What a beautiful observation. At the Guatemalan archaeological site called Topoxté, which is a 90% artificial island built during the Classic and Postclassic Mayan period, there is a surprising population of rats. I do not know if this phenomenon obeys conditions related to human occupation and later abandonment, but it is a fact that could be elucidated.

Ground squirrels in North America are also quite common in archaeological sites. In Alaska they are regularly found in burrowing into archaeological sites where they will gnaw on bones to extract calcium. In California they are considered a pest on archaeological sites due to site disturbance. While trying to distinguish whether squirrel bones in the sites were intrusive or part of the ancient diet I spent some time looking at burrowing habits. Members of this group tend to prefer loose soils of small particle sizes (areas where rocks are less common), however, when looking into California ground squirrels they were found to burrow around large rocks and roots to take advantage of the protection they can offer from larger burrowing predators. You could probably get information about soil preferences from agricultural journals. Farmers tend to dislike ground squirrels and in the USA much of the literature on burrowing is related to eradicating crop pests. There is some specific habitat data for your species on the IUCN red list (http://www.iucnredlist.org/details/summary/20472/0) and since it is considered a vulnerable species you might be able to find a biologist interested in investigating further. Good luck!

European ground squirrels require specific habitats. Natural low-grassy areas and/or artificial are favourite on condition that are well enlightened lean soils.  Possibly, is it the situation of the archaeological sites you you are investigating now?

Thank you a lot for the answers!

Mrs. Stephanie A. E. Jolivette, what you are describing is truly an important thing. If these little guys likes to gnaw on bones for extracting calcium I suppose the density of burrows can represent a clue to estimate the location of the necropolis. I will keep this observation in mind. Also, the reference you made is very helpful! Thank you! 

Mr. Alberto Catalano, the site is located  on an inter-fluvial terrace and meets the conditions you described above. Bellow you can see how the site looks like. The ground squirrels burrow are distributed mostly on the grassy higher parts, where the houses were located. Thank you! 

Mr. Danilo Callén, thank you for sharing the situation on Topoxté site, which is a fascinating one. 

Of course, that may be the reason that there are so many rats on the Sacred Island Topoxté. The island is "sacred" because it was the necropolis of the ruling dynasties in Yaxhá and in Tikal. It is also known as "Isla relicario".

The site you are  studying is really interesting. Thank you for the good photos.  I am concerned with aurignatian and epi-gravettian sites in my territory, but my group mates of the medieval section will welcome the conclusions of your investigation.  Thanks a lot!

Alexandru, the archaeological sites from Dobruja and South-eastern Romania where I excavated, in loess type deposits, were filled with these little creatures. I do not know however if they lived particularly in them and not outside. These sites were settlements (various periods). Don't forget that in many circumstances you can find more bones in a settlement than in a cemetery >)