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Coppa Et Al - aDNA Rome Science
Coppa Et Al - aDNA Rome Science
I
Italy and from Grotta d’Oriente in Sicily (12–15)
n the 8th century before the common era of genetic data from 127 ancient individuals, (fig. S17).
(BCE), Rome was one of many city-states spanning key events in Roman prehistory and As reported previously for WHG groups
on the Italian Peninsula. In less than history, allowing us to place genetic changes in (12, 14), these individuals show particularly
1000 years, it grew into the largest urban the context of a rich archaeological and histo- low heterozygosity, ~30% lower than that of
center of the ancient world (1–3). Rome rical record. early modern central Italians (7). After this
controlled territory on three continents, span- period, we see a sharp increase in heterozygos-
ning the entirety of the Mediterranean—or Results ity in the Neolithic Age and smaller increases
Mare Nostrum, “our sea,” as the Romans We generated whole-genome data for 127 an- afterwards, reaching modern levels by around
called it (1–3). As part of the Italian Peninsula, cient individuals from 29 archaeological sites 2000 years before present (fig. S6).
Rome occupies a distinctive geographic loca- in Rome and central Italy (Fig. 1 and table S1).
tion. It is partially insulated by the Alps to the Date estimates were obtained by direct radio- The Neolithic transition
north, which formed a natural barrier to move- carbon dating (n = 33 individuals) and in- The first major ancestry shift in the time series
ment of languages, material cultures, and people ference from archaeological context (n = 94) occurred between 7000 and 6000 BCE, coin-
(4, 5), and is also highly connected to regions (tables S2 and S3). We powdered the cochlear ciding with the transition to farming and
around the Mediterranean Sea, particularly after portion of the petrous bone, extracted DNA, introduction of domesticates including wheat,
Bronze Age advances in seafaring (2, 6). and built partially uracil-DNA glycosylase barley, pulses, sheep, and cattle into Italy (Fig.
Roman history has been extensively studied, (UDG)–treated libraries (7). Libraries were 2) (6, 16).
but genetic studies of ancient Rome have been screened for endogenous DNA concentration, Similar to early farmers from other parts
limited. To characterize the genetic composi- DNA damage patterns, and contamination. of Europe, Neolithic individuals from central
tion of Rome’s population throughout the tra- We performed whole-genome sequencing to Italy project near Anatolian farmers in PCA
jectory of the empire, we assembled a time series a median depth of 1.05× genome-wide cover- (13, 14, 17–19) (Fig. 2A). However, ADMIXTURE
1
Program in Biomedical Informatics, Stanford University, Stanford, CA, USA. 2Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA. 3Department of Genetics, Stanford
University, Stanford, CA, USA. 4Stanford University, Department of Anthropology, Stanford, CA, USA. 5DANTE Laboratory for the study of Diet and Ancient Technology, Sapienza Università di
Roma, Rome, Italy. 6School of Archaeology, University College Dublin, Dublin, Ireland. 7Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy. 8Department of Evolutionary
Anthropology, University of Vienna, Vienna, Austria. 9Dipartimento di Scienze Mediche, Università di Torino, Torino, Italy. 10Dipartimento di Biologia, Università di Pisa, Pisa, Italy. 11Ministero dei
Beni e delle Attività Culturali (retired), Rome, Italy. 12CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal. 13Soprintendenza Archeologia, belle arti e paesaggio per le
province di Sassari e Nuoro, Sassari, Italy. 14Dipartimento di Civiltà e Forme del Sapere, Università di Pisa, Pisa, Italy. 15Dipartimento di Studi Umanistici, Università degli Studi di Roma Tre,
Rome, Italy. 16Curatore beni culturali presso la Sovrintendenza Capitolina, Rome, Italy. 17Dipartimento di Studi Umanistici, Università degli Studi di Roma Tre, Rome, Italy. 18Soprintendenza
Speciale Archeologia Belle Arti e Paesaggio di Roma, Rome, Italy. 19Servizio di Bioarcheologia, Museo delle Civiltà, Rome, Italy. 20Christian and Medieval Archaeology, University of Rome Tor
Vergata, Rome, Italy. 21Università della Tuscia, DISUCOM Dipartimento di Scienze Umanistiche, della Comunicazione e del Turismo, Viterbo, Italy. 22Aix-Marseille University, Marseille, France.
23
Soprintendenza speciale Archeologia Belle arti e paesaggio di Roma, Rome, Italy. 24University College Dublin, Dublin, Ireland. 25Musei Vaticani, Reparto Antichità Greche e Romane, Vatican City.
26
Università L’Orientale Napoli, Naples, Italy. 27Dipartimento di Archeologia, Università di Foggia, Foggia, Italy. 28SABAP-LAZ Ministero dei Beni e delle Attività Culturali, Rome, Italy. 29Department
of Biology, Stanford University, Stanford, CA, USA.
*These authors contributed equally to this work.
†Corresponding author. Email: pritch@stanford.edu (J.K.P.); ron.pinhasi@univie.ac.at (R.P.); alfredo.coppa@uniroma1.it (A.C.) ‡These authors contributed equally to this work.
Italy 6000
Hunter-Gatherers
Predominant contribution of
10 Neolithic
Transition to farming-based
economy: wheat, barley, pulses, Anatolian/Iranian farmer ancestry to
3500 sheep, cattle. Population growth local population
Lazio
3 Copper Age
2300
Advances in travel: drafted chariots
and wagons in Near East/Steppe;
Rebound of Western Hunter-
Gatherer ancestry in Copper Age
Bronze Age more frequent long-distance individuals
Rome 900 seafaring in Mediterranean
Etruscan and Latin city-states form Presence of Steppe-related ancestry,
Iron Age 753 Mythical founding of Rome increase in Iranian Neolithic ancestry,
11 509 Roman Republic established
146 Roman territory extends to North
and appearance of North African
ancestry. Variable ancestry across
= Archaeological Roman
Republic Africa, Iberia, Greece individuals. Population approximates
site
Expansion continues to Near East modern Mediterranean populations.
27 BCE
27 BCE Augustus Caesar, 1st emperor Substantial ancestry shift towards
CE 117 CE Largest extent of Empire the Eastern Mediterranean and the
Imperial Rome
48 (population ~70 million)
Population of Rome ~1 million
Near East. Highly variable ancestry
across individuals
Fig. 1. Overview of study individuals, major events in Roman history, and key findings. Time periods covered in this study are shown by color
blocks, with reported samples represented by dots on the left side. A map of the sites from which individuals were sampled is shown in the top left.
Present-day Rome, and its administrative province Lazio, are shown.
reveals that, in addition to ancestry from north- ing into the Neolithic, locally or in neighbor- (Figs. 2B and 3B). Using qpAdm, we modeled
western Anatolia farmers, all of the Neolithic ing regions (tables S9 to S11). the genetic shift by an introduction of ~30 to
individuals that we studied carry a small amount 40% ancestry from Bronze and Iron Age noma-
of another component that is found at high The Iron Age and the origins of Rome dic populations from the Pontic-Caspian Steppe
levels in Neolithic Iranian farmers and Caucasus The second major ancestry shift occurred in (table S15), similar to many Bronze Age popu-
hunter-gatherers (CHG) (Fig. 2B and fig. S9). the Bronze Age, between ~2900 and 900 BCE lations in Europe (10, 13, 14, 19, 22). The pre-
This contrasts with contemporaneous central (Figs. 2 and 3, A and B, and tables S13 and S14). sence of Steppe-related ancestry in Iron Age
European and Iberian populations who carry We cannot pinpoint the exact time of this shift Italy could have happened through genetic ex-
farmer ancestry predominantly from north- because of a gap in our time series. change with intermediary populations (5, 23).
western Anatolia (fig. S12). Furthermore, qpAdm During this period, major technological de- Additionally, multiple source populations could
modeling suggests that Neolithic Italian farmers velopments increased the mobility of popula- have contributed, simultaneously or subsequently,
can be modeled as a two-way mixture of ~5% tions. The development of drafted chariots and to the ancestry transition before Iron Age. By
local hunter-gatherer ancestry and ~95% ances- wagons in the Near East and Pontic-Caspian 900 BCE at the latest, the inhabitants of cen-
try of Neolithic farmers from central Anatolia Steppe enabled movement over land (21). Ad- tral Italy had begun to approximate the gen-
or northern Greece (table S7), who also carry vances in sailing technologies facilitated easier etics of modern Mediterranean populations.
additional CHG (or Neolithic Iranian) ances- and more frequent navigation across the Medi- Although there is no direct historical or
try (fig. S12) (14). These findings point to terranean (3, 6), enabling the expansion of genetic information about the origins of Rome,
different or additional source populations Greek, Phoenician, and Punic colonies across archaeological evidence suggests that in the
involved in the Neolithic transition in Italy the “Great Sea” and beyond in the late Bronze early Iron Age, it was a small city-state, among
compared to central and western Europe. Age and Iron Age. many culturally and politically similar Etruscan
During the late Neolithic and Copper Age, We collected data from 11 Iron Age individ- and Latin neighbors (24–26). Their contact
there is a small, gradual rebound of WHG an- uals dating from 900 to 200 BCE (including with Greek and Phoenician-Punic colonies is
cestry (Fig. 2B and fig. S24), mirroring findings the Republican period). This group shows a evident in the incorporation of materials not
from ancient DNA studies of other European clear ancestry shift from the Copper Age, in- available locally, such as ivory, amber, and
populations from these periods (10, 13, 18, 20). terpreted by ADMIXTURE as the addition of ostrich eggshell, and design motifs such as
This may reflect admixture with communities a Steppe-related ancestry component and an lions, sphinxes, and palmettes, into Etruscan
that had high levels of WHG ancestry persist- increase in the Neolithic Iranian component art and culture (3, 6).
Prehistoric
WHG Mesolithic
Western Population Anatolia
+/- 2SD(PC) Neolithic
Hunter- Iran
-0.10 Gatherer Copper Age
Steppe Iron Age &
Morocco Republic
Lithuanian
Steppe
Finnish Eneolithic
-0.05 Icelandic
Basque Russian Imperial
N.Spanish
S.French English Ukrainian Rome
French
Croation
Spanish
Sardinian N
N.Italian
PC1
Tuscan
Historic
Greek
0
an
C.Italian Chechen
S.Italiann Late
Yemenite Jewish
Morocco Present
Hunter-Gatherer (C.Italian)
0.10
0.05 0 -0.05 0 0.5 1 Time
PC2 Proportion Period
Fig. 2. Overview of the genetic structure of 127 ancient individuals temporal clusters. The colored labels indicate five source populations
from central Italy. (A) Individuals reported here (colored points) projected used for supervised ADMIXTURE. (B) Supervised ADMIXTURE analysis
onto a principal component space defined by modern-day individuals. performed with Western hunter-gatherer (WHG), Neolithic Anatolian,
Crosses represent variation (±2 SDs) of published ancient (black) and Neolithic Iranian, Eneolithic Steppe, and Morocco hunter-gatherer
modern (gray) populations. Black circles and arrows highlight three major (Iberomaurusian) as the source populations (k = 5).
The Iron Age individuals exhibit highly var- differentiation between the Etruscans and continued for much of the next 300 years,
iable ancestries, hinting at multiple sources Latins in allele sharing with any preceding reaching as far as Britannia, Morocco, Egypt,
of migration into the region during this period or contemporaneous population (|Z-score|<2), and Assyria. Rome itself had a population of
(Figs. 2A and 3B). Although we were able to although the power to detect subtle genetic over 1 million people, and it is estimated that
model eight of the 11 individuals as two-way differentiation is limited by the small sam- the empire had a population of between 50
mixtures of Copper Age central Italians and ple size. and 90 million (1). The empire facilitated the
a Steppe-related population (~24 to 38%) using In contrast to prehistoric individuals, the movement and interaction of people through
qpAdm, this model was rejected for the other Iron Age individuals genetically resemble mod- trade networks, new road infrastructure, military
three individuals (p < 0.001; table S16). Instead, ern European and Mediterranean individuals, campaigns, and slavery. Beyond the boundaries
two individuals from Latin sites (R437 and and display diverse ancestries as central Italy of the empire, Rome engaged in long-distance
R850) can be modeled as a mixture between becomes increasingly connected to distant com- trade with northern Europe, sub-Saharan
local people and an ancient Near Eastern munities through new networks of trade, colo- Africa, the Indian subcontinent, and across Asia
population (best approximated by Bronze Age nization, and conflict (3, 6). (1–3, 16). Although these contacts have been
Armenian or Iron Age Anatolian; tables S17 well documented, little is known about the
and S18). An Etruscan individual (R475) car- Imperial Rome and the expanding empire genetic impacts.
ries significant African ancestry identified During the Republican (509 to 27 BCE) and During the Imperial period (n = 48 indi-
by f-statistics (|Z-score|>3; fig. S23) and can Imperial (27 BCE to 300 CE) periods, Rome viduals), the most prominent trend is an an-
be modeled with ~53% ancestry from Late grew from a city-state on the Tiber river into an cestry shift toward the eastern Mediterranean
Neolithic Moroccan (table S19). Together these empire that spanned the entire Mediterranean and with very few individuals of primarily
results suggest substantial genetic heteroge- and extended onto all three surrounding con- western European ancestry (Fig. 3C). The dis-
neity within the Etruscan (n = 3 individuals) tinents (3, 6). Rome’s overseas expansion began tribution of Imperial Romans in PCA largely
and Latin (n = 6) groups. However, using during the Punic Wars (264 to 146 BCE) against overlaps with modern Mediterranean and Near
f-statistics, we did not find significant genetic Carthage in present-day Tunisia (27). This growth Eastern populations, such as Greek, Maltese,
A Copper Age (3500 BCE - 2300 BCE) D Late Antiquity (300 CE - 700 CE)
Finnish
Basque
Basque English Russian Germany
Late Roman R31
French R106
Spanish Ukrainian
N.Italian
Sardinian
S.Italian Greek Rome R104
Cypriot Iranian
Palestinian Syrian
PC1 Moroccan Jordanian 405 CE
PC2 Egyptian Western Roman Empire
B Iron Age & Roman Republic (900 BCE - 27 BCE) E Medieval & Early Modern (700 CE - 1800 CE)
Sweden LateLithuania
Antiquity
Viking
Denmark LBA Denmark BA England Germany
NE IberiaRoman Early Medieval
Hungary IA Antiquity R1286
Hungary
Moldova Lombard
Scythian
R475
R64
R37 R116
R80
R132
117 CE 2000 CE
Roman Empire Italy
Fig. 3. Ancestry shifts of the Roman population during the historic era. political body encompassing Rome at the date specified at the bottom,
(A to F) In each panel, the PCA (left) shows reported individuals (red points); with the blue arrow indicating the approximate direction of gene flow.
a bold ellipse describes variation across individuals in this time period, whereas No source provides an adequate fit for the Imperial Roman population
fainter ellipses are from preceding panels (multivariate t-distribution at a (C). Individuals identified as outliers by an f4 test are labeled with their
0.80 confidence level). In blue are potential incoming sources identified by sample IDs (table S27). Present-day populations are represented by gray
qpAdm modeling. The map (right) illustrates the territorial expanse of the points, with labels shown in (A).
Cypriot, and Syrian (Figs. 2A and 3C). This shift tions that have not yet been identified or fall into five distinct clusters (Fig. 4A). Notably,
is accompanied by a further increase in the studied. only 2 out of 48 Imperial-era individuals fall in
Neolithic Iranian component in ADMIXTURE Although the data show a shift in the an- the European cluster (C7) to which 8 out of
(Fig. 2B) and is supported by f-statistics (tables cestry averaged across all Imperial individuals 11 Iron Age individuals belong. Instead, two-
S20 and S21): compared to Iron Age individ- (referred to as “average ancestry” henceforth) thirds of Imperial individuals (31 out of 48)
uals, the Imperial population shares more toward eastern populations, the PCA results belong to two major clusters (C5 and C6) that
alleles with early Bronze Age Jordanians ( f4 also suggest variation in ancestry within the overlap in PCA with central and eastern Medi-
statistics Z-score = 4.2) and shows significant population. To further characterize this, we terranean populations, such as those from
introgression signals in admixture f3 for this assessed haplotype sharing using Chromo- southern and central Italy, Greece, Cyprus,
population, as well as for Bronze Age Lebanese Painter (11), a method more sensitive than allele and Malta (Fig. 4B). An additional quarter (13
and Iron Age Iranians (Z-score < −3.4). frequency–based approaches such as PCA. Spe- out of 48) of the sampled Imperial Romans
We attempted to fit the Imperial population cifically, we measured the genetic affinity be- form a cluster (C4) defined by high amounts
as a simple two-way combination of the pre- tween each ancient Italian individual and a set of haplotype sharing with Levantine and Near
ceding Iron Age population and another popu- of modern Eurasian and North African pop- Eastern populations, whereas no pre-Imperial
lation, either ancient or modern, using qpAdm. ulations by the total length of the haplotype individuals appear in this cluster (Fig. 4AC). In
Some populations producing relatively better segments shared between them (Fig. 4A) (7). PCA, some of the individuals in this cluster
fits come from eastern Mediterranean regions We clustered ancient individuals by their relative also project close to four contemporaneous
such as Cyprus, Anatolia, and the Levant (table haplotype sharing with modern populations individuals from Lebanon (240 to 630 CE)
S22). However, none of the tested two-way and then labeled the resulting clusters by pro- (fig. S18) (28). In addition, two individuals (R80
models provides a good, robust fit to the data, ximity to modern populations in PCA (Fig. 4B). and R132) belong to a cluster featuring high
suggesting that this was a complex mixture ChromoPainter analysis reveals diverse ances- haplotype sharing with North African popula-
event, potentially including source popula- tries among Imperial individuals (n = 48), who tions (C4) and can be modeled with 30 to 50%
North African ancestry in explicit modeling influence from the eastern Mediterranean than were commonly from the east (29). Temples
with qpAdm (table S28). elsewhere in the Empire. and shrines to Greek, Phrygian, Syrian, and
The shift in average ancestry and increase in Supporting this, there is evidence for the Egyptian gods were also common, and the
complexity in the genetic composition follow long-term settlement of people from the east earliest known synagogue in Europe was estab-
the empire’s territorial expansion to encircle in Rome. The most common language for lished in the Roman port-town of Ostia (3, 16).
the entire Mediterranean (3). This connected inscriptions, after Latin, was Greek; other There is also well-documented evidence for
Rome with people and cultures across the languages, such as Aramaic and Hebrew, were connections between Rome and the west. For
Mediterranean in unprecedented ways; how- also used. Additionally, birthplaces recorded example, slaves were brought back to Rome from
ever, our data show considerably more genetic in burial inscriptions indicate that immigrants these regions following imperial expansions,
A Haplotype sharing between modern populations and ancient individuals Proportion 0.05
0.04
High
Haplotype 0.03
Newly reported ancient Italian and Roman individuals Sharing 0.02 Low
Sardinia Sardinian
(High Neolithic Spanish
Farmer ancestry) N. Italian
C. Italian
Southern Bulgarian
Europe & Romanian
Mediterranean Greek
S. Italian
Basque
Central & British
Northern Norwegian
R8
R4
R3
R11
R3
R17
R1
50
37
1
04
6
Iron & Republic
Imperial Rome Ancestry C1 C2 C3 C4 C5 C6 C7
Late Antiquity Cluster Near
Medieval & WHG Sardinian/ North
Neolithic African Eastern Eastern Mediterranean Mediterranean European
Early Modern
Yemenite Jewish
Medieval &
Morocco Iberomaurusian
(Hunter-Gatherer) Early 40% 60%
Modern
PC2
Fig. 4. Haplotype sharing between ancient Italian individuals and present-day with their sample IDs. Annotations beneath the heatmap denote the
population reveals fine population genetic structure. (A) Total length of time period for each individual and an identifier for the ancestry cluster.
haplotype segments shared between present-day populations (rows) and (B) PCA with study individuals (points) colored on the basis of their cluster
reported study individuals (columns) (fig. S22). K-means clustering was membership in (A). (C) A mosaic plot showing the haplotype cluster
performed on rows and columns. Individuals mentioned in the text are labeled membership [defined in (A)] for each time period (rows).
such as Scipio Africanus’s victory over Carthage from a late Imperial period individual from (such as belts, seals, and jewelry) and also as a
and Julius Caesar’s conquest of Gaul (1, 3, 16). Bavaria or modern Basque individuals (table burial space. Five of the seven individuals from
Rome also received large amounts of trade S24). The precise identity of the source pop- this site are classified into the European cluster
goods from the western Mediterranean, such ulations and the admixture fractions should (C7) (Fig. 4 and fig. S17) and can be modeled as
as wine, garum, and olive oil from Gaul and not be interpreted literally, given the simpli- a mixture of the preceding Roman Imperial
Iberia; and grain, salt, and Tyrian purple dye fied admixture model assumed and the lack population and individuals from the Lombard-
from western North Africa (2, 3, 16, 30). Un- of data for most contemporaneous ancient associated cemeteries in Collegno and Hungary
expectedly, few Imperial individuals (n = 2) populations (7). This ancestry shift is also re- (table S28).
have strong genetic affinities to western flected in ChromoPainter results by the drastic
Mediterranean populations, suggesting rela- shrinkage of the Near Eastern cluster (C4), The Medieval period and increasing ties
tively limited immigration from the western maintenance of the two Mediterranean clusters to Europe
provinces. (C5 and C6), and marked expansion of the In the Medieval and early modern periods
One possible explanation for the predomi- European cluster (C7) (Fig. 4C). (n = 28 individuals), we observe an ancestry
nance of gene flow from the east into Rome is This shift may have arisen from reduced shift toward central and northern Europe in
the higher population density in the eastern contacts with the eastern Mediterranean, PCA (Fig. 3E), as well as a further increase in
Mediterranean than the west. Historians have increased gene flow from Europe, or both, the European cluster (C7) and loss of the Near
suggested that the large population size and facilitated by a drastic reduction in Rome’s Eastern and eastern Mediterranean clusters
the presence of megacities, such as Athens, population in this period to less than 100,000 (C4 and C5) in ChromoPainter (Fig. 4C). The
Antioch, and Alexandria, may have driven a individuals, due to conflicts and epidemics Medieval population is roughly centered on
net flow of people from east to west during (1, 3). After the move of the capital and the modern-day central Italians (Fig. 3F). It can
Rome’s position as a genetic crossroads of Shaped the Modern World (Princeton Univ. Press, Princeton, comments and discussions; L. Vitousek for assistance with Fig. 1;
peoples from Europe and the Mediterranean. N.J., 2007). and the Chan Zuckerberg Biohub for sequencing. Funding: This
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