Ancient DNA signatures in modern breeds

1. Ancient DNA signatures in modern breeds Paolo Ajmone Marsan Università Cattolica del S. Cuore, Piacenza, Italy paolo.ajmone@unicatt.it

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 PAST • Phylogenetic relationship between species and the origin of the tree of life • Prehistorical migrations • Historical migrations • Genealogical studies • Paternity testing • Individual identification PRESENT

5. Domestic animals molecular genetics Since domestication

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. 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. Grigia Alpina Rendena 15 Italian breeds Pezzata Rossa It. Valdostana P.R. Piemontese Cabannina Romagnola Mucca Pisana Calvana Marchigiana Chianina Maremmana Podolica Cinisara Modicana 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 0 0 1 1 1 1 0 0 1 0 0 0 0 0 M1 M2 1 0 1 0 1 1 0 1 0 1 0 1 1 0 Binary matrix 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 0 M2 1 0 1 0 1 1 0 1 0 1 0 1 1 0 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. 0,15 Calvana 0,1 Chianina Italian Red Pied 0,05 It, Fresian Marchigiana Valdostana Red Pied Romagnola Alpine Grey It. Limousine Mucca Pisana 0 Cabannina Maremmana -0,1 -0,05 0 0,05 0,1 0,15 Piedmontese Rendena Podolica -0,05 It. Brown Modicana -0,1 -0,15 Cinisara -0,2 Relationship among Italian breeds NORTH CENTRE-SOUTH PCOA1 PCOA2 ALPINE PODOLIAN

14. Microsatellites typingMultidimensional 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. Bostaurus mtDNA HVRI region diversity Troy et al., Nature, 2000 Domestication centre Reduced Median Networks

19. Breeds analysed Rendena 11 Italian Breeds analysed (N=164) Italian red pied Piedmontese N=47 Romagnola 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. MPD 3.5±1.8 MPD 2.0±1.4 MPD 1.9±1.1 MPD 4.0±2.0 MPD 3.6±1.9 MPD 1.5±1.2 Centre Europe Near East Italy 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 • The largest bovine in the world. • The bull "Donetto" at the age of 8 reached 1.780 Kg! Calvana

28. Maremmana Cabannina

29. 0,15 Calvana 0,1 Chianina Italian Red Pied 0,05 It, Fresian Marchigiana Valdostana Red Pied Romagnola Alpine Grey It. Limousine Mucca Pisana 0 Cabannina Maremmana -0,1 -0,05 0 0,05 0,1 0,15 Piedmontese Rendena Podolica -0,05 It. Brown Modicana -0,1 -0,15 Cinisara -0,2 Relationship among Italian breeds NORTH CENTRE-SOUTH PCOA1 PCOA2 ALPINE 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. Crop rotation • Olive pressing to obtain olive oil • Wine making • Metallurgy • Ceramics • Crafting Cultural exchange with Greeks The Oriental period (VIII - VI sec. a.C.)

37. Tauromachia

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

39. 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.

40. Most related modern population • modern Tuscans Gene flow with • Anatolia populations mtDNA analysis from Etruscan remains (Vernesi et al., 2001 Proc. Natl. Acad. Sci. USA 98, 13460-13463.

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 • - 1426 sequences of Homo sapiens mtDNA HVRI region Sequences of populations living in the same regions of cattle sampling were retrieved

42. * * N.S. * Loss of diversity

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

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. 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)