Scientific Causes of the Plague
Update 2012, a note by Monica Green, Professor of History, School of Historical and Religious Studies, Arizona State University, received on Sept. 17, 2012:
"Plague studies are in the midst of being revolutionized because of work in genomics. On the one hand, phylogenetic work is able to reconstruct the history of the pathogen, Yersinia pestis, itself. This does indeed show that the organism evolved in central Eurasia, but it's by no means clear precisely where. The main work on this matter is: Giovanna Morelli, et al., “Yersinia pestis Genome Sequencing Identifies Patterns of Global Phylogenetic Diversity,” Nature Genetics 42, no. 12 (December 2010), 1140-45. Unfortunately, there are some claims in this essay that no historian would agree with: e.g., that there were plague epidemics in "China." The assumption is that China has always had the boundaries it does currently; however, the place in central Eurasia where the origin of the plague bacillus would be located was never within the confines of what constituted "China" in the Middle Ages. For a very helpful guiding hand through all that has happened over the past decade and a half in this area of research, see:
Lester K. Little, “Plague Historians in Lab Coats,” Past and Present 213 (2011), 267-90. 
On the mapping question in general, there is a superb article that deconstructs the whole "mapping" question:
David Mengel, “A Plague on Bohemia? Mapping the Black Death,” Past and Present no. 211 (May 2011), 3-34.