Learn English – Is the punctuation in this sentence correct

In this case is more a matter of aspect than tense.

English has both tense and aspect, but encodes them ambiguously, using the same words, particles and morphemes for both.

If you use the past tense for the subclause like this: "I asked mum how come my sister didn't feed him." Then you are also making the aspect a single action at a single point in time, instead of the habitual aspect that is needed here.

The most important thing in this context is that it's still possible, when the whole sentence is spoken, for the little sister to feed them. The concept that (s)he asked his/her mum about is still current. So in the subclause the habitual aspect is given through the simple present form.

If you use the perfect it's possible to make it past tense and continuous aspect: "I asked mum how come my little sister hasn't been feeding them" but then you lose some of the emphasis that it's still possible for her to be doing it now.

Pardon me for not knowing any technical terms. Your sentence -

Because male lions' manes are affected by temperature, becoming shorter and lighter in warmer weather, they are of interest to scientists researching climate change.

• contains an ... uh ... inserted clause, or whatever the hell it's called: becoming shorter and lighter in warmer weather.

If you put it in parenthesis, you could also reword it thus:

(they become shorter and lighter in warmer weather)

And the resulting sentence would look like this:

Because male lions' manes are affected by temperature (they become shorter and lighter in warmer weather), they are of interest to scientists researching climate change.

From which you could conclude that in your original sentence the word "becoming" stands in for "they become," no more and no less.

Et voila. I hope this helps.