\chapter{One}
\section{A section}
\lipsum \cite{Chomsky1986,Chomsky1995}
\subsection{A subsection}
\lipsum[1]
\subsection{Another subsection}
\lipsum[2]
\section{Another section}
\lipsum[3]

\bibliographystyle{apalike}
\bibliography{MSU-thesis-testfile}
\begin{appendices}
  \chapter{An appendix}
  \chapter{An appendix}
\end{appendices}
% Add before bibliography call

%\makebibliographypage