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A new hypothesis of the origin of the plague microbe in the Mongolian bobak (Marmota sibirica Radde, 1862) populations in Central Asia during the Pleistocene is based on the ideas of its relative phylogenetic recency. The Late Pleistocene cooling, which induced a deep freezing of the grounds in southern Siberia, Mongolia, and Manchuria, is considered as an inducer of speciation. The main ecological factors of the plague microbe evolution include the species specific behavior of the Mongolian bobak as it prepared to hibernate related to its occurrence in arid petrophytic landscapes and the larval parasitism of the flea Oropsylla silantiewi Wagn., 1898 in winter. Genesis of the plague foci is divided into two periods: natural-historical and biosocial. During the first period, the primary natural foci in Eurasia were formed and, during the second period, synanthropic (rat) and secondary natural foci appeared with the participation of humans in Africa, The New World, and on some tropical islands.