I have found the Data::Table to be a nice module for these types of tasks. It borrows some ideas from R that are helpful for handling tabular data (it has an implementation of the melt and cast functions inspired by the R reshape module). You can accomplish your task with the following code (assuming that your data is saved in a file named data.csv). The author of Data::Table has also made additional documentation/information available here: https://sites.google.com/site/easydatabase/

Data in data.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
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#!/usr/bin/env perl

use strict;
use warnings;

use Data::Table;
use Statistics::Lite qw(mean stddev);

my $dt = Data::Table::fromCSV("data.csv");

print "Original Data Table\n";
print "===================\n";
print $dt->tsv;
print "\n\n";

my $melt = $dt->melt(['Month', 'Zone', 'Replicate']);

print "Melt Table\n";
print "==========\n";
print $melt->tsv;
print "\n\n";

my $cast_mean = $melt->cast(
    ['Month', 'Zone'],
    'variable',
    Data::Table::STRING,
    'value',
    \&mean
); 

print "Cast (mean)\n";
print "===========\n";
print $cast_mean->tsv;
print "\n\n";

my $cast_stddev = $melt->cast(
    ['Month', 'Zone'],
    'variable',
    Data::Table::STRING,
    'value',
    \&stddev
); 

print "Cast (stddev)\n";
print "=============\n";
print $cast_stddev->tsv;

exit;
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Original Data Table
===================
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


Melt Table
==========
Month    Zone    Replicate    variable    value
Sept    1    1    SpeciesA    5
Sept    1    1    SpeciesB    10
Sept    1    1    SpeciesC    15
Sept    1    2    SpeciesA    0
Sept    1    2    SpeciesB    5
Sept    1    2    SpeciesC    10
Sept    1    3    SpeciesA    5
Sept    1    3    SpeciesB    0
Sept    1    3    SpeciesC    5
Sept    2    1    SpeciesA    5
Sept    2    1    SpeciesB    5
Sept    2    1    SpeciesC    5
Sept    2    2    SpeciesA    10
Sept    2    2    SpeciesB    15
Sept    2    2    SpeciesC    10
Sept    2    3    SpeciesA    0
Sept    2    3    SpeciesB    0
Sept    2    3    SpeciesC    5


Cast (mean)
===========
Month    Zone    SpeciesA    SpeciesB    SpeciesC
Sept    1    3.33333333333333    5    10
Sept    2    5    6.66666666666667    6.66666666666667


Cast (stddev)
=============
Month    Zone    SpeciesA    SpeciesB    SpeciesC
Sept    1    2.88675134594813    5    5
Sept    2    5    7.63762615825973    2.88675134594813
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