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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 first generate a de novo genome assembly of the black rat. We then
sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three
modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in
Europe and North Africa. Analyses of our newly reported sequences, together with published
mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterra-
nean 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.