What Ancient DNA Studies Tell Us About Human Infection?

What ancient DNA studies tell us about human infection?

Eske Willerslev Prince Philip Professor, University of Cambridge, UK Lundbeck Foundation Professor, Copenhagen University, Denmark ESCMID eLibrary © by author GLOBAL HUMAN POPULATION MOVEMENTS THROUGH TIME

CA: Central Anatolia; FC: Fertile Crescent; IP: Iberian Peninsula; ESCMID eLibraryPCS: Pontic–Caspian steppe. © by author THE INTERNATIONAL WEEKLY JOURNAL OF SCIENCE

Early human expansions revealed in 787 genome sequences PAGES XXX, 201, 207 & 238 THE DNA OF ANCIENT MIGRATIONS

GENETIC DISEASES PERSONALIZED MEDICINE PLANETARY SCIENCE NATURE.COM/NATURE 13 October 2016 £10 A KIND ALL GENOMES CHANGING FACE Vol. 538, No. 7624 OF LIVING MATTER OF THE MOON The ‘lethal mutations’ Bias towards a ‘European’ NASA’s orbiter measures the that pose no threat genomics must be corrected contemporary cratering rate ESCMID eLibraryPAGE 154 PAGE 161 PAGE 215 © by author ESCMID eLibrary © by author ESCMID eLibrary © by author ESCMID eLibrary © by author IDENTIFYING GENETIC VARIANTS UNDER SELECTION (CHANGE IN METABOLISM)

➔ ESCMID eLibrary © by author Population decline of farmers

ESCMIDShennan et al., Nat. Comm.eLibrary 2013 © by author Pontic steppes

Allentoft et al. Nature (2015)

Early Bronze Age ESCMID5,000 years BP eLibrary © by author INDO-EUROPEAN LANGUAGES

Ca. 42% of todays human population (3.2 billion) speaks an ESCMIDIndo-European language as a first languageeLibrary © by author COMPETING MODELS

Anatolian hypothesis Out-Of-India hypothesis

Armenian Hypothesis Steppe hypothesis

ESCMID eLibrary © by author EUROPE THROUGH TIME

Allentoft et al. Nature (2015) ESCMID eLibrary © by author BOTAI, OKONEVO: DOMESTICATION OF THE HORSE c. 5500 BP

ESCMID eLibrary © by author ESCMID eLibrary © by author Damgaard et al. Science (2018)

ESCMID eLibrary © by author THE ANATOLIAN (HITTITE) “PROBLEM”

• Earliest-attested of the Indo-European languages split in early Bronze Age ~5000 BP

• Oldest traces through Assyrian texts ~4000 BP and later through Hittite cuneiform ~3600 BP

• No genomic evidence of migration from the steppe to Anatolia ESCMID eLibraryDamgaard et al. Science (2018) © by author Allentoft et al. Nature (2015)

Mid-to-late Bronze Age 4,100-3,200 years BP ESCMID eLibrary © by author THE DISPERSAL OF INDO-IRANIAN LANGUAGES TO SOUTH ASIA

ESCMID eLibraryDamgaard et al. Science (2018) © by author ESCMID eLibrary © by author THE ADVENT MOUNTED WARRIORS c. 3200 BP

Where did the Scythian confederation emerge?

A Black Sea origin contrasted a Southern Siberian?

ESCMID eLibraryDamgaard et al. Nature (2018) © by author THE EMERGENCE OF HUNNIC TRADITION c. 2200 BP

Damgaard et al. Nature (2018) ESCMID eLibrary © by author THE ADVENT OF TURKIC LANGUAGES

> 200 000 000 people

ESCMID eLibrary © by author MEDIEVAL STEPPES: SHIFTING KHANATES

Jochi Khan’s Golden Horde

Damgaard et al. Nature (2018) ESCMID eLibrary © by author ESCMID eLibrary © by author Three Pandemics

• 1st, Plague of Justinian, 541-544 AD (541-750 AD) • Depopulation of 50 to 60% (other diseases as well) - collapse of the Byzantine Empire • 2nd, Black Death, 1347-1351 AD (until 18th century) • Black Death epidemic killed 30 to 50% of the European population • Economic, politic and demographic impact • 3rd pandemic (1855 - mid 20th century) • Started in China (Yunnan), spread via ships world-wide (1890ies) ESCMID~12 mill deaths eLibrary © by author Yersinia pestis and plague

• Plague is caused by gram-negative bacteria Yersinia pestis: 4.5Mb + 3 plasmids • Highly similar to ancestor Y. pseudotuberculosis, main differences: • Two extra plasmids pMT1 and pPCP1 • Pseudogenes: Loss of function mutations in many genes ESCMID• Key virulence genes: ymt (pMT1) eLibrary and pla (pPCP1) © by author Plague life-cycle

• Host: Rodents/animals, fleas, human

• Flea bite infested animal, Y. pestis biofilm -> blockage of flea gut -> very hungry flea -> more bites -> new infections

• Flea bite -> bubonic plague (buboes) or septicemic plague (blood) -> pneumonic plague (may also spread via droplets)

• Mortality of the different plague infections:

• Bubonic 40-60% (~10%), Septicemic 99-100% (30-50%), Pneumonic 99- 100% ESCMID eLibrary © by author Plague is still around today

A re-emerging disease + class A bioterrorism agent! Yosemite National Park ESCMID eLibraryUSA - 2017 © by author Authentic?

1. Not contamination in lab (7 of 101 samples) + empty negative extraction controls

2. Ancient reads: Highly fragmented + typical DNA damage patterns

3. Correlated DNA damage of Y. pestis and Human DNA

4. Higher read affinity for Y. pestis compared to Y. pseudotuberculosis

5. Naïve Bayesian classifier classifies samples as Y. pestis ESCMID6. Reads evenly distributed across eLibrary genome as expected © by author 2. Ancient DNA damage

5’ 3’

C->T

C->T G->A

ESCMIDStart of reads End of reads eLibrarySimilar damage for plasmids! © by author 3. Correlated DNA Decay

ESCMID eLibrary © by author ESCMID eLibrary © by author Virulence: ymt

Phospholipase D - required for survival in flea gut

All samples except youngest (900 BC) missing 19kb region

Statistical sign. (wilcox) ymt

ymt acquired through horizontal gene transfer (transposons) ESCMIDymt in >97% modern samples eLibrary © by author ESCMID eLibrary © by author Divergence estimates

pseudotuberculosis / pestis split MRCA for all known pestis strains

ESCMID eLibrary © by author JUSTINIAN PLAGUE (541-542)

Estimated death 25 Mill. c. 13% of world population

ESCMIDDamgaard et al. Science (2018) eLibrary © by author PATOGENES

ESCMID eLibrary © by author ESCMID eLibrary © by author ESCMID eLibrary © by author ESCMID eLibrary © by author ESCMID eLibrary © by author ESCMID eLibrary © by author ESCMID eLibrary © by author ESCMID eLibrary © by author ESCMID eLibrary © by author ESCMID eLibrary © by author ESCMID eLibrary © by author The three oldest ancient genotype A sequences lack a 6 nucleotide insertion at the C-terminus of the core gene, that ESCMIDis found in all modern genotype A sequences eLibrary © by author ESCMID eLibrary © by author ESCMID eLibrary © by author ESCMID eLibrary © by author ACKNOWLEDGEMENTS

Present and former group members and associates, Centre for GeoGenetics

M. Raghavan M. Allentoft A. S-Orlando M. Ilardo F. Demeter E. Lorenzen

M. Rasmussen M. Pedersen A-S Malaspinas H. MColl P. Damgaard A. Pohaska

National and international collaborators All authors on the papers

St. Johns College, Cambridge University of Copenhagen University of Cambridge R. Nielsen K. Kristiansen T. Jones The Wellcome Trust Sanger Institute S. Rasmussen L. Orlando D. Meltzer

Main economic support The Danish National Research Foundation The Lundbeck Foundation Novo Nordic Foundation M. Sikora F. Racimo B. Muehlemann Carlsberg Foundation D. Smith M. Lahr R. Foley Wellcome Trust ESCMID KU2016eLibrary © by author FUTURE

• Blitzkrieg: humans cause megafauna extinctions within 1000 years after contact (incl. hyperdisease)

• Climate: climatic change cause megafauna extinctions

ESCMID eLibrary © by author ESCMID eLibrary © by author ESCMID eLibrary © by author ESCMID eLibrary © by author ESCMID eLibrary © by author RECENT REVIEWS

ESCMIDPericúes FuegianseLibrarySurui © by author ESCMID eLibrary © by author ESCMID eLibrary © by author MEGAFAUNAL EXTINCTIONS

• Blitzkrieg: humans cause megafauna extinctions within 1000 years after contact (incl. hyperdisease)

• Climate: climatic change cause megafauna extinctions

• Substitution rate orders of magnitude lower than observed from modern data alone. • B19 was thought to have an mrca in the 1800s, which has now been dated to 12.600 years ago. • HBV is now dated to 8.6 to 17.8 thousand years ago, depending on the evolutionary model vs 1500ya. ESCMID eLibrary © by author ESCMID eLibrary © by author EARLY PEOPLING OF THE AMERICAS

Bering land bridge theory

Ice free corridor Pacific coastal route Solutrean Theory

First entrance: Clovis (13-12,6 ka cal yr BP) versus pre-Clovis (older than 13 ka cal yr BP)

Kennewick c. 9.000 years old ESCMID eLibrary © by author ESCMID eLibrary © by author THE INTERNATIONAL WEEKLY JOURNAL OF SCIENCE

Early human expansions revealed in 787 genome sequences PAGES XXX, 201, 207 & 238 THE DNA OF ANCIENT MIGRATIONS

Andaman Islanders similar Austro-asiatic rice farmers from China Kradai speakers from China ESCMIDto Hòabìnhians and Austro-nesians from TaiwaneLibrary © by author ESCMID eLibrary © by author ESCMID eLibrary © by author Pedersen et al. Royal . Phil. Trans. B. (2015) ESCMID eLibrary © by author Factors known to be associated with human phenotype

Y. pseudotuberculosis Modern Y. pestis ?

Fecal/oral transmission Flea-borne transmission (Mild pathogenic) (Pneumonic + bubonic) ESCMID eLibrary © by author Plague evolution

Y. pseudotuberculosis Bronze Age Y. pestis Modern Y. pestis

Fecal/oral transmission Respiratory transmission Flea-borne transmission (Mild pathogenic) (Pneumonic plague) (Pneumonic + bubonic) ESCMID53,000 BC 3,700 BC eLibrary3,500 BC / 1,000 BC © by author ESCMID eLibrary © by author ESCMID eLibrary © by author