Historical Y. pestis genomes reveal the Black Death as source of ancient and modern plague pandemics

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Short Article
Historical Y. pestis Genomes Reveal the European
Black Death as the Source of Ancient and Modern
Plague Pandemics
Graphical Abstract
Highlights
dThree historical Yersinia pestis genomes from the second
plague pandemic in Europe
dLow genetic diversity of the pathogen during the Black Death
dIndication for link between the Black Death and 19
th
century
plague pandemic lineages
dConnection between post-Black Death outbreaks in Europe
supports a local plague focus
Authors
Maria A. Spyrou, Rezeda I. Tukhbatova,
Michal Feldman, ..., Alexander Herbig,
Kirsten I. Bos, Johannes Krause
Correspondence
herbig@shh.mpg.de (A.H.),
bos@shh.mpg.de (K.I.B.),
krause@shh.mpg.de (J.K.)
In Brief
Spyrou et al. have sequenced historical
Yersinia pestis genomes from victims of
the Black Death and subsequent
outbreaks in Europe. Their data suggest a
connection between the Black Death and
the modern-day plague pandemic as well
as the persistence of plague in Europe
between the 14
th
and 18
th
centuries.
Spyrou et al., 2016, Cell Host & Microbe 19, 874–881
June 8, 2016 ª2016 Elsevier Inc.
http://dx.doi.org/10.1016/j.chom.2016.05.012

Cell Host & Microbe
Short Article
Historical Y. pestis Genomes Reveal
the European Black Death as the Source
of Ancient and Modern Plague Pandemics
Maria A. Spyrou,
1
Rezeda I. Tukhbatova,
2,3
Michal Feldman,
1
Joanna Drath,
4
Sacha Kacki,
5
Julia Beltra
´n de Heredia,
6
Susanne Arnold,
7
Airat G. Sitdikov,
2,3
Dominique Castex,
5
Joachim Wahl,
4,8
Ilgizar R. Gazimzyanov,
3
Danis K. Nurgaliev,
9
Alexander Herbig,
1,
*Kirsten I. Bos,
1,
*and Johannes Krause
1,4,
*
1
Max Planck Institute for the Science of Human History, Jena 07743, Germany
2
Laboratory of Paleoanthropology & Paleogenetics, Kazan Federal University, Kazan 420008, Russian Federation
3
Institute of Archaeology named after A. Kh. Khalikov, Tatarstan Academy of Sciences, Kazan 420012, Russian Federation
4
Department of Archeological Sciences, University of Tuebingen, Tuebingen 72070, Germany
5
PACEA, CNRS Institute, Universite
´de Bordeaux, Pessac 33615, France
6
Museu de Historia de Barcelona, Barcelona 08002, Spain
7
State Office for Cultural Heritage Management Baden-Wu
¨rttemberg, Esslingen 73728, Germany
8
State Office for Cultural Heritage Management Baden-Wu
¨rttemberg, Osteology, Konstanz 78467, Germany
9
Institute of Geology and Petroleum Technologies, Kazan Federal University, Kazan 420008, Russian Federation
*Correspondence: herbig@shh.mpg.de (A.H.), bos@shh.mpg.de (K.I.B.), krause@shh.mpg.de (J.K.)
http://dx.doi.org/10.1016/j.chom.2016.05.012
SUMMARY
Ancient DNA analysis has revealed an involvement
of the bacterial pathogen Yersinia pestis in several
historical pandemics, including the second plague
pandemic (Europe, mid-14
th
century Black Death un-
til the mid-18
th
century AD). Here we present recon-
structed Y. pestis genomes from plague victims of
the Black Death and two subsequent historical out-
breaks spanning Europe and its vicinity, namely Bar-
celona, Spain (1300–1420 cal AD), Bolgar City, Russia
(1362–1400 AD), and Ellwangen, Germany (1485–
1627 cal AD). Our results provide support for (1) a sin-
gle entry of Y. pestis in Europe during the Black Death,
(2) a wave of plague that traveled toward Asia to later
become the source population for contemporary
worldwide epidemics, and (3) the presence of an his-
torical European plague focus involved in post-Black
Death outbreaks that is now likely extinct.
INTRODUCTION
Yersinia pestis evolved from the closely related zoonotic entero-
bacterium Y. pseudotuberculosis (Achtman et al., 1999) to
become one of the most virulent pathogens known to humans.
Its recent identification in ancient human material from Altai,
Siberia suggests it caused human infections as early as 5,000
years ago, though its ability for flea-borne transmission leading
to bubonic disease might have been absent in these older, diver-
gent lineages (Rasmussen et al., 2015). To our knowledge, bu-
bonic plague, and presumably also the pneumonic and septice-
mic forms, have been the likely culprit of three major pandemics,
namely the Plague of Justinian (Eastern Roman Empire, 6
th
and
8
th
centuries AD), the second-wave plague pandemic (Europe,
mid-14
th
century Black Death until the mid-18
th
century AD),
and the third plague pandemic that started during the late 19
th
century in China. Differences in mortality rate and epidemiology
of the three pandemics initiated controversy over whether they
shared a common etiologic agent (Cohn, 2008). In recent years,
however, ancient DNA (aDNA) has confirmed a Y. pestis involve-
ment in both historical pandemics (Bos et al., 2011; Haensch
et al., 2010; Wagner et al., 2014).
The Black Death claimed up to 50% of the European population
between 1347 and 1353 (Benedictow, 2004). The disease is
thought to have arisen from plague foci in East Asia and to have
spread into Europe via trade routes (Morelli et al., 2010). Its origin,
however, is still contentious due to a lack of convincing archeo-
logical or documentary evidence from the early 14
th
century in
East Asia (Sussman, 2011). Ancient Y. pestis genomes obtained
from medieval victims have indicated the presence of a radiation
event immediately preceding the Black Death that gave rise to
most of the strain diversity circulating in the world today (Bos
et al., 2011; Cui et al., 2013). Based on the relationship of ancient
European and modern genomes, it was recently suggested that a
wave of plague might have traveled from Europe toward Asia after
the Black Death, eventually settling in China and later giving rise
to the third pandemic (Wagner et al., 2014). Genomes from its
purported route are, however, missing in the discussions, and
are needed to add legitimacy to the model.
After the Black Death, plague continued to strike Europe for
another four centuries through subsequent outbreaks that
ceased at the end of the 18
th
century (Benedictow, 2004). The
reasons for its sudden disappearance in Europe are unknown.
Sylvatic plague foci have a nearly worldwide presence today,
but are absent in Europe (Gage and Kosoy, 2005; Tikhomirov,
1999). The question of whether the recurrent European plague
outbreaks of the 14
th
to 18
th
centuries were the result of multiple
reintroductions of plague into Europe, or rather were attributed
to now-extinct European plague foci, is still being explored.
Previous studies that draw upon aDNA and climatic data favor
the former hypothesis. Through a SNP-based PCR approach,
874 Cell Host & Microbe 19, 874–881, June 8, 2016 ª2016 Elsevier Inc.

purportedly distinct plague lineages were identified in different
areas of Europe during the 14
th
century and were thought to
have entered via different pulses (Haensch et al., 2010). In addi-
tion, plague outbreaks documented in some of the main Mediter-
ranean ports were found to coincide with extreme climate fluctu-
ations in Central Asia, suggesting that recurrent maritime imports
of plague from Asia might have been responsible for post-Black
Death plague outbreaks (Schmid et al., 2015). By contrast, others
have suggested a long-term persistence of plague in Europe (Sei-
fert et al., 2016). Using a PCR SNP-typing approach of putative
plague material from Southern and Northeastern Germany, iden-
tical Y. pestis SNP profiles were identified in strains circulating
within Europe between the Black Death and 17
th
century AD (Sei-
fert et al., 2016), implying a single source population for the Euro-
pean plagues of that time period. A further genome-wide analysis
of Y. pestis strains from the Great Plague of Marseille (1720–1722)
has identified a previously uncharacterized lineage of Y. pestis
that descends from a strain present during the Black Death
(Bos et al., 2016). While the lineage is considered to represent
an historical plague focus potentially responsible for post-Black
Death European outbreaks (Bos et al., 2016), the use of material
from a highly operational Mediterranean center that linked West-
ern Europe with the East (Signoli et al., 1998) makes identification
of the disease source elusive.
Here, we aim to address three outstanding questions regarding
Y. pestis history. First, we investigate the possibility of disease
entry via multiple pulses during the Black Death by comparing
the genotype of a strain from the pandemic’s early phase to those
circulating in other areas later in the pandemic. Material from Bar-
celona, Spain, one of the Mediterranean cities through which
plague entered southern continental Europe, is compared to
Black Death genomes from London. Second, we evaluate the
likelihood of the proposed eastward migration of strains from Eu-
rope to Asia after the Black Death through the analysis of human
remains from a 14
th
century plague burial in the Volga region of
Russia. Third, we take a further step toward understanding the
relationship of post-Black Death outbreaks in Europe and eval-
uate the likelihood of a local reservoir. For this, we investigate a
16
th
century plague outbreak in Southwestern Germany and
compare it to both a London outbreak that occurred soon after
the Black Death and to the Great Plague of Marseille, France in
1722. Following the success of previous genomic investigations
of ancient bacterial disease (Bos et al., 2011, 2014, 2016; Schue-
nemann et al., 2011, 2013; Wagner et al., 2014), we employ
similar methods of DNA capture and high-throughput
sequencing to retrieve the genomes of three historical Y. pestis
strains. Our results suggest (1) limited Y. pestis diversity during
the early phase of the Black Death, and likely a single entry into
Europe; (2) a wave of plague that traveled eastward after the
Black Death and later gave rise to the 19
th
century pandemic;
and (3) an involvement of the same plague lineage in two post-
Black Death European epidemics that are 200 years apart.
RESULTS
Archaeological Sites and Dating
Samples were collected from a mass grave in Barcelona, Spain, a
single grave in Bolgar City in Russia, and a mass grave in
Ellwangen, Germany (Figure 1 and Supplemental Experimental
Procedures). Aside from the Bolgar City site that was dated to
the second half of the 14
th
century using coin artifacts known to
have been minted after 1362 (Supplemental Experimental Proce-
dures and Figure S1), archaeological dates were not available. To
estimate or confirm the historical period during which each of the
outbreaks occurred, radiocarbon dates from bone fragments and
tooth roots were obtained. The dates yielded were 1300–1420
cal AD for Barcelona, 1298–1388 cal AD for Bolgar City, and
1486–1627 cal AD for Ellwangen (Figure 1 and Table S1).
Screening for Y. pestis
A total of 223 DNA extracts from teeth of 178 individuals
were evaluated for the presence of Y. pestis DNA through a
Figure 1. Samples and Their Respective Locations
(A) Tooth sample that was positive for Y. pestis (3031) and mass grave picture from the plague burial in Barcelona.
(B) Y. pestis-positive tooth sample and picture of infected individual (2370) from the Ust’-Ierusalimsky tomb of Bolgar City.
(C) Picture of mass grave in Ellwangen, and two tooth samples from individual 549_O, found positive for the plague bacterium.
Cell Host & Microbe 19, 874–881, June 8, 2016 875

species-specific quantitative PCR (qPCR) assay targeting the
plasminogen activator (pla) gene located on the PCP1 plasmid
(Schuenemann et al., 2011)(Supplemental Experimental Proce-
dures). Results indicated 53 potentially positive DNA extracts
stemming from 32 individuals. All extraction and PCR blanks
were free of amplification products. Amplification products
were not sequenced, as samples from potentially positive indi-
viduals were directly turned into double-stranded next-genera-
tion sequencing libraries and were used for whole-genome array
capture. After capture, three individuals had sufficient Y. pestis
DNA for genome-level analysis. These were tooth specimens
3031 from Barcelona, 2370 from Bolgar City, and 549_O from
Ellwangen (Figure 1,Table S1 and Supplemental Experimental
Procedures).
Y. pestis Genome-Capture Results
Whole-genome array capture was performed using the ch-
romosome of Y. pseudotuberculosis (Chain et al., 2004)
Figure 2. Yersinia pestis Phylogeny
(A) Maximum Parsimony phylogenetic tree of 141
modern and 10 historical Y. pestis strains. 3,351
SNP positions were considered for the phylogeny.
The reconstructed tree shows the topology of the
new isolates from Barcelona, Bolgar City, and Ell-
wangen relative to previously sequenced modern
and ancient Y. pestis strains. Asterisks (*) indicate
bootstrap values of 100. Collapsed branches are
represented by triangles, to enhance tree clarity.
Strains belonging to Branch 1 are represented in
red, Branch 2 in yellow, Branch 3 in blue, Branch 4
in orange, and Branch 0 in black. Ancient Branch 1
strains are indicated by their archaeological or
radiocarbon date and by a (+). Because of the great
number of derived SNP positions of the 0.PE3
lineage, its branch was reduced to adjust scaling of
the tree. Geographic region abbreviations corre-
spond to: CHN (China), USA (United States of
America), MDG (Madagascar), IND (India), IRN
(Iran), MNM (Myanmar), RUS (Russia), GB (Great
Britain), DE (Germany), FRA (France), SP (Spain),
MNG (Mongolia), NPL (Nepal), FSU (Former Soviet
Union), AGO (Angola), CGO (Congo), and UGA
(Uganda).
(B) A magnified version of Branch 1 is shown to
enhance its resolution. The branch of lineage
1.ANT was manually reduced to adjust tree scaling.
A detailed description of p1-p7 SNPs is given in
Table 1 (see also Table S2,Table S3,Table S4 and
Figure S2).
and the Y. pestis plasmids pMT1 and
pCD1 as template for probe design
(Supplemental Experimental Procedu-
res). Array captures produced aver-
age genomic coverage of 10.3-fold for
Barcelona 3031, 19.3-fold for Bolgar
City 2370, and 4.9-fold for Ellwangen
549_O (Table S1 and Table S2). Owing
to its low coverage, data presented
for sample 549_O are from a pool
of two independent libraries produ-
ced from two teeth of the same individual (Table S1 and
Table S2).
Phylogenetic Analysis of Historical Y. pestis Genomes
Our ancient genomes were then added to a Y. pestis phylogeny
constructed from previously published genomes including 130
modern genomes (Cui et al., 2013), 7 historical genomes (Bos
et al., 2011, 2016), and 11 newly available modern Y. pestis
strains from the Former Soviet Union (Zhgenti et al., 2015)(Table
S3). Our maximum parsimony tree revealed that the modern
Former Soviet Union genomes group with what was previously
thought to be diversity restricted in China, specifically lineage
0.ANT3 (Cui et al., 2013). They also add further diversity to
the 2.MED1 lineage and, importantly, to the 0.PE2 lineage,
which is the second deepest branch in the Y. pestis phylogeny
(Figure 2A, Figure S2, and Table S3). This reveals a more exten-
sive Y. pestis diversity outside of China than was previously
thought.
876 Cell Host & Microbe 19, 874–881, June 8, 2016

All three reconstructed historical genomes group in Branch 1,
and all possess diagnostic SNP positions here referred to as
‘‘p1’’ and ‘‘p2’’ (Table 1), which were previously identified in his-
torical Y. pestis genomes from the Black Death (Bos et al., 2011)
(Figure 2B, Table 1). The positioning of the strains reported here
in the phylogeny confirms their authenticity as ancient. To date,
all Y. pestis genomes isolated from the historic 2
nd
plague
pandemic group in Branch 1.
We find no detectable differences between our Black Death
strain from Barcelona and three previously genotyped strains
from London 1348–1350 (Bos et al., 2011). The Bolgar City strain,
however, contains additional differences in four positions
compared to Black Death isolates: two of these are shared
with London individual 6330 (positions p3 and p4, Figure 2B
and Table 1), one is shared with all modern Branch 1 strains
(p6), and one is unique to this individual (p7, Figure 2B). Addition-
ally, the Ellwangen strain groups in a sub-branch of Branch 1,
together with five strains previously typed from the Great Plague
of Marseille (L’Observance), 1720–1722 (Figure 2B) (Bos et al.,
2016). Our analysis reveals 20 positions shared with the strains
from L’Observance and three unique SNPs (Table S4). That the
Ellwangen strain is ancestral to the Observance strains comes
as no surprise given the older age of the samples (Figure 2B).
This ‘‘Ellwangen-Observance’’ lineage originates from Black
Death strains currently represented by the isolates from London
and Barcelona. Like the strain from Marseille, that from Ellwan-
gen does not share additional derived positions with other
ancient or modern strains (Figure 2B), as no modern descen-
dants have as yet been identified in this sub-branch.
DISCUSSION
Our genomes from Barcelona, Bolgar City, and Ellwangen group
on the same phylogenetic branch (Branch 1), adding further legit-
imacy to the notion that the Black Death and subsequent plague
outbreaks in Europe, as well as the worldwide third pandemic,
were caused by the same Y. pestis lineage (Figure 2,Figure S2,
and Figure 3). Further analysis of ancient and modern strains of
this branch could reveal important clues to explain why this
particular lineage was involved in both the second and third
pandemic.
Our analysis reveals that the strain from Barcelona is identical
to a previously sequenced Black Death Y. pestis strain from Lon-
don (1348–1350). Barcelona was one of the main entry points for
the Black Death into Europe, with historical reports suggesting
the disease first entered there in the spring of 1348 (Gottfried,
1983). In London, the earliest reports of the illness are from
autumn 1348 (Benedictow, 2004). This indicates a contemporary
presence of the same strain in both southern and northern
Europe, supporting the notion of a single wave entry, with low
genetic diversity in the pathogen. Historical sources indicate
that plague first came into view in 1347, with outbreaks in the
southern islands of Crete, Sicily, and Sardinia, followed by entry
into mainland Europe via the heavily trafficked ports of Genoa
and Marseille. Samples from these locations and those further
afield from its purported source population in East Asia may pro-
vide us with relevant details regarding the microevolution of a
highly virulent pathogen at the beginning of a mass pandemic.
The key finding of our study stems from the analysis of an his-
torical Y. pestis strain from the Volga region in Russia (Figure 3).
This genome has added legitimacy to an important link between
the second and third plague pandemics hypothesized elsewhere
(Wagner et al., 2014). Under this model, Y. pestis spread from
Europe to Asia after the Black Death and gave rise to both the
1.IN lineages of the Yunnan Province of China (1.IN3) as well
as the 1.ORI strains associated with worldwide spread during
the third plague pandemic (Figure 2B, Figure 3, and Table S3)
(Wagner et al., 2014). That our sample from Bolgar City shares
one additional Branch 1 derived position with a strain circulating
in London during the second half of the 14
th
century provides
solid evidence of plague’s eastward travel subsequent to the
Black Death (Table 1,Figure 2B, and Figure 3). Of note, the
1.ANT lineage today restricted to Sub-Saharan Africa possesses
only an additional ten derived Branch 1 positions compared to
our Bolgar lineage (Table S4). A compelling possibility is that
this plague lineage was introduced via European presence in
the continent: its shared ancestry with the Bolgar lineage could
imply that it derives from an historical focus that existed along
the eastern path that Y. pestis traveled after the Black Death.
We therefore consider it possible that strains ancestral to these
African lineages may have caused disease in Europe during
the second wave and may one day be identified in ancient Euro-
pean skeletons.
As the geographical origins of the ‘‘p1’’ and ‘‘p2’’ SNPs are
unknown (Figure 2B), the possibility of Branch 1 lineages arising
from pre-existing diversity in Asia and independently dispersing
into Europe must be considered (Haensch et al., 2010). This
model is supported by climatic evidence, where regular
Table 1. SNP Description of Diagnostic Branch 1 Positions in the Newly Sequenced Ancient Y. pestis Genomes
SNP Name Position on Chromosome CO92 CO92 (Reference) Barcelona Bolgar City Ellwangen Gene
p1 189,227 C C C C pabA
p2 1,871,476 G G G G NC
a
p3
b
699,494 A G A G alt (rpoD)
p4 2,262,577 T G T G YPO1990
p5 4,301,295 G G G G recQ
p6 3,806,677 C T C T b0125 (hpt)
p7 3,643,387 G G T G YPO3271
a
Non-coding (NC).
b
The p3 SNP corresponds to the previously described s12 position present in a Black Death plague victim from the Netherlands (Haensch et al., 2010).
It is also present in a derived state isolate from London (6330), from which a complete genome is available (Bos et al., 2011).
Cell Host & Microbe 19, 874–881, June 8, 2016 877

westward pulses of plague from an Asian focus throughout the
second pandemic are thought possible (Schmid et al., 2015).
We find this model for the second pandemic difficult to reconcile
with our current data. Although it has been previously shown that
Y. pestis has an extremely variable substitution rate (Cui et al.,
2013), our Russian strain has only two additional derived substi-
tutions (p6, p7, Figure 2) compared to London Y. pestis genome
6330 (Bos et al., 2011), dated to 1350–1400. This close genetic
similarity suggests that our Russian strain represents a new
outbreak subsequent to that which occurred in London after
the Black Death. The alternative ‘‘Asian origin’’ model would
require a minimum of four separate lineages exiting together
from the same focus to account for the level of diversity observed
in Europe during the Black Death and its aftermath, i.e., (1) Lon-
don/Barcelona, (2) London 6330, (3) Bolgar City, and (4) Sub-Sa-
haran Africa. We regard the likelihood of such similar strains
leaving Asia in a short time frame to be low, but acknowledge
it would be possible if (1) their ancestral focus was in a location
particularly conducive to westward travel, or (2) there exists a
biological reason for their greater ease in rapid long-distance
travel. While the above scenarios could equally explain the
sole involvement of Branch 1 in contemporary plague outbreaks
outside of China, we regard a single exit followed by an eastward
travel as a more parsimonious explanation for the current data.
Under this scenario, historical strains carrying the previously
described ‘‘p3’’ SNP (Figure 2B) subsequently traveled east to
later become established in China, whereas those giving rise to
the Ellwangen-Observance lineage did not (Figure 3). Once in
the Former Soviet Union, plague likely became established in ro-
dent populations in an area accessible to western Russia and
evolved locally, as evidenced by the single unique derived posi-
tion in our strain from Bolgar City (Figure 2B and Figure 3). Given
that all modern Branch 1 lineages descend from a close hypo-
thetical relative of our Russian strain, these European forms
may well have given rise to the third plague pandemic in China
and beyond.
Consensus has not yet been reached regarding the role played
by the Russian region in the introduction of plague into Europe
during the Black Death (Alexander, 1980; Benedictow, 2004;
McNeill, 1998; Norris, 1977; Schmid et al., 2015). Drawing
Figure 3. Plague Introduction and Dispersal
Map describingour favored dissemination pattern of Y. pestisduring the second andthird plague pandemics.All strains includedin our dataset are depictedas points
on the map.Branch 1 strainsare in red and includeboth second pandemic(triangles) andmodern (circles)isolates. Branch2 strains are in yellow,Branch 3 strainsare in
blue,a single Branch 4 strainis in orange, andBranch 0 strainsare in black. Positioningof modern straindistributionon the map correspondsto geographiclocation, but
for the purposeof our study an accuratecoordinatesystem was not necessary.Red arrows indicateBranch 1 cyclingthrough Europe duringthe 14
th
century,eastward
travel out of Europe after the Black Death, and global dissemination from China during the third plague pandemic (see also Table S3).
878 Cell Host & Microbe 19, 874–881, June 8, 2016

upon historical and climatic data, scholars have adopted a
‘‘proximal origin’’ theory, which states that the Black Death erup-
ted from plague foci in the Caucasus and neighboring areas
(Alexander, 1980; Benedictow, 2004; Norris, 1977; Sussman,
2011; Varlik, 2015). Molecular investigations of the plague bacil-
lus, however, have pointed to China as both the birthplace of
Y. pestis itself and the origin of the Black Death (Cui et al.,
2013; Morelli et al., 2010). This is difficult to reconcile with the
strong East Asian sampling bias of the available data, coupled
with the fact that the second most basal Y. pestis lineage
sampled thus far stems from a rodent focus in the Former Soviet
Union (Cui et al., 2013)(Figure 3). In our current investigation, we
attempted to partially overcome this limitation by integrating
recently sequenced strains from the Caucasus region (Zhgenti
et al., 2015) in our Y. pestis phylogeny. To our surprise, these
strains grouped with some lineages previously thought to be
mostly or entirely restricted to China (Figure 2A). We therefore
highlight the need to expand the sampling region of both modern
and ancient Y. pestis to establish a more comprehensive under-
standing of its evolutionary history and modern ecology.
Our plague strain from the German city of Ellwangen is ances-
tral to those associated with the Great Plague of Marseille
(L’Observance), an epidemic that occurred in France some 200
years later (Figure 2B). This branch descends directly from the
strain circulating in both London and Barcelona during the Black
Death and does not possess the additional Branch 1 positions
present in the London 6330 and Bolgar lineages described
above. That the Ellwangen genome shares 20 positions with
the Marseille strain and has three unique positions (Table S4)
suggests the two share a common genetic history and diverged
from the same source population in advance of the 16
th
century
Ellwangen outbreak. A previous study has pointed to natural
plague foci in Asia as likely sources of the multiple plague out-
breaks in Europe following the Black Death (Schmid et al.,
2015). An alternative model, however, proposes a local European
source for plague, given the high number of documented spo-
radic epidemics in isolated rural areas throughout the second
wave. Alpine rodent species are considered one possible reser-
voir (Carmichael, 2014). Both models are explored in recent
aDNA analyses of post-Black Death European plague material
(Bos et al., 2016; Seifert et al., 2016), though at a resolution too
low to strongly favor one hypothesis over the other. Based on
modern epidemiological data, no known plague foci exist within
Europe; however, several foci are suspected to exist in areas
along the former Silk Road, the most prolific of which are imme-
diately to the east of the Caspian Sea (Gage and Kosoy, 2005).
The geographical location of the city of Ellwangen, and the seem-
ingly restricted outbreak here, however, makes the introduction
of disease via trade routes outside of Europe unlikely. We rather
view our data as more supportive of a European reservoir for the
disease. As only a small rodent focus with limited exposure to a
susceptible host species is thought to be theoretically sufficient
to initiate a large-scale human plague epidemic (Keeling and
Gilligan, 2000), plague’s presence in this proposed European
reservoir need not have been large. The Ellwangen-Observance
lineage contains no known extant descendants; hence, this
focus may no longer exist (Figure 2B), and its extinction may
have coincided with the sudden disappearance of plague in
Europe. The popular theory of an 18
th
century domestic rodent
replacement of Rattus rattus by Rattus norvegicus (Appleby,
1980) could still carry some traction. The black rat is a well-
known harbinger of plague in several locations where Y. pestis in-
fections persist today (Duplantier et al., 2005; Vogler et al., 2011),
and though brown Norway rats have a similar susceptibility to
plague infection (Anderson et al., 2009), their different ecological
niche and comparatively reduced contact with humans in a
domestic setting may have slowed the transmission of disease
entering from a neighboring sylvatic population.
Our phylogeny is compatible with popular demographic sce-
narios wherein the Black Death cycled through the Mediterra-
nean (Barcelona), spread to Northern Europe (London), subse-
quently traveled east into Russia (Bolgar), and eventually made
its way into China, its presumed origin and ultimate source of
the modern plague pandemic (Figure 3). The most parsimonious
interpretation of our data holds that, in the course of its travels, a
minimum of one plague lineage was left behind along its route
that persisted long enough to later diversify and give rise to at
least two subsequent epidemics—one in 16
th
century Germany
and one in 18
th
century France (Bos et al., 2016). The above pro-
posal, however, is unlikely to explain the full spectrum of Y. pestis
diversity and plague epidemics during the notorious so-called
‘‘second wave’’ plague pandemic; a unidirectional dispersal of
Y. pestis is unlikely, as multiple factors are sure to have contrib-
uted to its spread in humans and other host species. The epi-
demics in Germany and France, for example, stemmed from
only one of possibly several historical plague foci within Europe
or its vicinity. Concurrent plague foci harboring strains related to
our Bolgar lineage, to the lineage identified in late 14
th
century
London, or potentially others not yet identified may have been
responsible for additional second wave plague outbreaks.
Currently there is a lack of ancient Y. pestis data from the pro-
posed entry and end points of the Black Death in Europe (Gott-
fried, 1983). Genetic analyses of putative plague material from
these regions would be essential in unraveling additional key fea-
tures related to the paths traveled by the Black Death and the
legacy it left behind.
EXPERIMENTAL PROCEDURES
Array Design and Captures
A one-million-feature Agilent microarray was designed with an in-house probe
design software using the chromosome of Yersinia pseudotuberculosis (NCBI:
NC_006155) (Chain et al., 2004), as well as the Y. pestis (CO92) plasmids pMT1
(NCBI: NC_003134) and pCD1 (NCBI: NC_003131). DNA extracts from pla-
positive samples (Supplemental Experimental Procedures) were turned into
double-stranded DNA libraries as described before (Meyer and Kircher,
2010). Serial hybridization-based array capture was performed using previ-
ously established methods (Hodges et al., 2009)(Supplemental Experimenta l
Procedures).
High-Throughput Sequencing and Read Processing
Following high-throughput sequencing on Illumina platforms, all pre-process-
ing mapping and genotyping steps were performed using the automated pipe-
line EAGER (Peltzer et al., 2016). For SNP filtering, the MultiVCFAnalyzer
custom java program was applied to all vcf files to comparatively filter all de-
tected SNPs (Supplemental Experimental Procedures).
Phylogenetic Reconstruction
A SNP table was used as input for phylogenetic reconstruction. Phylogenetic
trees were generated using the Maximum Parsimony (MP) and Maximum
Likelihood (ML) methods available in MEGA6.06 (Tamura et al., 2013),
Cell Host & Microbe 19, 874–881, June 8, 2016 879

discarding alignment columns with more than 5% missing data. The
three newly reconstructed Y. pestis strains from Barcelona, Bolgar City, and
Ellwangen were analyzed alongside seven previously sequenced historical
strains from the second plague pandemic (Bos et al., 2011, 2016) and 141 pub-
lished modern Y. pestis strains (Cui et al., 2013; Zhgenti et al., 2015). A
Y. pseudotuberculosis strain (IP32953) (Chain et al., 2004) was used as out-
group for rooting the tree, and all its derived SNPs were removed to scale
branch lengths (Supplemental Experimental Procedures).
ACCESSION NUMBERS
Raw sequencing reads produced for this study have been deposited at the Eu-
ropean Nucleotide Archive (ENA) under accession number ENA: PRJEB13664.
SUPPLEMENTAL INFORMATION
Supplemental Information includes Supplemental Experimental Procedures,
two figures, and four tables and can be found with this article online at
http://dx.doi.org/10.1016/j.chom.2016.05.012.
AUTHOR CONTRIBUTIONS
J.K., K.I.B, A.H., and M.A.S. conceived the study; M.A.S., R.I.T., M.F., and
K.I.B. performed laboratory work; M.A.S., A.H., K.I.B., and J.K. analyzed
data; J.B.d.H., S.A., D.C., J.W., I.R.G., A.G.S., and D.K.N. provided archaeo-
logical material and archaeological context information; J.D., S.K., D.C., J.W.,
and I.R.G. performed anthropological and paleopathological examination;
M.A.S., K.I.B., A.H., and J.K. wrote the manuscript with contribution from all
co-authors.
ACKNOWLEDGMENTS
We are grateful to Cosimo Posth, Marcel Keller, and all other members of the
Department of Archaeogenetics of the Max Planck Institute for the Science of
Human History for their suggestions, as well as the three anonymous reviewers
for their comments. We thank Annette Gu
¨nzel for graphical support. We thank
Rainer Weiss for facilitating excavations in Ellwangen and for providing access
to photographic material. We acknowledge the following sources of funding:
European Research Council starting grant APGREID (to J.K.) and Social Sci-
ences and Humanities Research Council of Canada postdoctoral fellowship
grant 756-2011-501 (to K.I.B.), the Maison des Sciences de l’Homme d’Aqui-
taine (projet Re
´gion Aquitaine) and the French Research National Agency (pro-
gram of investments for the future, grant ANR-10-LABX-52) (to D.C.), the
Russian Government Program of Competitive Growth of Kazan Federal Uni-
versity and the Regional Foundation of Revival of Historical and Cultural Mon-
uments of the Republic of Tatarstan (to R.I.T., I.R.G., A.G.S., and D.K.N). Part
of the data storage and analysis was performed on the computational resource
bwGRiD Cluster Tu
¨bingen funded by the Ministry of Science, Research and
the Arts Baden-Wu
¨rttemberg, and the Universities of the State of Baden-Wu
¨rt-
temberg, Germany, within the framework program bwHPC.
Received: March 4, 2016
Revised: April 23, 2016
Accepted: May 13, 2016
Published: June 8, 2016
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Cell Host & Microbe, Volume 19
Supplemental Information
Historical Y. pestis Genomes Reveal
the European Black Death as the Source
of Ancient and Modern Plague Pandemics
Maria A. Spyrou, Rezeda I. Tukhbatova, Michal Feldman, Joanna Drath, Sacha
Kacki, Julia Beltrán de Heredia, Susanne Arnold, Airat G. Sitdikov, Dominique
Castex, Joachim Wahl, Ilgizar R. Gazimzyanov, Danis K. Nurgaliev, Alexander
Herbig, Kirsten I. Bos, and Johannes Krause

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Supplemental Figures and Tables
Figure S1
Supplemental Figure 1, Related to Figure 1. Archaeological artifacts associated with the Bolgar
City site.
(A-L) Coin artifacts associated with the burial of individual 2370 from Bolgar City, Ust’Jerusalem
tomb, were minted and released during the times of Murad Khan and Abdullah Khan ibn Uzbeg Khan
and date the burial to the second half of the 14th century, in the period after 1362 AD.

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Figure S2
Supplemental Figure 2, Related to Figure 2 and Figure 3. Maximum Likelihood phylogeny.
Maximum Likelihood phylogenetic tree of 141 modern and 10 historical Y. pestis strains. A Y.
pseudotuberculosis strain was used as outgroup (IP32953). 3351 SNP positions were considered for the
phylogeny. The reconstructed tree shows the topology of the newly sequenced isolates from Barcelona,
Bolgar City and Ellwangen relative to previously sequenced modern and ancient Y. pestis strains.
Asterisks (*) indicate bootstrap values of 100. Collapsed branches are represented by triangles, to
enhance tree clarity. Strains belonging to Branch 1 are represented in red, Branch 2 is represented in
yellow, Branch 3 is represented in blue, Branch 4 is represented in orange and Branch 0 is represented
in black. Ancient Branch 1 strains are indicated by their archaeological or radiocarbon date and by a
(+). Because of the great number of derived SNP positions of the 0.PE3 lineage, its branch was reduced
to adjust scaling of the tree. Geographic region abbreviations correspond to: CHN (China), USA
(United States of America), MDG (Madagascar), IND (India), IRN (Iran), MNM (Myanmar), RUS
(Russia), GB (Great Britain), DE (Germany), FRA (France), SP (Spain), MNG (Mongolia), NPL
(Nepal), FSU (Former Soviet Union), AGO (Angola), CGO (Congo) and UGA (Uganda).

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Table S1
Supplemental Table 1, Related to Figure 1 and Table S2. Sample description, screening results
and sequencing statistics.
Sample ID
Site
Tooth type
Dates cal AD
Archaeological
dating
Copies of pla
(copies/µl)
CO92
Chromosomal
fold-coverage
3031
Barcelona
Molar
1300-1420a
-
174
10.3x
2370
Bolgar City
Molar
1298-1388b
1362-1400 ADc
553
19.3x
549_O
Ellwangen
Molar/ Incisor
1485-1627b
-
3/2
4.9xd
aPublished in (Beltrán de Heredia Bercero, 2014)
bRadiocarbon dates produced for this study, presented in calibrated year AD (1 sigma)
cArchaeological dates point to the second half of the 14th century, and specifically the period after 1362
AD (see also Supplemental Experimental Procedures and Figure S1)
dPooled data from four independent serial capture experiments, using two libraries generated from two
tooth samples belonging to the same individual

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Table S2
Supplemental Table 2, Related to Figure 2. Read processing and mapping statistics
Sample
ID
Site
Number of pre-processed
reads before mapping
Number of
mapped reads
Duplication
factor
Number of mapped reads
after map quality filtering
Average coverage
on CO92
Chromosome
Percentage of CO92
chromosome covered
3-fold
3031
Barcelona
60,516,261
2,116,962
2.43
870,477
10.3
89.88%
2370
Bolgar
47,595,565
4,183,226
2.49
1,682,954
19.28
91.46%
549_O
Ellwangen
145,645,509
2,120,360
4.79
442,573
4.91
73.56%

!
Supplemental Experimental Procedures
Information on archaeological sites and aDNA specimens
Saints Màrtirs Just i Pastor, Barcelona, Spain
The Barcelona mass grave was discovered in 2012 during an excavation campaign performed in the
sacristy of the Saints Màrtirs Just i Pastor church, and is likely the first Black Death burial discovered
in Spain. The burial was only partially excavated due to security restrictions (i.e. it’s proximity to the
sacristy’s walls) and its western part was destroyed by the foundations of the gothic church. The pit
was 1.50 m deep, and estimated to have been 5.5 m long and 4 m wide. Individuals were deposited in
11 successive layers, each layer containing between 4 and 15 skeletons. During the excavation, the
skeletons of 120 individuals were recovered, of which 50 non-adults (i.e. less than 20 year-old) and 70
adults, out of an estimated number of 350-400 individuals buried in the pit (Beltrán de Heredia
Bercero, 2014). Due to partial excavation of the burial, most of the skeletons recovered were
incomplete. Most of the individuals were lying on their back, with their upper limbs in a flexed
position (hands on the thorax or abdomen), and their lower limbs extended. None of the individuals
were in prone position, and only a few were on their side. Regarding burial methods, no coffins were
used. Bodies were directly placed in the grave all together, and the pit was subsequently filled with
earth. The excavation, however, revealed textile remains (linen and hemp), suggesting that bodies were
wrapped in shrouds. It is noteworthy that a layer of lime was deposited on top of the accumulation of
cadavers; this is the only one example of use of such prophylactic material in a medieval plague pit
(Kacki, 2014; Schotsmans et al., 2015). For this study, 49 teeth were removed from 18 individuals and
used for biomolecular analysis. According to osteological examination of long bone length and dental
development, individual 3031 from Barcelona, from which a Y. pestis genome was recovered, was
most likely a 6-9 year old non-adult, whose sex could not be determined. Although the skeleton was
only partly preserved, there was no detectably diagnostic feature of a specific pathological condition.
Stress markers such as cribra orbitalia and mild developmental dental defects (linear enamel
hypoplasia), however, may indicate malnutrition earlier in life.
Ust’-Jerusalem necropolis and Bolgar City mausoleum, Russia
The medieval city of Bolgar was situated on the bank of the Volga River, 30 km downstream from its
confluence with the Kama River and some 130 km from modern Kazan (Tatarstan, Russian
Federation). Bolgar City was an early settlement of the civilization of Volga-Bolgars, which existed
between the 7th and 15th centuries AD and was intermittently capital of Volga Bulgaria between the
10th and 15th centuries (Sitdikov, 2014). Bolgar City was also the first capital of the Golden Horde in
the 13th century. The UNESCO World Heritage Committee declared the ancient Bolgar hill fort as a
World Heritage Site in 2014. The Ust’-Jerusalem necropolis was excavated between 1996 and 2003,
covers an 800 sq. m. area and includes 318 single burials (Vasiliev, 2004). Palaeodemographic analysis
revealed a high infant mortality rate (over 57% of the group), which may have been attributed to
unfavorable social and environmental conditions, early childbirth in women, and a significant lack of
food resources (Boruckaya, 2003). For the current investigation, material was chosen from the
anthropological collections of the Ust’-Ierusalimsky tombs (Figure 1b) and the Bolgar city mausoleum
(Vasiliev, 2004). A total of 95 teeth were extracted from 93 individuals and used for ancient DNA
analysis. A complete skeleton was recovered from the plague victim (2370) of the Ust’Jerusalem tomb
in Bolgar City. Anthropological analysis revealed a 35-40 year old male, whose burial was not
consistent with medieval Muslim funerary practices (Figure 1b). Coin artifacts that were discovered
during excavation of the burial dated the site to the second half of the 14th century. Grave artifacts
associated specifically with individual 2370 consisted of 12 silver coins (Figure S1), the earliest of
which date to 1362 AD. Such coin types are considered to have been minted and released during the
times of Murad Khan and Abdullah Khan ibn Uzbeg Khan of the Golden Horde (Bosworth, 1996), who
ruled between 1362 and 1370 AD (Figure S1).
“Marktplatz” Ellwangen, Germany
Excavations of the Ellwangen “Marktplatz” that were initiated as a tribute to the 1250th anniversary of
the city, revealed a burial ground proposed to have been used for about a millennium, with human
remains unearthed spanning form the 8th to the 18th centuries AD (Arnold, 2014). The cemetery
contained 3 mass graves and 14 multiple burials amongst single burials. To-date, a total of 800
individuals has been identified and unearthed. The mass graves included a total of 102 individuals, and
presented a case of unstructured burial practices clearly reflecting an event of mass mortality (Wahl,
2014). It is possible that part of the multiple burials were also attributed to the same catastrophic event.

!
No signs of warfare were detected in the remains, and skeletal indications of infectious disease were
unspecific and not uniform across the individuals. Microscopical analyses detected the presence of
intestinal parasites among skeletal material, possibly indicating unhygienic living conditions of the
population. Within the mass graves, 80% of individuals were determined to be non-adults (<20 years)
with an average age of 9.4 years (Wahl, 2014). In addition, the multiple burials contained a total of 73,
mostly incomplete, skeletons that were distributed across 14 graves with 2 to 10 individuals in each
grave. In this case the average age was much higher, estimated to 17.4 years. For the present study, 79
teeth were removed from 67 individuals for ancient DNA analysis. Individual 549_O from Ellwangen,
from which a Y. pestis genome was reconstructed, was identified as a 12-14 year old non-adult, whose
sex could not be confidently determined. In this case, the skeletal material recovered was also
incomplete, with non-specific bone changes and dental defects, including calculus formation (Figure
1c).
DNA Extraction from archaeological material
Extractions were performed for a total of 223 tooth samples, isolated from potential plague victims. 50
mg of pulverized dental pulp, was removed using a dental drill, as preserved pathogen DNA is more
likely to reside in the dried blood vessels of the pulp chamber (Schuenemann et al., 2011). All
procedures were carried out in the dedicated ancient DNA laboratory of Paleogenetics in the University
of Tübingen. DNA extraction was performed according to a previously described protocol (Dabney et
al., 2013), with a rotation of 12-16h at 37oC during an initial lysis step. A negative control was
included for every 10 samples, and one positive extraction control for every extraction slot.
Screening for pla
Initial screening was performed to evaluate the presence of Y.pestis DNA in all samples, by using the
species-specific gene plasminogen activator (pla). 223 DNA extracts were qPCR screened for the
presence of the pla gene, located in the pPCP1 plasmid using a previously described approach
(Schuenemann et al., 2011). 79 samples were from Ellwangen (67 individuals), 49 from Barcelona (18
individuals), 95 from Bolgar city (93 individuals). Amplification products were not sequenced.
Potential Y. pestis positive samples were subsequently used for further screening using an established
whole-genome array capture method (Hodges et al., 2009).
Array design
A one million feature Agilent microarray (Hodges et al., 2009) was designed using an in-house probe
design software, both for screening and whole-genome reconstruction purposes. In order to prevent
hybridization capture bias for a certain Y. pestis reference sequence, probes were prepared using the
chromosome of the bacterium Yersinia pseudotuberculosis (Accession number: NC_006155), which is
the closest known relative of Y. pestis, with up to 97% identity in chromosomal genes (Achtman et al.,
1999; Chain et al., 2004). The Y. pestis (CO92) plasmids pMT1 (Accession number: NC_003134) and
pCD1 (Accession number: NC_003131) were also included in the design. A complete set of 976,658
probes was generated for the array.
Array captures
60 µl of extract was used to produce double stranded DNA libraries, as described before (Meyer and
Kircher, 2010), for all positive samples. Blank library controls and extraction blanks were also
included in every library preparation slot. As the characteristic cytosine deamination accumulating
within DNA molecules over time may challenge downstream analyses (Briggs et al., 2007; Sawyer et
al., 2012), an initial UDG and endonuclease VIII treatment (USER enzyme) was used to remove uracil
residues and subsequently repair DNA fragments (Briggs et al., 2010). Unique double index DNA
barcodes (Kircher et al., 2012) were attached onto libraries through a 10-cycle amplification reaction,
using universal IS5/IS6 primers. Post indexing, libraries were amplified using AccuPrime Pfx or
Herculase II Fusion DNA polymerase to accomplish a 19 µg pool of samples. 1ug of a positive control
was added to make up a final 20 µg pool that served as template for array capture. A separate pool was
made for extraction and library blank controls, and was tested on a separate array to avoid cross talk
between samples and blanks. Hybridization-based array capture was performed using previously
established methods (Hodges et al., 2009). Hybridization of template to the probes took place over a
two-night incubation step at 65 °C. Following array elution, captured template was re-amplified with
universal IS5/IS6 primers using Herculase II Fusion DNA polymerase to achieve 20 µg of product that
would serve as template for a subsequent capture step (serial capture). Identical array design and
methodology were used for the second round of capture. Following elution, products were again

!
amplified as described above and subsequently diluted down to 10nM for high throughput sequencing.
Sequencing was performed on HiSeq 2500 and NextSeq 500 Illumina platforms.
High throughput read pre-processing and mapping pipeline
High throughput sequencing produced up to 123,690,558 raw paired-end reads per sequencing run per
library. All pre-processing, mapping and genotyping steps were performed using the automated
pipeline EAGER (Peltzer et al., 2016). Adaptors were clipped from all reads produced by the Illumina
platforms and overlapping reads were merged. Subsequent quality filtering and length filtering
removed reads shorter that 30 bp. All reads were then mapped with BWA (Li and Durbin, 2010) using
Y. pestis CO92 as a reference genome (Parkhill et al., 2001), the first complete Y. pestis genome to be
sequenced (Accession number: AL590842.1). To avoid cross mapping from multiple DNA sources,
mapping parameters used included a stringency of 0.1 (-n parameter) and a map quality filter of 37
(Table S1).
SNP calling
SNP calling was performed using the UnifiedGenotyper of the Genome Analysis Toolkit (GATK)
(DePristo et al., 2011) on the newly produced ancient mapped data, alongside previously published
ancient and modern Y. pestis data. A total of 152 samples were considered for this study. A vcf file was
produced for every sample using the “EMIT_ALL_SITES” option, which generates a call for every
genomic site. The MultiVCFAnalyzer custom java program was applied to all vcf files to
comparatively filter all the detected SNPs, and produce a multiple alignment of variable positions in
which a SNP was called when present in at least one of the samples in the dataset. Homozygous SNPs
were called when covered at least 3-fold with a minimum genotyping quality of 30. Respectively, a
reference base was called when supported by 3 independent fragments with the same quality threshold.
In case of a heterozygous position, a SNP or reference base was called when at least 90% of the reads
covering the position support it. If none of the options was possible, an “N” was inserted at the
corresponding positions. In the current dataset, a total of 3,444 variant positions were called.
Phylogenetic reconstruction
After SNP filtering, a SNP table was used as input for phylogenetic reconstruction encompassing a
total of 3,444 SNP positons. Phylogenetic trees were generated, using the Maximum Parsimony (MP)
and Maximum Likelihood (ML) methods available in MEGA6.06 (Tamura et al., 2013), discarding all
alignment columns with more than 5% missing data, which caused the removal of 93 SNP positions.
The Maximum Likelihood phylogeny was inferred assuming a General Time Reversible (GTR) model
and a Nearest-Neighbor-Interchange (NNI) tree inference option. The total amount of remaining
positions to be considered was 3,351. 1000 pseudo-replicates were carried out to assess tree robustness
by the bootstrapping method for both phylogenetic methods. A total of 152 samples were used for
generation of the phylogeny. The three new strains reported in this study include a Black Death strain
from Barcelona, a strain from Bolgar city dating to the second half of the 14th century AD (1362-1400),
and a 16th century AD strain from Ellwangen. Data from previously sequenced ancient and modern Y.
pestis strains included five strains from the 18th century plague of Marseille (Bos et al., 2016), one
sequence from Black Death victims from London 1348-1350 (8291-1197-8124), one strain from
London 1350-1400 (6330) and 141 modern Y. pestis strains (Cui et al., 2013; Zhgenti et al., 2015). A
previously published ancient strain recovered from victims of the Plague of Justinian (Wagner et al.,
2014) was omitted from the analysis, as it does not contribute to the interpretation of our results, and
the low coverage of this genome could negatively influence the robustness of our phylogeny. A Y.
pseudotuberculosis strain (IP32953) (Chain et al., 2004) was used as an outgroup for rooting the tree,
and all its derived SNPs were removed to scale branch lengths.

!
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Genome announcements 3.

Table&S3,&Related&to&Figure&2&and&Figure&3.&Geographical&regions&of&Y.#pestis&genomes&used&for&SNP&calling&and&phylogeny
Strain&identifier Branch& Lineage Country Newly&integrated&Caucasus&strains&
0.ANT1a_42013 0 0.ANT1 China Newly&sequenced&historical&strains
0.ANT1b_CMCC49003 0 0.ANT1 China
0.ANT1c_945 0 0.ANT1 China
0.ANT1d_164 0 0.ANT1 China
0.ANT1e_CMCC8211 0 0.ANT1 China
0.ANT1f_42095 0 0.ANT1 China
0.ANT1g_CMCC42007 0 0.ANT1 China
0.ANT1h_CMCC43032 0 0.ANT1 China
0.ANT2_B42003004 0 0.ANT2 China
0.ANT2a_2330 0 0.ANT2 China
0.ANT3a_CMCC38001 0 0.ANT3 China
0.ANT3b_A1956001 0 0.ANT3 China
0.ANT3c_42082 0 0.ANT3 China
0.ANT3d_CMCC21106 0 0.ANT3 China
0.ANT3e_42091b 0 0.ANT3 China
Kyrgyzstan_790 0 0.ANT3 Kyrgyzstan
0.PE2_PEST-F 0 0.PE2 Georgia
0.PE2b_G8786 0 0.PE2 Georgia
Armenia_14735 0 0.PE2 Armenia
Armenia_1522 0 0.PE2 Armenia
Georgia_1412 0 0.PE2 Georgia
Georgia_1413 0 0.PE2 Georgia
Georgia_1670 0 0.PE2 Georgia
Georgia_3067 0 0.PE2 Georgia
Georgia_3770 0 0.PE2 Georgia
Georgia_8787 0 0.PE2 Georgia
0.PE3_Angola 0 0.PE3 Angola
0.PE4_Microtus91001 0 0.PE4 China
0.PE4Aa_12 0 0.PE4 China
0.PE4Ab_9 0 0.PE4 China
0.PE4Ba_PestoidesA 0 0.PE4 Georgia
0.PE4Ca_CMCCN010025 0 0.PE4 China
0.PE4Cc_CMCC18019 0 0.PE4 China
0.PE4Cd_CMCC93014 0 0.PE4 China
0.PE4Ce_CMCC91090 0 0.PE4 China
M0000002 0 0.PE4 China
0.PE7b_620024 0 0.PE7 China
1.ANT1_Antiqua 1 1.ANT1 Congo
1.ANT1_UG05-0454 1 1.ANT1 Uganda
1.IN1a_CMCC11001 1 1.IN1 China
1.IN1b_780441 1 1.IN1 China
1.IN1c_K21985002 1 1.IN1 China
1.IN2a_CMCC640047 1 1.IN2 China
1.IN2b_30017 1 1.IN2 China
1.IN2c_CMCC31004 1 1.IN2 China
1.IN2d_C1975003 1 1.IN2 China
1.IN2e_C1989001 1 1.IN2 China
1.IN2f_710317 1 1.IN2 China
1.IN2g_CMCC05013 1 1.IN2 China
1.IN2h_5 1 1.IN2 China
1.IN2i_CMCC10012 1 1.IN2 China
1.IN2j_CMCC27002 1 1.IN2 China
1.IN2k_970754 1 1.IN2 China
1.IN2l_D1991004 1 1.IN2 China
1.IN2m_D1964002b 1 1.IN2 China
1.IN2n_CMCC02041 1 1.IN2 China
1.IN2o_CMCC03001 1 1.IN2 China
1.IN2p_D1982001 1 1.IN2 China
1.IN2q_D1964001 1 1.IN2 China
1.IN3a_F1954001 1 1.IN3 China
1.IN3b_E1979001 1 1.IN3 China
1.IN3c_CMCC84038b 1 1.IN3 China
1.IN3d_YN1683 1 1.IN3 China
1.IN3e_YN472 1 1.IN3 China
1.IN3f_YN1065 1 1.IN3 China
1.IN3g_E1977001 1 1.IN3 China
1.IN3h_CMCC84033 1 1.IN3 China
1.IN3i_CMCC84046 1 1.IN3 China
1.ORI1_CA88 1 1.ORI1 U.S.A
1.ORI1_CO92 1 1.ORI1 U.S.A
1.ORI1a_CMCC114001 1 1.ORI1 China
1.ORI1b_India195 1 1.ORI1 India
1.ORI1c_F1946001 1 1.ORI1 China
1.ORI2_F1991016 1 1.ORI2 China
1.ORI2a_YN2179 1 1.ORI2 Myanmar
1.ORI2c_YN2551b 1 1.ORI2 China
1.ORI2d_YN2588 1 1.ORI2 China
1.ORI2f_CMCC87001 1 1.ORI2 China
1.ORI2g_F1984001 1 1.ORI2 China

!"#$%&'()*++, ! !"#$%& -'./0
!"#$%&.(-1--2!3333!0 ! !"#$%& -'./0
!"#$%&.(-1--2!!333!4 ! !"#$%& -'./0
!"#$%,(%5&67 ! !"#$%, 108090:;0<
!"#$%,(1=37>!3&3 ! !"#$%, 108090:;0<
!"#$%,0(?@6+ ! !"#$%, 108090:;0<
&"A*B!(*CD0E7!+ & &"A*B! *CD0E
&"A*B!0(,F33G & &"A*B! -'./0
&"A*B!4(,F&3& & &"A*B! -'./0
&"A*B&0(& & &"A*B& -'./0
&"A*B&4(,7!33! & &"A*B& -'./0
&"A*B&;(-1--,F633! & &"A*B& -'./0
&"A*B&8(=!HH+33+ & &"A*B& -'./0
&"A*B&C(=!HH+3!3 & &"A*B& -'./0
&"A*B&I(-1--,FG33& & &"A*B& -'./0
&"A*B,0(-1--H&3!3 & &"A*B, -'./0
&"A*B,4(-1--H733! & &"A*B, -'./0
&"A*B,;(-1--H+33! & &"A*B, -'./0
&"A*B,8(-1--H+336 & &"A*B, -'./0
&"A*B,C(-1--+633! & &"A*B, -'./0
&"A*B,I(-1--!3F33, & &"A*B, -'./0
&"A*B,9(-1--7!3&3 & &"A*B, -'./0
&"A*B,'(-1--!3+33& & &"A*B, -'./0
&"A*B,.(-1--+F33! & &"A*B, -'./0
&"A*B,J(K!H7H33F & &"A*B, -'./0
&"A*B,L(76+! & &"A*B, $M::.0/NOC8C<0P.Q/
&"A*B,E(6,7 & &"A*B, $M::.0/NOC8C<0P.Q/
&"1?R!4(&73+ & &"1?R! -'./0
&"1?R!;(&+7F & &"1?R! -'./0
&"1?R!8(&73F & &"1?R! -'./0
&"1?R!(2%1!3 & &"1?R! %<0/S2M<8.:P0/
$M::.0/OC8C<0P.Q/(&HFF & &"1?R! $M::.0/NOC8C<0P.Q/
ATC<40.J0/(!7&& & &"1?R! ATC<40.J0/
&"1?R&4(H! & &"1?R& -'./0
&"1?R&;(2!!H6,33& & &"1?R& -'./0
&"1?R&8(A!H6,33! & &"1?R& -'./0
&"1?R&C(6,,G & &"1?R& -'./0
&"1?R,0(U!H+,33& & &"1?R, -'./0
&"1?R,4(-1--!&733&4 & &"1?R, -'./0
&"1?R,;(%!H+H33, & &"1?R, -'./0
&"1?R,8(U!H6G33& & &"1?R, -'./0
&"1?R,I(%!H63337 & &"1?R, -'./0
&"1?R,9(-1--HH!3, & &"1?R, -'./0
&"1?R,'(-1--H33&6 & &"1?R, -'./0
&"1?R,.(-1--H&33F & &"1?R, -'./0
&"1?R,J(%&33!33! & &"1?R, -'./0
&"1?R,L(-1--!&33, & &"1?R, -'./0
&"1?R,E(%!HHF33+ & &"1?R, -'./0
&"1?R,V(WKA*!! & &"1?R, -'./0
&"1?R,/(WKA*!& & &"1?R, -'./0
&"1?R,Q(%!HH!33! & &"1?R, -'./0
&"1?R,D(-1--!3633F & &"1?R, -'./0
,"A*B!0(64 , ,"A*B! -'./0
,"A*B!4(-1--6!33! , ,"A*B! -'./0
,"A*B!;(-!H6+33! , ,"A*B! -'./0
,"A*B!8(6!3&! , ,"A*B! -'./0
,"A*B&0(1=UX+ , ,"A*B& 1Q/9QE.0
,"A*B&4(1=UX6 , ,"A*B& 1Q/9QE.0
,"A*B&;(1=UXH , ,"A*B& 1Q/9QE.0
,"A*B&8(1=UX!! , ,"A*B& 1Q/9QE.0
,"A*B&C(1=UX, , ,"A*B& 1Q/9QE.0
F"A*B!0(1=UX!& F F"A*B! 1Q/9QE.0
G!&F(G&H!(!!H6& ! 0/;.C/PNY<0/;'N! =<C0PNY<.P0./
+,,3 ! 0/;.C/PNY<0/;'N! =<C0PNY<.P0./
#YW!36 ! 0/;.C/PNY<0/;'N! O<0/;C
#YW!!3 ! 0/;.C/PNY<0/;'N! O<0/;CN
#YW!!+ ! 0/;.C/PNY<0/;'N! O<0/;CN
#YW!&F ! 0/;.C/PNY<0/;'N! O<0/;CN
#YW!,6 ! 0/;.C/PNY<0/;'N! O<0/;C
Y0<;CEQ/0NZ,3,![ ! 0/;.C/PNY<0/;'N! WD0./N
YQE90<NZ&,63[ ! 0/;.C/PNY<0/;'N! $M::.0/NOC8C<0P.Q/
?EE\0/9C/NZ7FH(#[ ! 0/;.C/PNY<0/;'N! =C<V0/]
Y.pseudotuberculosisNZ%5,&H7,[ QMP9<QMD QMP9<QMD O<0/;C

Table&S4,&Related&to&Figure&2.&SNP&table&including&non-unique&and&unique&SNPs&of&all&second&pandemic&Y.#pestis&strains&sequenced&to-date
Position Reference OBS107 OBS110 OBS116 OBS124 OBS137 Ellwangen Bolgar Barcelona London&(8124_8291_11972) London&(6330)
29368 GTTTTTT. . . .
74539 CTTTTTTTTT T Ellwangen-Observance;shared;SNPs;N=20
100383 C T T T T T N . . . . Ellwangen;Unique;SNPs;N=3
130643 GAAAAAAAAA A SNP;positions;between;Bolgar;and;1.ANT;N=10
155747 AGGGGGNGGG G
169412 CTTTTTT.. . .
173032 C T T T T T . . . . .
186060 CTTTTTT.. . .
190040 CNANNNN. N. .
190041 T G G N N N N . N . .
190049 GNNNNNNNAN N
200723 C T T T T T . . . . N
217009 GTTTTTT. . . .
225436 T A A A A A N . . . .
226722 C T T T T T . . . . N
286528 TAAAAANAAA A
300041 C N N N N T . . . . .
325836 TCCCCCCCCC C
400143 GAAAAAA. . . .
477107 C T T T T T . . . . .
480773 C T T T T T . . . . .
482327 G T T T T T . . . . .
528975 A N N C N N . . . . .
545488 TCCCCCCCCC C
571183 GNNNANNNNN N
699494 AGGGGGG. GG .
699647 TCCCCCCCCC C
862385 T G G G G G N . . . .
867712 CAAAAAA. . . N
868549 G C C C C C N . . . .
869820 A G G G G G N . . . .
877258 TCCCCCNCCC C
899158 C T T T T T . . N . .
951295 C T T T T T N . . . .
961795 C T N T T T T . . . N
965281 C A A A A A . . . . .
1017647 T C C C C C N N N C C
1025278 TGGGGGGGGG G
1098675 ACCCCCCCCC N
1159539 T A A A A A . . . . .
1168951 G T T T T T . . . . .
1178178 TCCCCCNCCC C
1178459 TCCCCCCCCC C
1189479 C T T T T T . . . . .
1232222 CTTTTTT.. . .
1254157 CTTTTTT.. . .
1272559 TCCCCCCCCC C
1306718 TCCCCCCCCC N
1308719 G A A A A A N . . . N
1378105 G T T T T T . . . . .
1385780 TCCCCCCCCC C
1398797 CNNNNNANNN N
1439084 T . N N A N . . . . .
1439085 A . N N C N . . . . .
1440851 G T T T T T . . . . .
1451124 T G G G N G N . . . N
1458573 T A A A A A . . . . N
1466798 T N N C C C N . . . .
1481292 C N T T N T . . . . N
1481381 G A N N N N . . . . .
1481393 G A N N A A . . . . .
1511518 A N N N N G . . . . .
1512930 AGGGGGNGGG G
1549630 A N G G G G N . . . N
1586982 C A A A A A . . . . .
1614945 T G G G G G N . . . N
1644408 C A A A A A N . . . .
1708192 C A A A A A . . . . .
1713927 C A A A N A . . . . N
1724647 C T T T T T . . . . .
1735263 ACCCCCCCCC C
1749443 TCCCCCCCCC C
1808946 TCCCCCCCCC C
1871129 T C C N N N . . . . .
1883743 C T N N N N . . . . N
1883750 A T N N N N . . . . N
1935112 C A A A A A . . . . .
1952848 GAAAAAA. . . .
2022335 ACCCCCCCCC C
2071670 G T T T T T N . . . N
2076353 C T T T T T . . . . .
2098628 TCCCCCCCCC C
2105332 C T T T N T N . . . N
2105376 A N G G G G . . . . N
2262577 TGGGGGG. GG .
2264654 C A A A A A . . . . N
2277583 GAAAAANANA A
2278317 AGGGGGGGGG G
2281061 C N A A A A N N N . .
2292030 CTTTTTT.. . .
2300659 TGGGGGNGGG G
2356003 TAAAAAAAAA A
2414599 T C C C C C . . . . N
2472383 A G G G G G . . . . .
2507983 T G G G G G N . . . .
2508389 TCCCCCCCCC C
2519931 CTTTTTT.. . .
2575152 GAAAAANAAA A
2596736 A G G G G G . . . . N
2671194 G A A A A A N . . . .
2684793 AGGGGGGGGG G
2727385 A G G G G G . . . . .
2739149 CAAAAANAAA N
2744933 AGNGGGNGGG G
2877295 GAAAAAA. . . .
2903882 TGGGGGGGGG G
2913027 A.....T... .
2918297 T G G G G G . . . . .
2934972 CGGGGGNGGG G
2936268 GAAAAAAAAA A
2950954 GAAAAANAAA N
2958327 CTTTNTTTTN N
2964936 A G G G G G . . . N N
2973013 C T T T T T N . N . .
3025157 GNNN. NNNAN N
3030042 GTTTTTT. . . N
3085079 AGGGGGGGGG N

3098104 C N A A A A N . N . N
3145523 ACCCCCCCCC C
3190399 AGGGGGGGGG G
3229407 T C C C C C N N N . .
3244204 AGGGGGGGGG G
3253104 G N N N N N T . . . .
3254908 GAAAAAA. . . .
3267118 AGGGGGNGGG G
3269577 G N T T T T N . . . N
3269613 G A N N . . . . . . .
3269615 C T N N N N . . . . .
3299755 CNNNNNN. T N N
3324959 AGGGGGGGGG G
3336063 CN....T... N
3362591 AGGGGGGGGG G
3387542 CNNNNNNNTN N
3397040 AGGGGGGGGG N
3407572 A T T T T T . . N . N
3421335 AGGGNGGGGG N
3442617 ATTTTTNTTT N
3540139 GAAAAAA. . . .
3564026 CTTTTTTTTT T
3571531 AGGGGGGGGG N
3610371 C T T T T T . . . . .
3613964 C A A A A A . . . . N
3616733 AGGGGGGGGG N
3620114 G A A A A A . . . . .
3620500 G A A A A A N . . . N
3643387 G......T.. N
3645151 CGGGGGGGGG G
3667806 AGGGGGGGGG G
3726726 AGGGGGGGGG N
3761046 GANNNNNN. N N
3764396 C A A A N A A . N N N
3782640 G A A A A A N . . . N
3806677 CTTTTTT.TT T
3824821 G A A A A A . . . . N
3872698 CTTTTTT.. . N
3888808 C..T...... .
3944305 C A A A A A . . . . .
3973746 CTTTTTNTTT T
3973901 G A A A A A . . . . .
3988141 C T T T T T . . . . .
3989422 C.....A... .
4082562 TCCCCCCCCC C
4083536 AGGGGGGGGG G
4134121 A T T T T T . . . . N
4150574 CAAAAAA. . . .
4173149 A C C C N C N C N N N
4190286 C A A A A A N N N . N
4194600 GAAAAAAAAA A
4200639 C A A A A A N . . . N
4208536 A G G G G G N . . . N
4232240 C T N N N N . . . . N
4236782 C N N T N N . . . . .
4236789 C N N G N N N . . . .
4242260 GTTTTTT. . . N
4243823 ATTTTTTTTT N
4296702 GNNNNNNTNN N
4301295 G......... T
4363505 C T T T T T . . . . .
4371886 AGGGGGGGGG G
4396236 G T T T T T . . . . N
4421278 GNNNANNNNN N
4421633 TCCCCCCCCC C
4421689 AGGGGGNGGG G
4456212 C A A A A A N N N . .
4518401 GAAAAAAAAA A
4527483 AGGGGGNGGG N
4567317 C . N A N N N . . . N
4579183 AGGGGGGGGG G
4616904 T C C C C C . . . . .
4634287 AGGGGGGGGG G
4642828 G A A A A A N . . N N