereas at best 5-10% comes from ancient Yemen and 1-5% comes from the native Ethio Hunter-Gatherers and that's that.