Ancient DNA signatures in modern breeds

Paolo Ajmone Marsan

Università Cattolica del S. Cuore, Piacenza,

Italy

paolo.ajmone@unicatt.it

One past revealed to us in many ways

No source is unbiased…..

Integration of disciplines

When combining records in a synthesis, their unique characteristics are to be considered:

-Makers of a certain style of pottery may have left no descendants…..

-Artifacts can move through trade, with no gene flow….

-Gene flow can occur across languages……..

- ………..

Records are independent reflextion of a single past but they need not all tell us the same thing!

Different strata of the past are accessible through the analysis of genetic diversity

• Phylogenetic relationship between species and the origin of the tree of life

• Prehistorical migrations

• Historical migrations

• Genealogical studies

• Paternity testing

• Individual identification

PAST

PRESENT

Since domestication

Domestic animalsmolecular genetics

DNA diversity

• Variation among modern individuals is shaped by cumulative past processes

• Extracting information on any one past period or events requires careful interpretation, to isolate it from previous and subsequent processes

• Neutral markers are perhaps the most representative records of the past, not biased by natural/human selection

Towards a strategy for the conservation of the genetic diversity of European cattle

European projectRESGEN EU project (PL98-118)RESGEN EU project (PL98-118)Towards a strategy for the conservation of genetic Towards a strategy for the conservation of genetic

diversity in European cattlediversity in European cattle

(www.androclus.vet.uu.nl/resgen/)(www.androclus.vet.uu.nl/resgen/)

Please, notice, no cellular phone

PiemonteseValdostana P.R.RendenaGrigia AlpinaPezzata Rossa It.Cabannina RomagnolaMucca PisanaCalvana ChianinaMaremmanaMarchigianaPodolicaCinisaraModicana

Jersey

Menorquina

Betizu

Normande

EringerEvolene

Jutland

HungarianGrey

Vestland Red Polled

Telemark

FinnishAyrshire

Limousine

Frisona

Bruna I.

29 Razze

606 individui

Piacenza

15 Italian breeds

Modicana

Cinisara

Podolica

Marchigiana

Maremmana

Chianina

CalvanaMucca Pisana

Romagnola

Piemontese

Valdostana P.R.Rendena

Grigia Alpina

Pezzata Rossa It.

Cabannina

AFLPAFLP

M10 0 1 1 1 1 0 0 1 0 0 0 0 0

M2

Binary matrix

A B C D E F G H I J K L M N

A B C D E F G H I J K L M N------------------------------------------------------------M1 0 0 1 1 1 1 0 0 1 0 0 0 0 0M2 1 0 1 0 1 1 0 1 0 1 0 1 1 0M3 …

1 0 1 0 1 1 0 1 0 1 0 1 1 0

Northern Europe

Southern Europe

Central Europe

Reynolds distance

Relationship among European breeds

iii

iii

ynolds yx

yxD

1

)( 2

21

Re

Neighbour Joining tree

Dimensions needed to represent genetic relationship/distance

Principal Components

PCOA1

PC

OA

2

-0,2

-0,15

-0,1

-0,05

0

0,05

0,1

0,15

-0,1 -0,05 0 0,05 0,1 0,15

It, FresianItalian Red Pied

Valdostana Red Pied

Cabannina

It. Limousine

RendenaPiedmontese

Mucca Pisana

Podolica

Maremmana

Cinisara

It. BrownModicana

MarchigianaRomagnola

Chianina

Calvana

Alpine Grey

Relationship among Italian breeds

ALPINE PODOLIAN

NORTH CENTRE-SOUTH

Microsatellites typingMultidimensional analysis

D Laloë, K Goudarzi

1st dimension

2nd d

ime

ns

ion

Mitochondrial DNA

• about 1% of total DNA (15-20 kb, 37 genes)

•Haploid and maternally inherited

•No recombination

•Higher mutation rate compared to nuclear DNA

Mitochondrial DNA

Constructing a median network from SSR haplotypes

Domestication centre

Bos taurus mtDNA HVRI region diversity

Reduced Median Networks

Troy et al., Nature, 2000

Breeds analysed 11 Italian Breeds

analysed(N=164)

Modicana

Cinisara

Podolica

Maremmana

Chianina

Calvana

RomagnolaPiedmontese

RendenaItalian red pied

Cabannina

N=47

N=66

N=51

Centre Europe Near EastItaly

Pairwise differences in sequences

Pairwise differences in constant and expanding populations

Mismatch distribution of populations expanded at different times

Center

South

North

Italian bovines

Centre Europe Near EastItaly

MPD1.9±1.1

MPD2.0±1.4

MPD1.5±1.2

MPD3.5±1.8

MPD4.0±2.0

MPD3.6±1.9

Central Italian breeds seem to share a differenthistory compared to that of other Italian breeds

Do these breeds have anything in common?

Chianina

•The largest bovine in the world.

•The bull "Donetto" at the age of 8 reached 1.780 Kg!Calvana

Maremmana

Cabannina

PCOA1

PC

OA

2

-0,2

-0,15

-0,1

-0,05

0

0,05

0,1

0,15

-0,1 -0,05 0 0,05 0,1 0,15

It, FresianItalian Red Pied

Valdostana Red Pied

Cabannina

It. Limousine

RendenaPiedmontese

Mucca Pisana

Podolica

Maremmana

Cinisara

It. BrownModicana

MarchigianaRomagnola

Chianina

Calvana

Alpine Grey

Relationship among Italian breeds

ALPINE PODOLIAN

NORTH CENTRE-SOUTH

• Romans called the elephants taken by Hannibal “bulls from Lucania” (about 215 B.C.).

•L. IUNIUS MODERATUS COLUMELLA (I sec A.C.)

De Re Rustica - Liber VI

“[…] l’Umbria ne produce di grandissimi e bianchi (Umbria produces huge and white (bovines)); ma anche di rossicci, non meno pregiati sia come indole sia come struttura fisica. L'Etruria ed il Lazio li hanno tarchiati, ma forti nel lavoro. Gli Appennini danno bovini robustissimi […]”

Historical information

•In VI – VII sec. B.C. Numa Pompilio (Roman king) introduced in Rome the use of sacrifying to gods huge white bovines used in field working

Small size of domestic bovines

Bos primigenius: 2,20 – 2,30 m

Iron age: 1,10 – 1,20 m

Is there any link with the onset of Etruscan civilisation?

Etruscan had a powerful military and trading fleet and reached the Aegean

sea and Anatolia

Strabone, citing Eforo, reports that Greeks that were founding Naxos (734 B.C.) were afraid of

Etruscan attacks.

Etruscan navy controlled trade in west Mediterranean

630 – 500 a.C.

Distribution of etruscan ceramics with red figures 350 – 270 B.C.

Cultural exchange with Greeks

•Wine making

•Olive pressing to obtain olive oil

•Crop rotation

•Metallurgy

•Ceramics

•Crafting

The Oriental period (VIII - VI sec. a.C.)

Tauromachia

•What about genetics?

•History -> Herodotus

•Linguistics -> European or Semitic?

•Archaeology -> different opinions

On-going debate on the origin of this civilisation

Local development, with Eastern influences or Eastern Mediterranean provenience?

Genetic data from modern populations

- Francalacci et al. (1996 Am. J. Phys. Anthropol. 100, 443-460.) modern mtDNA sequences suggested the presence in Tuscany of an ancient European mtDNA diversity component, subsequently enriched by migrational waves, possibly from the Middle East.

- Cavalli-Sforza and coauthors assayed nuclear markers in modern humans living in Tuscany (1994 History and geography of

human genes - Princeton University Press, Princeton, NY, USA). They detected a genetic discontinuity in these when compared to nearby Italian populations, explained either as an immigration from elsewhere or by the ancient expansion of a local isolated population.

mtDNA analysis from Etruscan remains

(Vernesi et al., 2001 Proc. Natl. Acad. Sci. USA 98, 13460-13463.

Most related modern population

• modern Tuscans

•Anatolia populations

Gene flow with

Extended analyses

Dataset of cattle mitochondrial sequences-237 Bos taurus mtDNA sequences from animals reared in Continental Europe, Anatolia, Near East

and Africa. Total bovine mtDNA dataset comprising 401 sequences.

Dataset of human mitochondrial sequences- 1426 sequences of Homo sapiens mtDNA HVRI

region Sequences of populations living in the same regions of cattle sampling were retrieved

Loss of diversity

**

*N.S.

Bovine extended datasetAll haplogroups (T, T1, T2 and T3)

Bovine extended dataset“European” haplogroup only (T3)

Human dataset

Bovine vs Human genetic distancesH

omo

sapi

ensDimension 1

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9

Bos taurus

Hom

o sa

pien

sDimension 1

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9

Bos taurus

Dimension 1

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9

Bos taurus

(r = 0.98; Mantel test = 0.99).

Admixture analysis

Parental population

Hybrid population Africa Europe Anatolia & Near East

Northern Italy 0.071 ± 0.087 1.114 ± 0.364 -0.1852 ± 0.442

Central Italy 0.028 ± 0.084 0.160 ± 0.297 0.812 ± 0.363

Southern Italy 0.197 ± 0.098 1.517 ± 0.405 -0.713 ± 0.486

Conclusion 1

Likely arrival of progenitors of Central Italian bovines from Eastern Mediterranean by the sea-route:

• significant presence of haplotype variants typical of the Near East (T, T1 and T2), but rare or absent in Europe;

• close genetic relationship between Central Italian, Anatolian and Near Eastern T3 haplogroup;

• sudden burst of diversity detected in Central Italian cattle, observed nowhere else in the Italian peninsula;

• statistical support by the comparison of the level of genetic diversity in the different areas investigated;

• major contribution of Anatolian and Near Eastern Bos taurus to Central Italian cattle mtDNA is confirmed by admixture analysis.

Conclusion 2

The migration hypothesis better explains the finding of parallel signatures in humans and cattle. Outlier behaviour points to the same direction: highly significant correlation between human and cattle genetic distance matrices.

Alternative hypothesis: trade. In this case only or mainly bovine mtDNA is expected to carry clear Eastern molecular signature. Data of Vernesi et al., Francalacci et al., and the MDS results support the conclusion that modern people from Tuscany possess mtDNA more related to Anatolian and Near Eastern populations than to Europeans.

Conclusion 3

Migrational event should pre-date the Roman age

Presence of the same cattle breeds in Central Italy at least since the I century B.C.

No later records of large import of cattle females and massive human immigrations from Eastern

Mediterranean shores in Tuscany.

Sea freight of bovines was technically possible. Not a huge number of animals had to be transported from

the Near East (high variability in Near East and population expansion contrasting the loss of

haplotypes by genetic drift)

Conclusion 4

The event is unlikely to date back to the Neolithic colonization of Italy (around 6,000

B.C.).

This process began in the southern part of the peninsula, where people arrived from the Balkans and gradually spread northward.

Archaeological remains from Italy are in favour of a relative cultural homogeneity until the

Bronze Age (2nd millennium B.C.)

Conclusion 4

These data support the Eastern origin of Etruscans, as reported by Herodotus (1.94) in the V century B.C.

Near Eastern populations and their cattle should have sailed and docked to Central Italy. The admixture of

people and animals with autochthonous Italian populations have likely originated the embryo of

Etruscan culture.

The period in which, likely, the Eastern migration occurred is compatible with the onset of the Etruscan civilisation (X-IX

sec B.C.).

Before Rome…..

All roads took nearby….. To Tarquinia (or Caere, Cerveteri, Chiusi…)?

ACKNOWLEDGEMENTS

- M. Pellecchia- R. Negrini- E. Milanesi- M. Patrini- L. Colli

- F. Salamini- A. Torroni- A Achilli- U. Tecchiati- O. Hanotte- M. Bruford