One way to deal with this is to employ a phase design:
AB
ABA
ABAB
where 'A' is baseline and 'B' is your treatment (x).
These types of design are very useful as the allow you to return to baseline to ensure that any effects of treatment are not due to uncontrolled factors. Also, you can randomize the order of 'A' and 'B' between the different enclosures:
Week 1 | Week
2 |
Week
3 |
Week
4 |
|
Pen
1 |
A |
B |
A |
B |
Pen
2 |
B |
A |
B |
A |
It is a good idea to plan to carry out at least one (preferably more than one) independent replication of the study.
Finally, don't forget that as you have not used random sampling (i.e., all of the animals have come from one farm) you cannot generalise your findings beyond this study! To do this, you would need to collect a random sample from the population.