\chapter{Introduction}
Intro things \lipsum
\cite{Munn1999,Chomsky1986}
\section{A section}
\lipsum[1]
\subsection{A subsection}
\lipsum[2]

\bibliographystyle{apalike}
\bibliography{MSU-thesis-testfile}

\begin{appendix}
\chapter{An appendix}
This is some text
\end{appendix}