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Ancient DNA and Population Turnover in Southern Levantine Pigs

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Ancient DNA and Population Turnover in Southern Levantine Pigs OPEN Ancient DNA and Population Turnover in SUBJECT AREAS: Southern Levantine Pigs- Signature of the EVOLUTIONARY BIOLOGY Sea Peoples Migration? PHYLOGENETICS Meirav Meiri1,2, Dorothee Huchon2, Guy Bar-Oz3, Elisabetta Boaretto4, Liora Kolska Horwitz5, Aren Maeir6, ZOOLOGY Lidar Sapir-Hen1, Greger Larson7, Steve Weiner8 & Israel Finkelstein1 ARCHAEOLOGY 1Institute of Archaeology, Tel Aviv University, Tel Aviv 69978, Israel, 2Department of Zoology, Tel Aviv University, Tel Aviv 69978, Received 3 4 30 May 2013 Israel, Department of Archaeology, University of Haifa, Haifa 31905, Israel, Weizmann Institute-Max Planck Center for Integrative Archaeology, D-REAMS Radiocarbon Dating Laboratory, Weizmann Institute of Science, Rehovot 76100, Israel, 5National Natural Accepted History Collections, Faculty of Life Science, The Hebrew University of Jerusalem, Jerusalem 91905, Israel, 6The Institute of 23 July 2013 Archaeology, The Martin (Szusz) Department of Land of Israel Studies and Archaeology, Bar-Ilan University, Ramat Gan 52900, Israel, 7Durham Evolution and Ancient DNA, Department of Archaeology, University of Durham, Durham DH1 3LE, United Kingdom, Published 8Kimmel Center for Archaeological Science, Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, 24 October 2013 Israel. Correspondence and Near Eastern wild boars possess a characteristic DNA signature. Unexpectedly, wild boars from Israel have requests for materials the DNA sequences of European wild boars and domestic pigs. To understand how this anomaly evolved, we sequenced DNA from ancient and modern Israeli pigs. Pigs from Late Bronze Age (until ca. 1150 BCE) Israel should be addressed to shared haplotypes of modern and ancient Near Eastern pigs. European haplotypes became dominant M.M. (meirav.meiri@ only during the Iron Age (ca. 900 BCE). This raises the possibility that European pigs were brought to the gmail.com) region by the Sea Peoples who migrated to the Levant at that time. Then, a complete genetic turnover took place, most likely because of repeated admixture between local and introduced European domestic pigs that went feral. Severe population bottlenecks likely accelerated this process. Introductions by humans have strongly affected the phylogeography of wild animals, and interpretations of phylogeography based on modern DNA alone should be taken with caution. hylogeographic studies use phylogenetic methods and geographical contexts to reveal evolutionary histories of species to follow migrations and contraction/expansion processes1,2. Recent studies of mitochondrial DNA (mtDNA) of wild boar (Sus scrofa) found strong phylogeographic structure across its entire distri- P 3–7 bution range with European, Near Eastern and East Asian pigs falling into separate clades . This structure has enabled researchers to infer past events in the history of wild boars, such as postglacial recolonisation of northern Europe from southern refugia8. Violation of this phylogeographic structure was used to infer human movements and translocations across Europe and the Pacific4,5,9. During the Epipaleolithic and Neolithic periods, humans introduced wild boars into various regions across Eurasia (e.g.10–12). Since domestication, however, the assumption is that humans have mainly translocated do- mestic pigs rather than wild boars. It was remarkable, then, that Giuffra et al.3 reported that three modern wild boars from Israel possessed a European mtDNA haplotype. In contrast, studies have shown that modern wild boars from other Near Eastern countries (i.e., Egypt, Syria, Turkey, Armenia, Iraq and Iran) possess Near Eastern haplotypes5,7,9. Patterns observed using only modern mtDNA might not accurately represent earlier phylogeographic events such as migrations, translocations and extinctions (e.g.13–15). Therefore, ancient DNA is a powerful tool for revealing population histories, and can shed light on past events (e.g.16–18). Through the use of ancient DNA, we aim to elucidate the apparent paradox of the modern Israeli wild boar, and to determine just how far back this inconsistency extends. Today, wild boars are found in the Mediterranean region of Israel and south of the Dead Sea19. They have been part of the fauna of the southern Levant since at least the middle Pleistocene, ca.0.78 Mya20. Pigs were domes- ticated in the Neolithic21,22 and their remains are found at most archaeological sites in Israel. Their frequency, SCIENTIFIC REPORTS | 3 : 3035 | DOI: 10.1038/srep03035 1 SCIENTIFIC REPORTS SREP-13-02445-T.3d 14/10/13 12:16:50 www.nature.com/scientificreports however, varies greatly between sites as well as between periods according to their MC1R gene. Using ancient DNA techniques, we (e.g.23,24). Variation in the number of pig bones, and therefore in studied domestic pig bones from a diachronic series of Israeli archae- the past consumption of pork, depends on several factors, including ological assemblages dating from the Neolithic period to medieval climate, modes of life, as well as cultural and religious prefer- times (Fig. 1). For the ancient samples we analysed a short fragment ences25–27. Pig remains, however, are especially abundant in the of the mtDNA CR. We then compared our results to phylogenetic Israeli archaeological record in four periods: Middle Bronze II (ca. data on Asian and European pigs to elucidate the biogeographic 2000 BCE–1550 BCE); Iron I (ca. 1150-800 BCE) faunal assemblages affinities of our samples. in Philistia (the southern coastal plain) (e.g.23,28–30); assemblages from non-Jewish sites from the Roman (634-324 BCE) and Byzantine Results 23,27 periods (324-63 BCE) . There is extensive archaeological evidence Modern DNA. We analysed the DNA from 25 museum specimens of showing that during all these periods there were contacts between the modern wild boars from Israel using mtDNA CR (see Supplementary 31–33 Levant and Europe (e.g. ; needless to say, connections became Table S1). The phylogenetic tree of mtDNA CR was based on 621 bp, stronger with time). and is in agreement with previous studies of Sus scrofa5–7,9. Three In order to resolve the phylogeographic inconsistency that the supported clades are known – one European (with Italian samples modern Israeli wild boars have a different mtDNA signature from forming a divergent clade at the base of the group), and two Near their surroundings, we examined a combination of modern and Eastern – while the rest of the tree consists of East Asian pigs (Fig. 2). ancient DNA sequences of suids from Israel. We analysed DNA from All 25 modern wild boars from Israel as well as one Israeli boar a series of modern wild boars from museum collections representing sequence from GenBank (accession number AF136558) (Fig. 2) fell their full biogeographical distribution across the country, in order to within the European clade. Very little genetic diversity was found in assess the observation made by Giuffra et al.3 and examine whether the mtDNA CR between these wild boar sequences, with 21 samples their results reflected a genetic anomaly or a widespread pattern. sharing the same haplotype. Ancient DNA data enabled us to test whether this was a case of We also analysed the nuclear MC1R region in 17 modern wild shifting spatial and temporal patterns of haplotypes, and if so to boar specimens from Israel. A median-joining network, based on pinpoint when it had started. 963 bp of MC1R region demonstrates the differences between For the modern wild boar samples, we amplified a combination of European and Asian suids, and confirms that extant wild boars from mtDNA control region (CR), and nuclear Melanocortin receptor 1 Israel possess a European wild boar haplotype (identical to GenBank (MC1R) gene. This is the first time that Near Eastern wild boars have Accession numbers: EU443645-56 & GQ240942) (see Supplemen- been sequenced for MC1R gene that is associated with coat colour tary Fig. S1). variation (e.g.34,35). We chose this nuclear marker because a large geographical dataset is available for this gene. Moreover, recent stud- Ancient DNA. We successfully extracted and sequenced DNA from ies showed that pig coat colour is the result of strong selective pres- 34 out of 177 ancient domestic pig bones sampled from archaeolo- sures (e.g.36,37). Thus European and Asian pigs can be distinguished gical sites in Israel (Fig. 1). The overall success rate was 19%, which is Figure 1 | Map showing location of archaeological sites from which DNA was obtained. An asterisk marks Philistine Iron I sites. The map was created using the ArcGIS version 9.3.1. SCIENTIFIC REPORTS | 3 : 3035 | DOI: 10.1038/srep03035 2 www.nature.com/scientificreports Figure 2 | Modern pig phylogeny based on mtDNA. A Bayesian phylogenetic tree based on 621 bp of the mitochondrial CR with 100 haplotypes, representing 197 modern pig sequences. Desert Warthog (Phacochoerus aethiopicus) serves as an outgroup. The Bayesian posterior probabilities (above 0.8), and bootstrap supports (above 50%) are shown below and above the branches respectively. SCIENTIFIC REPORTS | 3 : 3035 | DOI: 10.1038/srep03035 3 www.nature.com/scientificreports the expected rate given the climate in the region38,39 (see Supplemen- European haplogroup in two specimens from the Roman period tary Fig. S2). The samples were collected from secure stratigraphic (MMP150, 211). These samples were re-extracted and multiple contexts associated with well-defined ceramic assemblages, which amplifications resulted in the same sequence. However, they are still provide secure
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