1 2 3 4 5

6 7 8 9 10 11 12

13 14 15 16 17 18

19 20 21 22 X Y

Weinheritonecopyofeachchromosomalpairfromourmotherandfather1-22Autosomes23rdpair:SexChromosomes

OurGenome:6BillionNucleoBdes/46chromosomes/mtDNA

Mitochondrial DNA mtDNA (~16.5 Kb)

A single nucleotide polymorphism (SNP)– an alteration at a single site in the DNA– is the most frequent type of variation in the genome. Currently, over 100 million SNPs have been identified in the human genome.

DNA microarray technology (SNP array) is used to detect SNPs within a population. SNP arrays are able to detect millions of different SNPs on all chromosomes in hundreds of samples in a single experiment.

Genome-wideData:SingleNucleoBdePolymorphism(SNP)

Genome-wideData:RelaBonshipsamongPresent-DayPopulaBons

PCA Admixture

Dendrogamor

PopulaBonTree

Individual“Ancestry”ProporBons

AnatomicallyModernHumans:AfricanOriginandGlobalDiaspora

~60Kya~3Kya

Hunter-GathererDispersals

Did Neolithic farmers genetically replace Hunter-gatherers? •  9homelandsofagricultureandherding(10.5-4.5kya)•  FoodProducGonconfersenormousadvantagetofarmersoverhunter-gatherers

(Diamond&Bellwood2003)

TradiBonalView:2MajorExpansionsintoEurope

7kya

•  Firstanatomicallymodernhumans(AMH)fromAfrica~45,000yearsago

•  NeolithicFarmersfromtheNearEastbeginning7,000-10,000yearsago

45kya

Genome-wideDataSupportEuropeasaMixtureofTwoPopulaBons

Skoglund et al. (2012) Sikora et al. (2014)

ContemporarySamples

HgGHgR HgI

EuropeanYChromosomes:MajorHaplogroups

R1bclade:Mostcommonpaternal

lineageinW.Europe

HgR1b

M269

P311

M312

U106

L21

U152

SRY2627

U198

L23

P107L11

L49

*

**

*

L1

L48

M65

M153

M126

M160

L2L20

L4

M37

M222

P66

*

*

*

a

a

a

b

a

bc

c

d

1 1

3

3

4

4

5

*

1

1

2

2

Europe:TheHgR1bControversy

Traditionally believed to be of Paleolithic (Hunter-Gatherer) origin

•  Carried by >110 million European men

•  Increases in frequency from east to west

Concluded that Mesolithic hunter-gatherer Y chromosomes were nearly replaced by those of incoming farmers (driven by improved technology—farming)

HaplogroupR-M269ExpandedWithFarming

Balaresqueetal.(2010)

DatesofearlyNeolithicsites FrequencyofHgR-M269 STRdiversitywithinHgR-M269

ContemporarySamples

Busbyetal.(2012)Current distribution is result of population dispersal after the Neolithic expansion

HaplogroupR-M269ExpandedA&erFarming

Traditional view challenged

Indirectapproach§  ExaminepaZernsofgeneGcvariaGonin

contemporaryhumansandinferpast

Directapproach§  RecoverDNAsequencesfromancientmaterialand

compareacrossdifferentGmeframes

Abletoinferwhethercontemporarypeopledescendfromlong-terminhabitantsofaregion,orfrompeoplewhoarrivedfromelsewhere—replacingoradmixingwithpreviousinhabitants

ImportanceofAncientDNAinReconstrucBngEuropeanPopulaBonHistory

0

20

40

60

80

100

120

140

160

180

1 2 3

2013 2014 2015

Number of Ancient European DNA Samples

1

2

3

4

1 Cave 1 of Treilles at St-Jean et St Paul (Aveyron, France) 5 kya (end of Neolithic)

2 Abellaner Cave (Catalonia, Spain) 5 kya (Epicardial Culture; end of Neolithic)

2013: First Look at Ancient Y Chromosomes (n=32)

3 Derenburg Cave (Meerenstieg Germany) 7 kya (LBK)

4 Ötzi 5.3 kya

N=22

N=6

N=3

N=1

Ancient Graves from End of Neotlithic (7 to 5 Kya)

Catalonia

Aveyron

Meerens>eg

Ötzi

1

2

3

4 G2a (20) I2a (2)

G2a (5) E1b1b1 (1)

G2a3 (1) F*(xG,H,I,J,K) (2)

G2a4-L91

1 Cave 1 of Treilles at St-Jean et St Paul (Aveyron, France) 5 kya (end of Neolithic)

2 Abellaner Cave (Catalonia, Spain) 5 kya (Epicardial Culture; end of Neolithic)

2013: First Look at Ancient Y Chromosomes (n=32)

3 Derenburg Cave (Meerenstieg Germany) 7 kya (LBK)

4 Ötzi 5.3 kya

Early Farmers carry Hg G

HgR1bnotfoundinancientsamplesda:ngto~5Ky

1 hunter-gatherer (~8 kya)

7 hunter-gatherers (~8 kya)

1 farmer (~7 kya)

Complete Genomes from Nine Ancient Europeans Lazaridisetal.Nature(2014)

FirststudytofullysequencegenomesofNeolithicandMesolithicEuropeans

2014

24kyagenomefromMal'taSiberia

•  West European Hunter-Gatherer (WHG), based on an 8 kya genomes from Loschbour, Luxembourg, and Motala, Sweden. The WHG meta-population also includes a Mesolithic individual from the La Brana Cave in Spain.

•  Early European Farmer (EEF), based on a 7.5 kya genome from Stuttgart, Germany belonging to the Neolithic LBK culture. The EEF meta-population includes Oetzi the Iceman and a Neolithic Funnelbeaker farmer from Sweden.

•  Ancient North Eurasian (ANE), based on the 24 kya genome from Mal'ta Siberia. The ANE meta-population also includes the late Upper Paleolithic sample from Central Siberia called Afontova Gora-2 (AG2).

ThreeMainEuropeanAncestralComponents

WHG(indigenousEuropeans) 0-50%EEF(NearEasternorigin) 32-93%ANE(likeancientSiberians) 1-18%

3 Ancestral Components in Contemporary Europeans

•  EEF component increases toward the South—peaking at just over 80% among Sardinians

•  In contrast, WHG component increases toward the North—peaking in East Baltic region at ~50%.

•  ‘ANE’ ancestry is present in nearly all Europeans today—peaking in Estonians & Scots at ~20%

•  Importantly, ANE component is not found in either farmers or HGs from central and western Europe during the Neolithic FirstFarmersonlyamixtureof2sourcepopula:ons

N S

0"

10"

20"

30"

40"

50"

60"

70"

80"

90"

100"

Estonian"

Lithuanian"

Icelandic"

Sco<

sh"

Norwegian"

Belarusian"

Ukranian"

Orcadian"

English"

Czech"

Fren

ch"

CroaHa

n"

Hun

garian"

Basque

"

Fren

ch"(S)"

Bulgarian"

Spanish"(N)"

Bergam

o"

Tuscan"

Albanian"

Greek"

Spanish"

Sardinian"

Sicilian"

Maltese"

Ashkenazi"

ANE WHG

EEF

3.ANEancestrycomponententeredthebroaderEuropeangenepooladertheNeolithic

New View: Three Source Migration Model

2. Second major infusion of people comes with expansion of agriculture—also from the Levant—beginning ~8 kya

1.Anatomicallymodernhunter-gatherersfirstmigratedintoEurope~45kyafromAfricathroughtheLevant

EuropeanHunter-GatherersEarlyEuropeanFarmersAncientNorthEurasians

Connecting the Dots: What does new model of European ancestry based on autosomal DNA mean for the NRY?

•  WhichpopulaGon(s)carriedthemostcommoncontemporaryNRYhaplogroupsintoEuropeandwhen?

•  HowdoestheANEancestrycomponentseeninautosomalDNAcorrespondtotheNRY?

Mesolithic Hgs Contemporary Hgs

(~8kya)

(~8 kya)

All Five Mesolithic Y Chromosomes Belong to Haplogroup I Lazaridisetal.Nature(2014)

FirststudytoreportNRYhaplogroupsofMesolithicEuropeans

SupportshypothesisthatHgIwascommoninpre-agriculturalEuropeans.ThishaplogroupremainsthemaincandidateforEurope'sPaleolithicpaternalheritage.InteresGngly,threeoftheresultsfellintohaplogroupI2a1b,andnoneintothepresentlylocallymorecommonI1.

Loschbour1: I2a1b

Motala2: I*(xI1, I2a2,CTS1293) Motala3: I2a1b Motala9: I*(xI1) Motala12: I21ab

1

2

3

N=22

N=6

N=3

N=1

1 Cave 1 of Treilles at St-Jean et St Paul (Aveyron, France) 5kya (end of Neolithic)

2 Abellaner Cave (Catalonia, Spain) 5kya (Epicardial Culture; end of Neolithic)

2014: More Ancient Y Chromosomes

3 Derenburg Cave (Meerenstieg Germany) 7kya (LBK)

4 Ötzi Chalcolithic (5.3 kya)

5

5 Starčevo Culture and LBK sites from Carpathian Basin Hungary (7.6-7.0kya) (Neolithic)

N=14 6

7 Chalcolithic Bell Beaker Kromsdorf, Germany (4.6kya Copper Age)

N=2

7

6 Dolmen of La Pierre Fritte, France (4.8kya) (Neolithic)

N=4

8 N=2

8 Corded Ware Eulau, Germany (4.6kya)

9 Lichtenstein Cave, Dorste, Germany Urnfield (3.0kya Bronze Age)

9 N=14

10 Jagodno, Poland Chalcolithic (4.8kya, Copper Age)

N=2

11 11 Mesolithic Hunter-Gatherers Motala, Sweden (8kya)

4

12 Mesolithic Hunter-Gatherer Loschbour, Luxembourg (8.2-7.9kya)

N=1 12

13 Mesolithic Hunter-Gatherer, La Brana Valdelugueros, Spain (7.0kya)

13 N=1

14 N=1

14 Pitted Ware Culture Gotland, Sweden (Mesolithic 4.8-4.0kya)

15 Vinkovci and Vukovar Croatia Starčevo Culture (7.6kya) (LBK)

15 N=3

10 N=2

W. Hunter-Gatherer

Near Eastern Farmer

Copper-Bronze Age

1

2

3

5 6

7

2 I* 1 I2 1 I2a1b*

8

9

11 I2a2b 2 R1a1 1 R1b (M343)

10

11 11 Mesolithic Hunter-Gatherers Motala, Sweden (8kya)

4

12 Mesolithic Hunter-Gatherer Loschbour, Luxembourg (8.2-7.9kya)

12

13 Mesolithic Hunter-Gatherer, La Brana Valdelugueros, Spain (7.0kya)

13

14

14 Pitted Ware Culture Gotland, Sweden (Mesolithic 4.8-4.0kya)

15 Vinkovci and Vukovar Croaita Starčevo Culture (7.6kya) (LBK)

15 20 G2a 2 I2a

5 G2a 1 E1b1b1

1 G2a3 2 F*(xG,H,I,J,K)

G2a2b

2I2a

1C1a2

1 G 1 I or J?

2 R1b (M269, M343)

2 R1a

1I2a1b*

1I2a

1G23G2a4G2a2b2F*1I1I1

2G2a1I2a1

1 Cave 1 of Treilles at St-Jean et St Paul (Aveyron, France) 5kya (end of Neolithic)

2 Abellaner Cave (Catalonia, Spain) 5kya (Epicardial Culture; end of Neolithic)

3 Derenburg Cave (Meerenstieg Germany) 7kya (LBK)

4 Ötzi Chalcolithic (5.3 kya)

5 Starčevo Culture and LBK sites from Carpathian Basin Hungary (7.6-7.0kya) (Neolithic)

7 Chalcolithic Bell Beaker Kromsdorf, Germany (4.6kya Copper Age)

6 Dolmen of La Pierre Fritte, France (4.8kya) (Neolithic)

8 Corded Ware Eulau, Germany (4.6kya)

9 Lichtenstein Cave, Dorste, Germany Urnfield (3.0kya Bronze Age)

10 Jagodno, Poland Chalcolithic (4.8kya, Copper Age)

MesolithicHG

NeolithicFarmers

MetalAge

F 2C 1I1 1 1I*/I2 5 7 11G 37 1R1b 3R1a 4E 1

6 48 20

2014: More Ancient Y Chromosomes

1st R1b!

Mesolithic Neolithic Metal Present

Thousands of Years Ago 8 7 6 5 4 3 2 1 0

Ancient NRY Haplogroup Frequencies

N=6 N=48 N=20

IG

R1b

Who were the ANE and how did they make such a large contribution to the European Gene Pool?

•  Two laboratories published papers in the same issue of Nature in June of 2015- both reaching the same conclusion. Massive migrations from the Russian Steppe in the Bronze Age represent the third major source of genetic material found in Europeans today

•  They extracted genetic material from bones and teeth collected from across Europe and as far east as Lake Baikal in Siberia. The age of the bones spanned five millennia, from 8,000 to 2,900 Ya

•  To get the 170 samples, they had to test >700 samples for DNA quality. All of the samples that they ultimately used for analysis had a well-documented archaeological context with radio carbon dates

2015

low-coveragegenomesfrom101ancientEurasians

genome-widedatafrom69ancientEuropeans

DavidReich EskeWillerslev

Genomics Supports Steppe Contribution to Bronze Age Europe

HG component Farmer component Steppe component

WillerslevTeam

~8Kya ~3Kya ~5kya ~2.8kya

BronzeAgeSteppeNeolithicfarmers

BronzeAgeEuropeans

MesolithicHG

•  Neolithic Europeans composed of HG and farmer mixture

•  Bronze Age Europeans have added ‘Pastoralist’ component suggested to derive from Yamnaya culture from the Pontic-Caspian steppe

•  Neolithic farmer component is absent in Yamnaya

Yamnaya

YamnayageneBccontribuBontoNeolithicEuropeanGenePoolReichTeam

WesternEuropeanHunter-Gatherer

EarlyNeolithicFarmer

YamnayaPastoralist

Ancien

tMod

ern

All European populations considered a three-way mixture of WHG, Neolithic Farmer, and Yamnaya Yamnaya related ancestry is lower in southern Europe and higher in northern Europe Supports steppe as a source for genes now found in Europe, with massive migration ~4,500 years ago

New View: Steppe Contribution to Europe

2. Second major infusion of people comes with expansion of agriculture—also from the Levant

1.Anatomicallymodernhunter-gatherersfirstmigratedintoEurope~45kyafromAfricathroughtheLevant

EuropeanHunter-GatherersEarlyEuropeanFarmersBronzeAgeSteppePastoralists

3.SteppecomponententeredbroaderEuropeangenepooladerNeolithic

After 7,000 years ago

Connecting the Dots: What do the new Autosomal data mean for the NRY (and mtDNA)?

•  WhichpopulaGon(s)carriedthemostcommoncontemporaryNRYhaplogroupsintoEuropeandwhen?

•  HowdoestheYamnayaancestrycomponentseeninautosomalDNAcorrespondtotheNRYandmtDNA?

Mesolithic Hgs Contemporary Hgs

•  In Europe, only a single R1b individual found before Late Neolithic

•  By contrast, R1a and R1b found in 60% of Bronze Age Europeans

•  Highest frequency of R1b found in Copper Age Yamnaya of Russian Steppe - same population that contributed autosomal Steppe component to Bronze Age Europeans

•  Combined results suggest that R1b spread into central and western Europe from the steppe after 5 kya

Origin of European R1b

Europe

Yamnaya

Asia & Russian Steppe

Bronze Age

R1b

R1b

R1a

G2a I/I2

I/I2 I/I2

R1b

R1a

C

I/I2

Cassidyetal.(2016)

Neolithic and Bronze Age Genes Established Ireland by 4 kya

NeolithicIrish

woman

3IrishBronzeAgemen

All3BronzeAgemencarriedHgR1bYchromosomes

Hunter-gatherer(WHG)

EarlyFarmer(EEF)

MetalAge(Steppe)

Combined evidence supports hypothesis that the current distribution of Hg R1b lineages in western Europe is the result of major population movements during the Metal Ages. Populations carrying R1b chromosomes appear to have nearly displaced western European Neolithic Y chromosomes What conferred advantage to post-Neolithic Steppe invaders?

AncientDNASupportsRecentSpreadofHgR1bacrosswesternEurope

TheBronzeAge:firstuseofmetalspecificallytocreateweapons.Thesword,spearandshieldwereallinventedinthisperiod(warrioridenGtybecameastandardpartofdailylife)

Post-NeolithicAdvantage:MetalWeapons?

TheIronAge:Firsttruemass-producGonofmetaltoolsandweapons.RevoluGonizesbothagricultureandwarfare.

3200to3000ya:Celtsmostdominantiron-agewarriors.RangingoverEurope,fromtheBriGshIslestoHungary,theCeltsforgedtoughswordsmadeofiron.

“By about 3300 years ago people across Europe were raging war in different ways. Thrusting weapons like the rapier were preplaced by edged weapons for slashing. Heavily armed horsemen, the warrior elites, used these weapons together with spears in group combat. Strong regional identities are reflected in styles of arms and armour at this time. The many hoards of weapons found provide graphic evidence of the armed struggle for wealth, property and power. Some of these are the personal hoards of arms possibly buried as offerings to the gods.” British Museum

Personal set of bronze arms (Late Bronze Age)

Indo-EuropeanInvasionsfromSteppes

Cultural / Technological Innovations Metal weapons, chariots, horses, domesticated animals, less reliance on agriculture/ more on dairy (milk)

SpreadofIELanguages SpreadofChariot

ExpansionsofIndo-EuropeanLanguages

EasternArmenian

AdapazarModernGreek

Nepali

Assamese

Oriya

BengaliBihariHindiPunjabiLahndaUrdu

Marathi

GujaraGSinhaleseRom

aniKashm

iriGerm

anSw

issGerman

Luxembourgish

EnglishNorw

egianFaroeseIcelandicRom

anianItalianLadinFriulianRom

anshProvencalWalloon

FrenchCatalanSpanishPortugueseCagliariNuorese

ScotsGaelicIrish

ClassicalArmenian

AncientGreek

VedicSanskrit

Avestan

OldChurchSlavic

Hilte

TocharianBGothic

OldHighGerm

an

OldEnglish

OldWestNorse

LaGn

OldIrish

5000

4000

3000

2000

1000

today

YearsAgo

TreeofIndo-Europeanlanguages

Supportshypothesisthatrootlanguage,proto-Indo-European,originatedinsteppesofeasternEurope

Afanasevoculture(5300YBP)

Balto-SlavicCulture(2600YBP)

CordedWareCulture(4900—4350YPB).

Maykopculture(5700—5000YPB)

HilteEmpire(3321–3322YPB)

CelGcDistribuGon:CoreHallstaZterritory,by2600YBPMaximalCelGcexpansion,by2275YBPLusitanianareaofIberiaCelGcspeakersintoEarlyModernperiodCelGclanguagesspokentoday

EarlyVedicPeriod(3700-3100YBP).

TarimBasin:easternremnantofIndo-Aryans(2500YBP).

Andronovo/Indo-Iraniancultures(3800–3400YBP)

ExpansionofGermanictribes:SeZlementsbefore2750NewseZlementsby2500NewseZlementsby2250NewseZlementsby2000

ExpansionsofMetalAgeCulture

BronzeAgeYchromosomesinEuropeans

>25% ancY Slovakia Switzerland Portugal Belgium Spain Austria

FtDNAdatabase

MET

EEF WHG

Loschbour Stuttgart Motala Motala MA1

Sardinian Spanish Bulgarian Greek Albanian Kalash

Basque French_South French Croatian Hungarian Icelandic Norwegian Orcadian Scottish Czech Enghlish Finnish Mordovian Russian Estonian Lithuanian Belorussian Ukranian Bedouin

Percentage Test European Hunter-gatherer Near Eastern Farmer Metal Age Invader

Thank you for listening!

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RuiHuMeaganPetersMichaelDavila