From the Popular Science link:
It may be a borderline-offensive schoolyard taunt, but "throws like a girl" has an element of truth. Studies suggest that girls often don't throw as well as boys. ... In fact, the "throwing gap," as it's called, is one of the biggest differences between the genders. It's not just the largest gap in physical activities--although it's the largest gap in that field--it's possibly the most salient gap. Period.
Literature on this put forward by Janet Hyde, professor of psychology and women's studies at the University of Wisconsin at Madison, for example, has shown the disparity.)
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[G]irls are more likely to, for example, throw in a dart-tossing motion or step forward with the incorrect foot, which means a weaker throw.
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Thomas pegs evolution for that, hypothesizing that throwing was the most important trait for hunting, and that the best (male) hunter was more likely to pass on his genes with the woman of his choosing.
Link: Popular Science: The genders are more alike than they are different, with one notable exception...