Clonal microevolution within Y. pestis
allows inferences about its evolutionary history, especially when placed in the context of the geographic sources of the isolates and historical records regarding waves of transmission. One important conclusion is that Y. pestis
probably evolved in China. Isolates from China are scattered over all four phylogenetic branches and average phylogenetic diversity among isolates is greater within China than other countries. Subsequently, Y. pestis
has spread from China to other areas on multiple occasions since the origins of branch 0. For example, we infer that Y. pestis
on branch 0 spread on multiple occasions to Mongolia, Siberia and central regions of the FSU, which is the most parsimonious explanation for the isolation there of strains with related microsatellite (MLVA) patterns13
Dates of several branching events postdate historical events with which they might be associated for reasons that are explored and analyzed in the Supplementary Note
. Genotypes from the Black Death in Europe dating to the mid-14th
century (~610 ya)14
map at or near the split between branches 1, 2 and 3, which occurred >728 ya. The geographical sources and evolutionary branch order of 2.MED subpopulations, which arose >545 ya, correspond with points along the former Silk Road15
(Supplementary Fig. 3B
), an extensive trade route from China to Western Asia between 200 BC and 1,400. Other 2.MED1 isolates have been found in Western China (R. Yang, pers. comm.), as well as Kazakhstan and the Caucasus13
, which supports the westward spread of 2.MED from China via trade articles that were carried along the Silk Road.
We also invoke extensive spread of Y. pestis
for the 1.ANT1 to 1.ANT3 populations that have only been isolated from East and Central Africa. The estimated age of 1.ANT1 (628-6,914 ya) slightly predates the extensive voyages from China led by Zheng He between 1409 and 1433 (Supplementary Fig. 3A
). These voyages involved up to 300 ships, up to ten times larger than those of contemporary European explorers, and carrying ~28,000 crewmen16
. It seems highly likely that these ships were infested by rats, which could have transmitted Y. pestis
from China to Africa. The geographic locations of 1.ANT isolates are consistent with the terminus of Zheng He's route, and suggest progressive evolution during migration from the coast. However, a causal association between 1.ANT in Africa and the voyages by Zheng He remains an unproven hypothesis. Plague may have been introduced to East Africa by an alternative route, such as the limited contacts between East Africa and China facilitated by Arab traders.
The third plague pandemic initially spread from Yunnan to Hong Kong5-7
prior to global dissemination in 1894. This pandemic was caused by Y. pestis
isolates from the youngest population on branch 1, 1.ORI, which evolved >210 ya. As expected, multiple 1.ORI isolates were found in China, including the oldest node of 1.ORI1. Subsequent global dispersion during the third pandemic was associated with multiple independent radiations of sub-branches 1.ORI1, 1.ORI2 and 1.ORI3.
1.ORI1 spread to northeast India from which six 1.ORI1.d strains were isolated. These may have been associated with a major epidemic in 1899 in Calcutta (now Kolkata) which is thought to have been infected from Hong Kong by 1896 5
. Historical records also document that plague was imported to the U.S.A. in 1899 via a plague ship from Hong Kong that docked in Hawaii and then in San Francisco17
. Plague broke out soon thereafter in both Hawaii (December, 1899) and San Francisco (March, 1900). Our data pinpoint the origin of modern plague in the continental U.S.A. to California as all extant Y. pestis
in the U.S.A. are the progeny of 1.ORI1.d, which was isolated three times in the vicinity of Los Angeles (Supplementary Fig. 4
) where plague-infected squirrels were observed by 191017
. 1.ORI1.d was also isolated in Hawaii, and its ancestor 1.ORI1.a was isolated in China, which is consistent with the historical records. The subsequent evolutionary path in the U.S.A. is marked by two descendent nodes containing five strains in central California. All 626 other isolates from diverse sources in the western U.S.A. are descendents of those nodes. Thus, all extant Y. pestis
in the U.S.A. are derived from a single import, possibly corresponding to bacteria introduced to San Francisco in 1899 that then spread to Los Angeles.
1.ORI2.a, a second descendent of 1.ORI1.a, probably also evolved in China because its descendent radiation ix spread from the Chinese-Vietnamese border to southern Vietnam and Burma and back to China (Supplementary Fig. 3E
inset). 1.ORI2.a strain 195 was isolated from Bombay in 1898, which is compatible with historical records showing that Bombay was infected by plague in 1896 via a ship from Hong Kong18
. But 1.ORI2.a was also the parent of multiple other radiations that reached Europe, South America, western and southern Africa and Southeast Asia (; Supplementary Fig. 3E
). For example, radiation viii to Hamburg in Germany and Argentina probably originated in India because plague was imported into Argentina in 1899 from Uruguay by a rice ship from India via Rotterdam19
. Several ships carrying plague-infected rats docked in Hamburg soon after 189420
but did not cause recorded cases of human plague there.
1.ORI2.a also gave rise to sub-branch 1.ORI3 that reached Madagascar. Our data are consistent with one single successful import event from India into Madagascar in 1898, which then differentiated further within Madagascar, finally reaching the highlands in 192111
, where it remains endemic. Alternatively, the original import in 1898 has no extant descendants, and 1.ORI3.k was imported after 1898 but before 1921. Still other scenarios invoking independent imports of the blue and red clusters (Supplementary Fig. 5
) after microevolution outside Madagascar are less likely, because they would need to account for the restricted geographical specificity of the red cluster within Madagascar. A descendent of 1.ORI3 spread from Madagascar to Turkey because three isolates from Turkey are descendents of nodes that likely evolved within Madagascar. Historical records document two cases of human plague from Madagascar that reached the Middle East in 193121
, which may have been the time period in which transmission to Turkey occurred.
In summary, we present a phylogeny of Y. pestis that covers a large part of its global evolutionary history since an origin in the vicinity of China. We also provide a postulated historical reconstruction for major migrations from East Asia to other continents. The phylogeny of this genetically monomorphic clone is based on an unambiguous reconstruction of the sequential accumulation of approximately 1,000 SNPs that have accumulated in different branches during that phylogenetic history. This extensive SNP-based framework will facilitate future investigations of under-sampled regions, such as Africa and the former Soviet Union, for which details are still lacking. It will also help to elucidate the basis of historical pandemics such as Justinian's plague and the Black Death through ancient DNA studies. This study thus provides a basis for more detailed analyses as well as a general paradigm for the reconstruction of historical pandemics.