This is because the @_ array is aliased to the parameters passed.

Its worth explaining aliasing a little better I think: I like to think of it as a reference that doesn't need dereferencing. Which is essentially how its implemented as well. :-)

while you lose out on readability.

Well, you could use for:

sub get_exon {
    my $end=pop;
    my $begin=pop;
    # alias $_[0] to $chromosome to avoid copy semantics speed penalty
    for my $chromosome (@_) {
      return substr($chromosome, $begin - 1, $end - $begin + 1);
    }
}
# or perhaps 
sub get_exon {
    my ($begin,$end)=@_[1,2];
    # alias $_[0] to $chromosome to avoid copy semantics speed penalty
    for my $chromosome (@_) {
      return substr($chromosome, $begin - 1, $end - $begin + 1);
    }
}
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But of course its not as efficient as the straight forward access to @_, but it is worth remembering that for (LIST) aliases the iterator var to the values being iterated over. As such this might be a nice middle ground between super-optimised and unreadable, and optimised and relatively readable.

:-)