Igor Lipovsky has extrapolated from Genesis a scenario for the house of Joseph as part of the Hyksos rule of Egypt that ended in about 1550 BCE. He does not hold to the Bible as a precise, literal record. However, he does see Genesis as showing us real relationships and data on the origins of Israel and its tribes. The house of Joseph developed in Egypt and moved back to Canaan with the Hyksos expulsion.
The two Joseph tribes are Ephraim and Manasseh. Genesis says that they derive from the principal sons of Joseph by a daughter of an Egyptian priestly family from On or Heliopolis (Genesis 46:20). Their birth order was Manasseh then Ephraim. But when aged and nearly blind Jacob-Israel blessed them, he blessed Ephraim first (Genesis 48:14). This explained why Ephraim became the greater tribe.
According to Lipovsky, Genesis was a basic narrative for the united nation of Judah and Israel that existed under David and Solomon.
But do we have any sources about Ephraim and Manasseh from before David and Solomon? It appears to me that we do.
We have the Song of Deborah in Judges 5, which many scholars say is probably the oldest composition in the Bible. There are many translation and even pointing problems (telling where words end and begin) with this passage. It seems to be written in a dialect of which we have no other examples, perhaps a Kenite dialect. So we should not be too confident about our translations. What seems clear is that it speaks of ten Israelite tribes. But these do not entirely agree with the later 12 tribes ideal.
For instance, there is no Manasseh tribe. Instead there is a tribe of Machir (Judges 5:14). Machir was supposed to be a son of Manasseh (Genesis 50:23). According to Numbers 32:39 and Joshua 17:1, Machir’s descendents established themselves across the Jordan in Gilead. However, the Song of Deborah seems to have another tribe of Gilead (Judges 5:17) and it has no tribe of Manasseh. Gilead may have been a related clan (1 Chronicles 7:17)
Anyway, this calls into doubt the notion that from the earliest times there was a well-known house of Joseph consisting of Ephraim and Manasseh. Also, possibly from a pre-monarchic tradition is the story of Gideon in Judges 6. Gideon is technically from the tribe and territory of Manasseh. But this is never mentioned. He was apparently not a hero of Manasseh the way Joshua was a hero of Ephraim.
As I said, you should not build much on translations of Judges 5, but for what its worth, one of the ways to translate Judges 5:14 is to say that Ephraim’s “root is in Amelek”. That may mean something if 1 Chronicles 7:21-24 also draws from a source that comes before the monarchy. First Chronicles is very late, but it used sources and we don’t know how early some of them may have been.
It is an odd passage and not well-known. It is either part of or has been inserted into a genealogy of Joshua. Here it is from the NET Bible, which puts it in parenthesis:
(Ezer and Elead were killed by the men of Gath, who were natives of the land, when they went down to steal their cattle. Their father Ephraim mourned for them many days and his brothers came to console him. He had sexual relations with his wife; she became pregnant and gave birth to a son. Ephraim named him Beriah because tragedy had come to his family. His daughter was Sheerah, who built Lower and Upper Beth Horon, as well as Uzzen Sheerah).
In this passage Ephraim does not seem to ever have been in Egypt. He has brothers (plural).
Especially note that the men of Gath are not called Philistines. So this passage seems to show knowledge of people who came before the Philistines. “Philistines” in Gaza is one of the reasons Lipovsky dates Genesis later
Ephraim’s sons, Ezer and Elead, got themselves hanged (or something) as cattle rustlers by the “natives of the land.” This implies conflict between foreign nomads and native settlers. It is hard to see this Ephraim as the son of an upper class priestly family from Egypt.
And, if this passage is part of the family tree of Joshua, the mention of Gath, Lower and Upper Beth Horon and Uzzen Sheerah, seems to imply that Joshua’s family came to the territory of Ephraim by a migration from the southwest rather than around from Egypt and across the Jordan. This would fit with Lipovsky.
Yet for Lipovsky’s scenario to work, you would have to think that Ephraim, a warrior in the Hyksos army according to him, was reduced to head of a wandering clan in Gaza after the Hyksos defeat at Sharuhen. This is possible. But it is quite a stretch.
So was the house of Joseph with the tribes of Ephraim and Manasseh as first tribes something that really existed from an early time? Perhaps it was Ephraim alone with Manasseh somehow tacked on later. I do not see much evidence for Manasseh as a thing before Solomon made it a district. Manasseh does not appear in the list of northern polities in 2 Samuel 2:9.
I would entertain the possibility that Ephraim had once existed as a nomadic clan in the hill country bordering Gaza. Perhaps its root was in Amelek whether that is a correct translation of Judges 5:14 or not.