RT Journal Article SR Electronic T1 A phylogeography of the second plague pandemic revealed through the analysis of historical Y. pestis genomes JF bioRxiv FD Cold Spring Harbor Laboratory SP 481242 DO 10.1101/481242 A1 Maria A. Spyrou A1 Marcel Keller A1 Rezeda I. Tukhbatova A1 Elizabeth A. Nelson A1 Aida Andrades Valtueňa A1 Don Walker A1 Amelie Alterauge A1 Niamh Carty A1 Hermann Fetz A1 Michaël Gourvennec A1 Robert Hartle A1 Michael Henderson A1 Kristin von Heyking A1 Sacha Kacki A1 Elizabeth L. Knox A1 Christian Later A1 Joris Peters A1 Jürgen Schreiber A1 Dominique Castex A1 Sandra Lösch A1 Michaela Harbeck A1 Alexander Herbig A1 Kirsten I. Bos A1 Johannes Krause YR 2018 UL http://biorxiv.org/content/early/2018/11/29/481242.abstract AB The second plague pandemic (14th - 18th century AD), caused by the bacterium Yersinia pestis, is infamous for its initial wave, the Black Death (1346-1353 AD), and its repeated scourges in Europe and the vicinity until the Early Modern Era. Here, we report 32 ancient Y. pestis genomes spanning the 14th to 17th century AD through the analysis of human remains from nine European archaeological sites. Our data support an initial entry of the bacterium from Eastern Europe and the absence of genetic diversity during the Black Death as well as low diversity during local outbreaks thereafter. Moreover, analysis of post-Black Death genomes shows the diversification of a Y. pestis lineage into multiple genetically distinct clades that may have given rise to more than one disease reservoir in, or close to, Europe. Finally, we show the loss of a genomic region that includes virulence-associated genes in strains associated with late stages of the second plague pandemic (17th - 18th century AD). This deletion could not be detected in extant strains within our modern dataset, though it was identified in a today-extinct lineage associated with the first plague pandemic (6th - 8th century AD), suggesting convergent evolution during both pandemic events.