sub makeArrays
{
    $lower = 10;
    $upper = 20;
    
        my @chroma;
    my @chromb;
    my $ranpop;
    
    $ranpop = int rand($upper - $lower + 1) + $lower;
    
    # @arrA and @arrD hold the same values, and
    # aren't modified - why do you need them both?
    # what is their purpose?
    my @arrA = ( 1 .. $ranpop );
    my @arrD = (1 .. $ranpop );

    my $limiter = 50;
    # you can write that shorter:
    # my @holda = map { int rand($limiter)} 1 .. $randpop;
    # my @holdb = map { int rand($limiter)} 1 .. $randpop;
    my @holda;
    my @holdb;
    while ($ranpop) 
    {
        my $genea = int rand ($limiter);
        push(@holda, $genea);    
        my $geneb = int rand ($limiter);
        push(@holdb, $geneb);
        $ranpop--;
    }

    # there's no need to copy these arrays
    # you can return \@holda and \@holdb directly.
    my @arrB = ( @holda );
    my @arrC = ( @holdb );
    return \@arrA, \@arrB, \@arrC, \@arrD;
}