@haplotypes = (); ## THIS IS AN ARRAY DECLARATION
.....
push @{ $haplotypes{ $currentPop} }, [ @temp ]; 
## THIS ...........^............^...................is a hash 
## with a numeric key, that increments from zero, by 1!


##</code><code>##

	 @temp = split;
	  push @{$haplotypes{$currentPop}}, [@temp];


##</code><code>##

    push @{ $haplotypes[ $currentPop ] }, [ split ];


##</code><code>##

	@{$TempList{$currentPop};} = ();
	while (@{$haplotypes{$currentPop};}) {
		push @{$TempList{$currentPop};}, splice(@{$haplotypes{$currentPop};}, rand @{$haplotypes{$currentPop};}, 1);
	}
	@{$haplotypes{$currentPop};} = @{$TempList{$currentPop};};


##</code><code>##

use List::Util qw[ shuffle ]; ## near the top of your program.
...

	@{ $haplotypes{$currentPop } } = shuffle @{ $haplotypes{$currentPop } };


##</code><code>##

    push @total, $currentPop;


##</code><code>##

  for($i = 0; $i <  $sampleSize{$_}/2; $i++) {


##</code><code>##

Use of uninitialized value in division (/)...