Though Joseph was one of the younger sons of Jacob, yet he was his eldest by his most just and best beloved wife Rachel, was himself his best beloved son, and had been the greatest ornament and support of his family, kept it from perishing in a time of famine, and had been the shepherd and stone of Israel, and therefore his posterity were very much favoured by the lot. Their portion lay in the very heart of the land of Canaan. It extended from Jordan in the east (Jos 16:1) to the sea, the Mediterranean Sea, in the west, so that it took up the whole breadth of Canaan from side to side; and no question the fruitfulness of the soil answered the blessings both of Jacob and Moses, Gen 49:25, Gen 49:26, and Deu 33:13, etc. The portions allotted to Ephraim and Manasseh are not so particularly described as those of the other tribes; we have only the limits and boundaries of them, not the particular cities in them, as before we had the cities of Judah and afterwards those of the other tribes. For this no reason can be assigned, unless we may suppose that Joshua being himself of the children of Joseph they referred it to him alone to distribute among them the several cities that lay within their lot, and therefore did not bring in the names of their cities to the great council of their princes who sat upon this affair, by which means it came to pass that they were not inserted with the rest in the books.

Beth-horon the nether - This city was about twelve miles from Jerusalem, on the side of Nicopolis, formerly Emmaus. - Calmet. See the note on Jos 10:10.

So the children of Joseph, Manasseh and Ephraim, took their inheritance. As it fell to them by the lot; by Manasseh is meant the half tribe of Manasseh, one half of that tribe having been settled by Moses on the other side Jordan; and next follows an account of the borders of the inheritance of Ephraim in particular, as that of the half tribe of Manasseh is given in Jos 17:1.
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Joshua 16:5

jos 16:5
jos 16:5
jos 16:5And the border of the children of Ephraim, according to their families, was thus,.... Or what follows is the description of it:

even the border of their inheritance on the east side was Atarothaddar, unto Bethhoron the upper; the first was on the south of the inheritance, and the latter on the north, as Masius has placed them: who has given us a type of this description, by which it appears that this lot is here described in its breadth from south to north.