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I have a question regarding how the rules of commas apply in a particular sentence. I cannot seem to work out what rules go with the following excerpt:

The desert savanna of the Neolithic Period, with its flora and fauna, gave way to increasingly arid conditions, and rainfall alone was never adequate for agriculture.

I understand the two independent clauses rule and the interruption rule about making sense if you take out the middle sentence between a pair of commas. This has four clauses, doesn't it? And so what rules should one use here?

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    Here, 'with its flora and fauna' is a parenthetical, in this case best set off by commas (rather than parentheses or dashes). Removing it leaves 'The desert savanna of the Neolithic Period gave way to increasingly arid conditions, and rainfall alone was never adequate for agriculture.' It's grammatical, and correctly punctuated, but I'm not too happy about 'savannah' giving way to 'increasingly arid conditions'. '... increasingly arid landforms' maybe. – Edwin Ashworth May 22 '15 at 22:44
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    The author is talking about a savannah biome, which has climatic conditions. When the climate changes, the biome "gives way to" its successor biome. Ordinary bio-talk. – John Lawler May 22 '15 at 22:49
  • Suggest splitting extract into two sentences: The desert savanna of the Neolithic Period, with its 'characteristic' flora and fauna, gave way to increasingly arid conditions. Consequently, rainfall was never sufficient to support agriculture. – Julie Carter May 22 '15 at 23:52
  • All above is good counsel. But there is a lot of leeway with commas. There are few firm rules about where you must use a comma; it's more important to learn rules on when not to use a comma. – Brian Hitchcock May 23 '15 at 3:31
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There are two clauses, which can be seen most easily if you strip out prepositional phrases:

The desert savanna gave way, and rainfall alone was never adequate.

Re-add most prepositional phrases, and it's still two clauses:

The desert savanna of the Neolithic Period gave way to increasingly arid conditions, and rainfall alone was never adequate for agriculture.

The commas surround another prepositional phrase and serve two purposes. One is to clarify that the phrase refers to "desert savanna" as opposed to "Neolithic Period". The use of commas also sets it off as a parenthetical, a "descriptive" phrase that adds details, as opposed to a "limiting" phrase that specifies which savanna the way "of the Neolithic Period" does.

The desert savanna of the Neolithic Period, with its flora and fauna, gave way to increasingly arid conditions, and rainfall alone was never adequate for agriculture.

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