Without even trying to understand what was required, a lot is already possible with DBD::CSV.

$ cat pm1072615.csv
Month,Zone,Replicate,SpeciesA,SpeciesB,SpeciesC
Sept,1,1,5,10,15
Sept,1,2,0,5,10
Sept,1,3,5,0,5
Sept,2,1,5,5,5
Sept,2,2,10,15,10
Sept,2,3,0,0,5
$ cat pm1072615.pl
#!/usr/bin/perl

use 5.14.2;
use warnings;

use DBI;

my $dbh = DBI->connect ("dbi:CSV:", undef, undef, {
    f_ext       => ".csv/r",
    });

my $sth = $dbh->prepare (qq;
    select month, zone, replicate, avg (speciesa)
    from   pm1072615
    group  by month,zone, replicate;
    );
$sth->execute;
while (my $row = $sth->fetch) {
    printf "%-5s %3d %3d %8.5f\n", @$row;
    }
$ perl pm1072615.pl
Sept    2   1  5.00000
Sept    2   2 10.00000
Sept    1   1  5.00000
Sept    1   3  5.00000
Use of uninitialized value in printf at pm1072615.pl line 19.
Sept    1   2  0.00000
Use of uninitialized value in printf at pm1072615.pl line 19.
Sept    2   3  0.00000
$
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