Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

Abstract

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we generated a de novo genome assembly of the black rat, 67 ancient black rat mitogenomes and 36 ancient nuclear genomes from sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of mitochondrial DNA confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.

A Theory of City Biogeography and the Origin of Urban Species

“…The black rat, Rattus rattus, evolved in southern India, potentially in association with the Indus River Valley civilization or its progenitors (Ervynck, 2002), and appears in the zooarchaeological record as early as the 3rd millennium BC in Mesopotamia. A few thousand years later they were present in the Mediterranean, and then widely spread by the Roman Empire by the thirteenth century AD (Yu et al, 2021). Indian Ocean trade networks also moved the black rat along the eastern coast of Africa and several islands beginning in the seventh Century AD.…”