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Ancient DNA signatures in modern breeds

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Presentation on theme: "Ancient DNA signatures in modern breeds"— Presentation transcript:

1 Ancient DNA signatures in modern breeds
Paolo Ajmone Marsan Università Cattolica del S. Cuore, Piacenza, Italy

2 One past revealed to us in many ways
No source is unbiased…..

3 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!

4 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 PRESENT

5 Since domestication Domestic animals molecular genetics

6 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

7 Please, notice, no cellular phone
European project RESGEN EU project (PL98-118) Towards a strategy for the conservation of genetic diversity in European cattle Towards a strategy for the conservation of the genetic diversity of European cattle Please, notice, no cellular phone (www.androclus.vet.uu.nl/resgen/)

8 15 Italian breeds 29 Razze 606 individui Modicana Cinisara Podolica
Marchigiana Maremmana Chianina Calvana Mucca Pisana Romagnola Piemontese Valdostana P.R. Rendena Grigia Alpina Pezzata Rossa It. Cabannina Piacenza Vestland Red Polled Finnish Ayrshire Telemark 29 Razze 606 individui Jutland Frisona Jersey Normande Piemontese Valdostana P.R. Rendena Grigia Alpina Pezzata Rossa It. Cabannina Romagnola Mucca Pisana Calvana Chianina Maremmana Marchigiana Podolica Cinisara Modicana Evolene Hungarian Grey Eringer Bruna I. Limousine Betizu Menorquina

9 AFLP A B C D E F G H I J K L M N M1 M2 Binary matrix
M1 M2 Binary matrix A B C D E F G H I J K L M N M M M3 …

10 Relationship among European breeds
Central Europe Southern Europe Northern Europe Reynolds distance Neighbour Joining tree

11 Dimensions needed to represent genetic relationship/distance

12 Principal Components

13 Relationship among Italian breeds
-0,2 -0,15 -0,1 -0,05 0,05 0,1 0,15 It, Fresian Italian Red Pied Valdostana Red Pied Cabannina It. Limousine Rendena Piedmontese Mucca Pisana Podolica Maremmana Cinisara It. Brown Modicana Marchigiana Romagnola Chianina Calvana Alpine Grey NORTH CENTRE-SOUTH PCOA1 ALPINE PCOA2 PODOLIAN

14 Microsatellites typing Multidimensional analysis
2nd dimension 1st dimension D Laloë, K Goudarzi

15 Mitochondrial DNA

16 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

17 Constructing a median network from SSR haplotypes

18 Bos taurus mtDNA HVRI region diversity
Troy et al., Nature, 2000 Domestication centre Reduced Median Networks

19 11 Italian Breeds analysed
Rendena 11 Italian Breeds analysed (N=164) Italian red pied Piedmontese Romagnola N=47 Cabannina Calvana Chianina Maremmana N=66 Podolica Cinisara Modicana N=51

20 Centre Europe Near East Italy

21 Pairwise differences in sequences

22 Pairwise differences in constant and expanding populations

23 Mismatch distribution of populations expanded at different times

24 Italian bovines South North Center

25 Central Italian breeds seem to share a different
Centre Europe Near East Italy MPD 3.5±1.8 4.0±2.0 3.6±1.9 MPD 1.9±1.1 2.0±1.4 1.5±1.2 Central Italian breeds seem to share a different history compared to that of other Italian breeds

26 Do these breeds have anything in common?

27 Chianina Calvana The largest bovine in the world.
The bull "Donetto" at the age of 8 reached Kg! Calvana

28 Maremmana Cabannina

29 Relationship among Italian breeds
-0,2 -0,15 -0,1 -0,05 0,05 0,1 0,15 It, Fresian Italian Red Pied Valdostana Red Pied Cabannina It. Limousine Rendena Piedmontese Mucca Pisana Podolica Maremmana Cinisara It. Brown Modicana Marchigiana Romagnola Chianina Calvana Alpine Grey NORTH CENTRE-SOUTH PCOA1 ALPINE PCOA2 PODOLIAN

30 Historical information
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 […]” 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 Romans called the elephants taken by Hannibal “bulls from Lucania” (about 215 B.C.).

31 Small size of domestic bovines
Iron age: 1,10 – 1,20 m Bos primigenius: 2,20 – 2,30 m

32 Is there any link with the onset of Etruscan civilisation?

33 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.

34 Etruscan navy controlled trade in west Mediterranean
630 – 500 a.C.

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

36 Cultural exchange with Greeks
The Oriental period (VIII - VI sec. a.C.) Wine making Olive pressing to obtain olive oil Crop rotation Metallurgy Ceramics Crafting

37 Tauromachia

38 the origin of this civilisation
On-going debate on the origin of this civilisation Local development, with Eastern influences or Eastern Mediterranean provenience? History -> Herodotus Linguistics -> European or Semitic? Archaeology -> different opinions What about genetics?

39 Genetic data from modern populations
Francalacci et al. (1996 Am. J. Phys. Anthropol. 100, ) 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.

40 mtDNA analysis from Etruscan remains
(Vernesi et al., 2001 Proc. Natl. Acad. Sci. USA 98, Most related modern population modern Tuscans Anatolia populations Gene flow with

41 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 sequences of Homo sapiens mtDNA HVRI region Sequences of populations living in the same regions of cattle sampling were retrieved

42 Loss of diversity * N.S.

43 Bovine extended dataset All haplogroups (T, T1, T2 and T3)

44 Bovine extended dataset “European” haplogroup only (T3)

45 Human dataset

46 Bovine vs Human genetic distances
(r = 0.98; Mantel test = 0.99).

47 Admixture analysis Parental population Hybrid population Africa Europe
Anatolia & Near East Northern Italy 0.071 ± 0.087 1.114 ± 0.364 ± 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 ± 0.486

48 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.

49 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.

50 Migrational event should pre-date the Roman age
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)

51 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.)

52 Conclusion 4 The period in which, likely, the Eastern migration occurred is compatible with the onset of the Etruscan civilisation (X-IX sec B.C.). 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. Before Rome….. All roads took nearby….. To Tarquinia (or Caere, Cerveteri, Chiusi…)?

53 ACKNOWLEDGEMENTS M. Pellecchia R. Negrini E. Milanesi M. Patrini L. Colli F. Salamini A. Torroni A Achilli U. Tecchiati O. Hanotte M. Bruford


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