From Tony Woodbury – a set of dissertations, and two papers, on the fascinating Chatino tonal systems. 

The Chatino dissertations that deal with tone are all at:

https://sites.google.com/site/lenguachatino/recursos-academicos

In particular, there are five dissertations, each on a different variety.

Villard, Stéphanie. 2015. The phonology and morphology of Zacatepec Chatino. Doctoral dissertation. University of Texas at Austin. pdf

Cruz, Emiliana. 2011. Phonology, tone, and the functions of tone in San Juan Quiahije Chatino. Doctoral dissertation. University of Texas at Austin. pdf

Campbell, Eric W. 2014. Aspects of the Phonology and Morphology of Zenzontepec Chatino, a Zapotecan Language of Oaxaca, Mexico. Doctoral dissertation. University of Texas at Austin. pdf  

Sullivant, John Ryan. 2015. The Phonology and Inflectional Morphology of Chá?knyá, Tataltepec de Valdés Chatino, a Zapotecan Language. Doctoral dissertation. University of Texas at Austin. pdf

McIntosh, Justin D. 2015. Aspects of phonology and morphology of Teotepec Eastern Chatino. Doctoral dissertation. University of Texas at Austin. pdf  

Also, for a historically oriented discussion of tonal morphology that touches on several of the above languages, here is a new “to appear” paper of mine:

https://drive.google.com/file/d/0B4-pvfKWqpprdERnaUprTjVDU28/view?usp=sharing

Finally, this is an overview of our tone work:

Cruz, Emiliana, & Anthony C. Woodbury. 2015. Finding a way into a family of tone languages: The story and methods of the Chatino Language Documentation Project.  Language documentation & conservation 8:490-524. Special Issue: Steven Bird & Larry Hyman (guest eds.), How to study a tone language.