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doi: 10.1111/j.1469-1809.2007.00414.x Differential Y-chromosome Anatolian Influences on the Greek and Cretan Neolithic R. J. King1 , S. S. Özcan2 , T. Carter3 , E. Kalfoğlu2 , S. Atasoy2 , C. Triantaphyllidis4 , A. Kouvatsi4 , A. A. Lin5 , C-E. T. Chow5 , L. A. Zhivotovsky6 , M. Michalodimitrakis7 and P. A. Underhill5, ∗ 1 Department of Psychiatry and Behavioral Sciences, 401 Quarry Road, Stanford University, Stanford, CA 94305-5722 2 Institute of Forensic Sciences, Istanbul University, Istanbul, Turkey 3 Department of Anthropology, McMaster University, Chester New Hall 524, 1280 Main Street West Hamilton, L8S 4L9, Ontario, Canada 4 Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University, Thessaloniki, 54124 Thessaloniki, Greece 5 Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5120 6 N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, Moscow, 119991, Russia 7 Department of Forensic Science, University of Crete, Heraklion, Greece Summary The earliest Neolithic sites of Europe are located in Crete and mainland Greece. A debate persists concerning whether these farmers originated in neighboring Anatolia and the role of maritime colonization. To address these issues 171 samples were collected from areas near three known early Neolithic settlements in Greece together with 193 samples from Crete. An analysis of Y-chromosome haplogroups determined that the samples from the Greek Neolithic sites showed strong affinity to Balkan data, while Crete shows affinity with central/Mediterranean Anatolia. Haplogroup J2b-M12 was frequent in Thessaly and Greek Macedonia while haplogroup J2a-M410 was scarce. Alternatively, Crete, like Anatolia showed a high frequency of J2a-M410 and a low frequency of J2b-M12. This dichotomy parallels archaeobotanical evidence, specifically that while bread wheat (Triticum aestivum) is known from Neolithic Anatolia, Crete and southern Italy; it is absent from earliest Neolithic Greece. The expansion time of YSTR variation for haplogroup E3b1a2-V13, in the Peloponnese was consistent with an indigenous Mesolithic presence. In turn, two distinctive haplogroups, J2a1h-M319 and J2a1b1-M92, have demographic properties consistent with Bronze Age expansions in Crete, arguably from NW/W Anatolia and Syro-Palestine, while a later mainland (Mycenaean) contribution to Crete is indicated by relative frequencies of V13. Keywords: Y-chromosome diversity, Neolithic Greece, Crete, bread wheat, maritime migration, Bronze Age Introduction The earliest archaeological evidence for Neolithic economies in SE Europe dates to c. 7000 cal BC, with the founding of a fully-fledged farming community at Knossos on the island of Crete, followed slightly later in the NW Peloponnese of mainland Greece (Efstratiou 2005; Perlès 2001: pp84–95; Runnels 2003). Concerning the origins of ∗ Corresponding author: Peter A. Underhill, Department of Genetics, 300 Pasteur Drive, Stanford University School of Medicine, Stanford, CA 94305-5120, Fax: 650 725 1534. phone: 650 723-5805. E-mail: under@stanford.edu 2008 The Authors C 2008 University College London Journal compilation   C agriculture in these Aegean contexts, it is an uncontested fact that both plant and animal husbandry first emerged at an earlier date in regions to the east, namely Anatolia, Cyprus and the Levant (Colledge et al., 2004; RowlyConwy 2003). The question thus becomes one of how Neolithic farming economies came to be introduced into SE Europe and from which external region(s) did the impetus originate? The argument is often polarized between two distinct models, namely: demic expansion of agropastoralists versus the cultural transmission of ideas (Pinhasi et al., 2005; though see Kotsakis 2003; Tringham 2000), the debate drawing upon a wide range of evidence, including archaeology, genetics and linguistics (Bellwood 2001). Annals of Human Genetics (2008) 72,205–214 205 R. J. King et al. In Crete, the process of ‘neolithisation’ appears to be relatively straightforward. With the island seemingly uninhabited prior to its colonization by Neolithic farmers (whose associated domestic animals and plants were foreign to Crete), research has thus focused largely on these peoples’ overseas origins and the routes by which they traveled (Broodbank & Strasser 1991; Efstratiou 2005: pp146–148). The situation on mainland Greece (henceforth ‘Greece’) is more complex, as here we do have evidence for a Mesolithic heritage (Galanidou & Perlès 2003; Runnels 2001), with a potential for contact between natives and migrants in the NW Peloponnese (Runnels 2003: pp126– 127). While patterns of genetic diversity in SE Europe and the eastern Mediterranean often display gradients (CavalliSforza et al., 1994; Semino et al., 2000), distinguishing those that might have related specifically to the spread of farming remains challenging. That said, data from the haploid Y-chromosome does seem to support the movement of Anatolian/Levantine agro-pastoralists from their SW Asian origins towards SE Europe (Semino et al., 2000). More specifically haplogroups E and J have been proposed as possible signatures of this dispersal (Semino et al., 2004), with a significant correlation between haplogroups E3b and J2 and the distribution of certain distinctive types of Neolithic material culture, from the Levant, via SE Europe, to parts of the east and central Mediterranean (King & Underhill 2002). Turning to the Aegean specifically, while this region has experienced post-Neolithic gene flows (Renfrew 1996: pp15–16), we emphasize the fact that the impact of founder effect is often maximal in situations when migrants settle previously unoccupied territory, as with Crete (Edmonds et al., 2004; Klopfstein et al., 2006). With demographic population expansions following initial colonization, it is possible that these genetic variants will persist and be detectable. Similarly, many of the localities in Greece that were first settled by Initial Neolithic [IN] agriculturalists appear to have been unoccupied for some time prior to the establishment of settled farming communities (Perlès 2001, 2003, Runnels 2003, Kotsakis 2003), a situation that could also lead to the retention of genetic varieties introduced by these early migrant agriculturalists. Patterns of Y-chromosome diversification also offer the possibility to dissect other prehistoric events subsequent to the arrival of Neolithic pioneers (Novelletto 2007). Recent Y-chromosome surveys concerning Greece (DiGiacomo et al., 2003) and Crete (Malaspina et al,. 2001; Martinez et al., 2007) discuss Neolithic migrations in the Mediterranean. In addition, other studies have supported the notion of one or more subsequent migrations into SE Europe (Cavalli-Sforza et al., 1994; DiGiacomo et al., 2004; Semino et al., 2004), poten206 Annals of Human Genetics (2008) 72,205–214 tially supporting earlier archaeological claims that population movements played a role in the emergence of the Aegean’s great Bronze Age cultures of the 3rd and 2nd millennia BC: the so-called Minoans of Crete and the mainland Mycenaeans (Caskey 1960: pp301–302; Coleman 2000; Hood 1990; Renfrew 1987, 1996). As a means of understanding the complexities of the neolithisation process in SE Europe and the Aegean, and the role of alleged population expansions at the start of the Neolithic, we investigate the components of the Y-chromosome phylogenies of Crete and Greece. The results of the study are then contrasted with data from a larger Mediterranean, SW Asian and Arabian context. This report investigates the local, micro-geographic variation of Y chromosome haplotypes, data that suggests strongly that the demic diffusion model has merit, whereby in the discussion section we address the following issues: 1) What is the degree of affinity between the pioneer Neolithic agriculturalists of Greece and Crete? 2) By extent, what does the combined genetic and archaeological data inform us with regard to the regional source(s) of these early farmers? 3) What do the genetic data tell us with regard to postNeolithic migrations to Crete and the role of demographic change in the emergence of the Bronze Age ‘Minoan’ culture? Methods Sampling Rationale and Details Using an informed consent process, 193 healthy adult males from the four main prefectures of Crete were sampled for DNA, a not entirely dissimilar strategy to that proposed by Renfrew for a study of the island’s molecular genetic history over a decade ago (Renfrew 1996: p16). These samples from Crete are independent from those reported in Martinez et al. (2007). A further 171 males were sampled from three areas in Greece in villages near known Initial Neolithic [IN] and Early Neolithic [EN] sites (Figure 1). These comprised Central Macedonia near the site of Nea Nikomedeia (n = 57); Thessaly within the southeast Larissa basin (n = 30) and near Sesklo/Dimini (n = 27); and in the NW Peloponnese, near the Franchthi Cave (n = 21) and Lerna (n = 36). Only individuals whose paternal grandfather was from the designated areas were sampled. Y-chromosome Polymorphisms Binary polymorphisms were genotyped either by DHPLC, RFLP or direct sequencing methodology following the hierarchy of the Y-chromosome phylogeny. The majority of the binary markers have been previously described (Cinnioğlu et al., 2004; Cruciani et al., 2006; Sengupta et al., 2006; Shen et al., 2004; Underhill et al., 2001). We report for the first time a new  C 2008 The Authors C 2008 University College London Journal compilation  Y-Chromosome Diversity in Greece and Crete Figure 1 Map of sample locations. The T1-T9 data points indicate the nine geographic regions in Turkey (Cinnioğlu et al., 2004). Data point correspondences: Cr (Crete); G1 (Nea Nikomedeia); G2 (Sesklo and Dimini); G3 (Lerna and Franchthi Cave). T to G tranversion substitution that defines an informative G2 sub-clade. The M406 site occurs at position 81 within a 370 nucleotide amplicon defined by the following PCR primers: F: 5′ -CCCCAAAAAGCTATTCTGTAA-3′ and R: 5′ -GAAGCACTTTAGAGCAGGG-3′ . All of the samples were also genotyped at 10 Y microsatellite loci previously described (Cinnioğlu et al., 2004) to compute mean haplotype variance within specific haplogroups defined by the binary markers. In addition, both the dinucleotide DYS413 and DYS445 tetranucleotide microsatellite loci were also analyzed in all hgHG J2aM410 related lineages. Statistical Analysis Analysis of molecular variance (AMOVA [Excoffier et al., 1992]) with pairwise Fst analysis of the haplogroup frequencies comparing Crete and the three Greek areas was performed using the Arlequin 2000 program (Schneider et al., 2000). To locate our data within a broader SW Asian and Mediterranean context a PC analysis was performed using published haplogroup frequencies from 16 Middle East and SE European regions, nine regions from Anatolia, together with the Crete and Greek samples. Ten YSTR loci DYS19, DYS388, DYS389I(CD), DYS389II(AB), DYS390, DYS391, DYS392, DYS393, DYS439 and DYS461(A7.2) were genotyped on haplogroup J2a-M410, J2b-M12, E3b1a2-V13 backgrounds. To ascertain the STR affinities between the three Greek regions, Crete and Anatolia, a PC analysis was performed on the 10 STR repeat scores on all M410 (xM319) backgrounds using the Rst covari2008 The Authors C 2008 University College London Journal compilation   C ance distance metric (Slatkin 1995). The M319 chromosomes were excluded because of their outlier microsatellite pattern on Crete (Malaspina et al., 2001, Martinez et al., 2007). See Electronic Supplementary Material as Table S1 in the online edition for YSTR haplotypes. Expansion times on selected M410 terminal backgrounds (M92 and M319) in Crete, and M12 and V13 backgrounds in Greece, were calculated using the method and evolutionary mutation rate of Zhivotovsky (2001, 2004). See Electronic Supplementary Material as Table S2 in the online edition for YSTR haplotypes. Results A total of 32 binary polymorphisms were typed to define 24 informative haplogroups. Figure 2 illustrates the Y-chromosome haplogroup phylogenetic relationships and frequencies for the observed haplogroups in the three Greek regions and Crete. In the Greek data overall, the most frequent haplogroups include E3b1a2-V13 (28%), R1b3-M269 (13%), R1a1-M17 (11%), I2a-P37 (9.0%), J2b-M12 (6%). In Crete, the most frequent haplogroups are R1b3-M269 (17%), G2-P15 (11%), J2a1-DYS413∗ (9.0%) and J2a1h-M319 (9.0%). The Fst analysis of the haplogroup frequencies demonstrates that Crete is significantly different from each of the three sampled Greek locations (p < 0.001). In turn, the Annals of Human Genetics (2008) 72,205–214 207 R. J. King et al. M94 M168 YAP M213 M35 M304 M258 M201 M9 P15 M78 M81 M123 M253 M267 M438 M172 M70 M20 M74 M207 M34 M410 P37 M223 M406 V13 M12 M306 DYS 413 18 M67 M319 M269 SRY1532 DYS 445-6 M92 M198 E3b3 G2d I1 I* I2 I2a I21b F J1 J2a J2a1b J2a1b1 J2a1h J2a1k J2b K* K2 L R2 R1b3 R1* R1a R1a1 J2a1 E3b2 G2 E3b1a E3b1a2 E3b 0 1.8 14.0 1.8 1.8 3.5 0 1.8 0 0 8.8 1.8 0 10.5 0 0 0 1.8 0 1.8 7.0 0 1.8 1.8 0 19.3 0 0 21.1 0 3.5 35.1 1.8 0 1.8 3.5 3.5 0 0 7.0 3.5 0 3.5 0 0 3.5 1.8 0 3.5 8.8 0 1.8 0 1.8 5.3 0 0 10.5 n Nea Nikomedeia 57 57 Sesklo/Dimini Lerna/Franchthi 57 193 Crete 0 0 35.1 0 0 1.8 3.5 1.8 0 5.3 12.3 1.8 0 1.8 0 5.3 5.3 1.8 0 1.8 1.8 1.8 1.8 0 0 15.8 0 0 1.8 0 0 6.7 0 2.1 8.8 2.1 4.1 0 5.7 0 8.3 1.6 6.7 5.2 2.6 8.8 2.6 3.1 0 2.1 0.5 0 17.0 0 0.5 8.3 1.6 1.6 Figure 2 Phylogenetic relationships and Y-chromosome haplogroup frequencies in mainland Greece and Crete. Haplogroup I clade structure as given in Underhill et al. (2007). Table 1 Fst analysis of haplogroup frequency Nea Nikomedeia Sesklo Lerna Crete ∗ Nea Nikomedeia Sesklo Lerna Crete 0 0.035∗ 0.038∗ 0.019∗ 0 0.003 0.065∗ 0 0.05∗ 0 p < 0.001 Nea Nikomedeia sample also differs from those of the other two Greek regions (Table 1). The Sesklo/Dimini and Lerna/Franchthi Cave regional data do not significantly differ from each other in the Y haplogroup frequencies. Inspection of Figure 2 results shows that Crete has a high frequency of haplogroup J2a-M410 (25.9%) with Lerna/Franchthi Cave (14.1%) and Sesklo/Dimini (8.8%) having intermediate frequencies of J2a. The northernmost sample-site, Nea Nikomedeia, has the lowest frequency of J2a-M410 (3.6%). The distinctive short 6 repeat motif allele pattern (Schrack et al., 2006) was detected in 1.8% of the samples from Nea Nikomedeia, 3.5% from Sesklo/Dimini and 1.8% from Lerna/Franchthi Cave and 2.6% of the samples from Crete, and specifically, 3.8% of the samples from Heraklion prefecture in Crete containing the IN site of Knossos. Haplogroup J2b-M12, the offsetting companion 208 Annals of Human Genetics (2008) 72,205–214 clade of J2a-M410, shows a trend of decreasing frequency from north to south, from 7% and 8.8% at Nea Nikomedeia and Sesklo, respectively, to 1.8% at Lerna/Franchthi Cave and 3.1% in Crete. E3b1a2-V13 is more frequent in Greece than in Crete ranging from 14.0% at Nea Nikomedeia, 35.1% at Sesklo/Dimini, 35.1% at Lerna/Franchthi Cave, to 6.7% in Crete. Furthermore the M78 defined chromosomes are almost entirely characterized by the V13 polymorphism in both Greece and Crete. Of the previously reported 26 M78 derived chromosomes in Turkey (Cinnioğlu et al., 2004), 22 carried the V13 polymorphism. A reanalysis of 26 M78 Y chromosomes from the Egyptian delta showed that none carried the derived marker V13 (Luis et al., 2004). In addition the new haplogroup G related SNP, M406 was found to occur at 4.2% in the Turkish samples previously described (Cinnioğlu et al., 2004). To investigate the population affinities of the Greek and Cretan data to other regional SE European, SW Asian, Egyptian and Arabian populations a PC analysis of haplogroup frequencies normalized to the same level of molecular diversification was conducted (Figure 3). Notable observations include: 1) the three Greek regional samples cluster with those from the Balkans. 2) Crete, on the other hand, clusters with the central and Mediterranean Anatolian samples together with those of southern Iran, Iraq, Lebanon and Jordan. 3) Egypt, Oman and the Bedouin  C 2008 The Authors C 2008 University College London Journal compilation  Y-Chromosome Diversity in Greece and Crete Figure 3 Principal Component Factor Analysis of Middle Eastern and South East European population affinities from the gene pool of Y-chromosome haplogroup frequencies. Albania, Bosnia, Croatia, FRYOM (Former Republic of Macedonia), Herzegovina, Serb (Serbia) Peričić et al. 2005; Bosnia2, Croatia2, Serb2 (Marjanovic et al., 2005); NIran, SIran (Reguerio et al., 2006); Egypt, Oman (Luis et al., 2004); Jordan from Amman (Flores et al., 2005); Iraq (Al-Zahery et al., 2003, Semino et al., 2004); Lebanon (Semino et al., 2000, Semino et al., 2004); Bedouin (Israel), unpublished. The T1-T9 data points indicate the nine geographic regions in Turkey (Cinnioğlu et al., 2004). G1, G2 and G3 labels are the same as given Figure 1. samples from the Negev tend to form an isolated cluster, distinct from the Greek and Cretan data. Vector analysis (not shown) demonstrates that the Balkan cluster is most associated with haplogroups J2b-M12, E3b1a-M78, I-M170 and R1a1-M17. The Crete and Anatolian cluster was most influenced by J2b-M410 while the Arabian Peninsula and north Egypt cluster by J1-M267. Since haplogroup J2a-M410 is hypothesized to be associated, at least in part, with the spread of agriculture (Sengupta et al., 2006), a PC analysis of YSTR haplotypes was conducted to investigate the Anatolian contribution to Greece and Crete. Figure 4 shows a plot of the PC factor scores for the three Greek regions, Crete, and the nine Anatolian regions for the M410 (xM319) haplotype data. The plot demonstrates an affinity between both Crete and Lerna/Franchthi Cave and central and Mediterranean 2008 The Authors C 2008 University College London Journal compilation   C Anatolia (T7/T6), with the two other Greek sample-sites (Nea Nikomedeia and Sesklo/Dimini) forming outliers in the plot. The M319 defined sub-clade was excluded from the PC analysis since its frequency is informative only in Crete. Estimates of the expansion time should be considered preliminary because of the small sample sizes and inherent uncertainties in the calibration of the YSTR molecular clock. These estimates for J2b-M12 and E3b1a2-V13 from Greece and J2a1h-M319 and J2a1b1-M92 from Crete are given in Table 2. The mean expansion time for J2b-M12 in Greece is consistent with a late Neolithic population expansion (Halstead 1994: p200), while V13 expands in the Peloponnese earlier than the IN presence there indicating that it may reflect a Mesolithic expansion. On the other hand M319 and M92 in Crete both have significantly Annals of Human Genetics (2008) 72,205–214 209 R. J. King et al. Figure 4 Principal Component Factor Analysis of the affinities of haplogroup J2a-M410 chromosomes (i.e. lineages), without the M319 representatives, from Turkey, Crete and mainland Greece, based upon10 Y-STR loci. The T1-T9 data points indicate the nine geographic regions in Turkey (Cinnioğlu et al., 2004). G1, G2 and G3 labels are the same as given Figure 1. Discussion Table 2 Haplogroup expansion times Mainland Greece Sample size Age (kya) J2b-M12 Nea Nikomedeia E3b2-V13 Seklo/Dimini E3b2-V13 Lerna/Franchthi E3b2-V13 Crete J2a1b1-M92 Crete J2a1h-M319 Crete J2b-M12 Crete E3b2-V13 10 6.7+/− 3.1 6 8.6+/− 4.0 20 4.3+/− 1.8 20 9.2+/− 4.3 5 5.1+/− 1.5 17 5.1+/− 2.2 5 0.9 +/− 0.9 13 3.1+/− 1.5 later expansion times, dating to the end of the Neolithic / beginning of the Early Bronze Age [EBA]. Haplogroup E3b1a2-V13 has an expansion time in Crete dating to the end of late Bronze Age (1100 BCE) arguably reflecting the presence of a mainland Mycenaean population in Crete. 210 Annals of Human Genetics (2008) 72,205–214 The results of our Y-chromosome survey provide a means to compare and contrast the role of migration in the establishment of the first Neolithic farming economies in Greece and Crete. Archaeological links had previously been drawn between the first settlers of Knossos and their central Anatolian predecessors/contemporaries, based on their common use of mud-brick technology and shared suites of domesticates, with particular reference made to bread wheat (Triticum aestivum). This is the predominant cereal from the earliest levels at Knossos (Evans 1994: p5), well attested in Anatolia, yet rare, if not completely absent from the archaeobotanical record of most Balkan and Greek IN sites (Perlès 2001: p62, p155). Moreover, a recent survey of archaeobotanical data has demonstrated that the suite of plants (including invasive weeds) recovered from the earliest levels of Knossos are known not only from earlier sites in central and Mediterranean Anatolia, but also Cyprus and the Levant (Colledge et al., 2004: pp42–44, Figs. 6– 7). Our Y-chromosome data allows us to explore the issue of possible parallelisms with the botanical patterns. For example, haplogroup J2a-M410 is frequent in central and  C 2008 The Authors C 2008 University College London Journal compilation  Y-Chromosome Diversity in Greece and Crete Mediterranean Turkey (Cinnioğlu et al., 2004) and Crete but rare in the northern Greek Neolithic sites (Figure 2). Furthermore the J2a1k-DYS445 sub-clade (Schrack et al., 2006) is present on Crete (Heraklion prefecture, 3.8%) and also occurs at high frequencies (7.3%) in regions T6 and T7. On the other hand, in Greece, the most frequent J2 haplogroup is J2b-M12 that is however rare (1.7%) in Anatolia (Cinnioğlu et al., 2004). In general when all Ychromosome data are considered, Crete clusters with near Eastern populations whereas mainland Greece groups with Balkan populations (Figure 3). Within mainland Greece there is differentiation among the three sampling sites. Most notable is Lerna/Franchthi Cave, in the Peloponnese region, which displays affinity to Crete with the exception of haplogroup E3b1a2-V13. This could reflect regional interaction between Crete, Peloponnese and Anatolia. The presence of haplogroups I and R1b in Crete are similar to levels reported by Martinez et al. 2007. The variety of haplogroup I in Crete is I2-M438∗ rather than I2aP37 which predominates in the Balkans. Interestingly, haplogroup R1b YSTR haplotypes showed affinity to those of Italy rather than the Balkans (Martinez et al., 2007). Moreover, the PC plot (Figure 4) of J2a(xM319) linked YSTR haplotypes shows a close genetic relationship between Crete and central / Mediterranean Anatolia (T6 & T7). The genetic data thus appears to support the long-held theory that the island’s colonists came from Anatolia (Evans 1921: p14), specifically those in those areas where the wellknown Neolithic sites of Aşıklı Höyük, Çatalhöyük and Hacılar (region T7), Mersin/Yumuktepe and Tarsus (region T6) were located. Within mainland Greece, only the data from the NW Peloponnese (Lerna/Franchthi Cave) exhibit a high frequency of J2a(xM319) lineages comparable to those in central and Mediterranean Anatolia (Crete to a large degree and Lerna/Franchthi Cave to a lesser degree). The Y-chromosome distinction between the Greek sites is significant as it mirrors other differences between the first farmers of north and south Greece. While Franchthi dates to the beginning of the 7th millennium BC, the IN of Thessaly is nearer the middle of the 7th millennium (Kotsakis 2003: p218; Perlès 2001: pp84–93). The implications are that distinct populations may have in part underwritten the regional differences witnessed in the establishment of farming economies. A much-debated topic is whether the earliest farmers to Greece arrived via terrestrial or maritime colonization routes (Perlès 2005). The absence of J2b-M12 in regions T1 and T8 (Cinnioğlu et al., 2004), i.e. those next to the land bridge from Anatolia to Greece, suggests that the first farmers of Greece and the Balkans are less likely to have come overland. The Thessalian and Greek Macedonian samples exhibit a high frequency (7–9%) of J2b-M12 with an approximate 2008 The Authors C 2008 University College London Journal compilation   C expansion time dating to the Neolithic era of c. 5000BC (Table 2). Previous work on the Balkans (Peričić et al., 2005; Marjanovic et al., 2005) regarding the frequency of J2b-M12 is consistent with our observations in Greece. The geographic origin of J2b-M12 remains unknown; however, Cinnioğlu et al., (2004) report its occurrence in SE Anatolia near the Euphrates River (T5) at 4.7%, i.e. the region with some of the first Neolithic communities to have been established beyond the original Levantine core, such as Çayönü, Göbekli Tepe and Hallan Çemi (Cauvin 2000: pp78–91). While the source of J2b-M12 chromosomes in Greece/Balkans remains unclear, it is likely to reside in those regions with an early Neolithic domestic economy based upon unleavened wheat such as present day Syria and the Levant. The calculated expansion time of haplogroup E3b1a2V13 in mainland Greece is 8,600 y BP at Nea Nikomedeia and 9,200 y BP at Lerna/Franchthi Cave and is consistent with the late Mesolithic/initial Neolithic horizon. These dates exceed those reported previously for Europe (Cruciani et al., 2007) that date to the Bronze Age. This discrepancy arises mainly because of differences in the choice of mutation rate used. Our choice of the evolutionary mutation rate is based upon its concordance with other episodes of rapid demographic growth (e.g. the Bantu Iron Age expansion in Africa and the colonization of New Zealand by Polynesians (Zhivotovsky et al., 2004). The expansion of E3b1a2-V13 in Crete provides a consistent internal control our choice of mutation rate. Namely the Late Bronze Age expansion date of 1100 BC coincides with the alleged arrival of mainland Mycenaean Greeks that is well documented in the archaeological and epigraphic record. The calculation of expansion times of terminal binary mutations from linked YSTR variance yields insight into post-Initial Neolithic demographic events in our study area. In Crete, the binary mutation M319 defines a unique J2a-M410 sub-haplogroup that is rarely observed elsewhere (Martinez et al., 2007). This category of chromosomes was first recognized because of an unusual DYS413 YSTR allelic pattern (Malaspina et al., 2000). The J2a1h-M319 haplogroup confirms this association. A reanalysis of the Anatolian data (Cinnioğlu et al., 2004) shows there were only two such chromosomes in this gene pool. Previously, mutation M319 was also reported in Iraqi and Moroccan Jews at 5% and 10% respectively (Shen et al., 2004). The J2a1h-M319 expansion time in Crete dates to 3100 BC, while haplogroup J2a1b1-M92 also has an expansion time dating to approximately 3100 BC (Table 2). The latter is found at relatively high frequencies in western Anatolia (T1 and T8) (Cinnioğlu et al., 2004; Semino et al., 2004). Our data are consistent with the proposal that haplogroup Annals of Human Genetics (2008) 72,205–214 211 R. J. King et al. J2a1b1-M92 is a signature of Bronze Age expansions in Europe (Di Giacomo et al., 2004). The archaeological implications of these data are tantalizing. A date of 3100 BC is a highly significant one for Aegean prehistorians, as it marks approximately the boundary between the Neolithic and Bronze Age on Crete (Manning 1995), a period associated with a series of major changes in settlement patterns, demography, material culture, technology, iconography and burial practices. Many scholars have suggested that new influxes of population were responsible for triggering these changes, a sociocultural impetus from which emerged the island’s famed Minoan culture. The new features associated with EBA Crete have been linked variously with Egypt/Libya, Syro-Palestine, the East Aegean/NW Anatolia and the Cyclades (Betancourt 2003; Branigan 1988: pp199–200; Evans 1924: px, pxiii; Hood 2000: p21; Nowicki 2002; Warren 1973, 1984). Regarding the purported link to Egypt/Libya, the majority of E3b1-M78 chromosomes are derived at V13, both in Crete and Greece, whereas all samples from northern Egypt lack the V13 SNP (Luis et al., 2004). This suggests that there has not been a recent genetic affinity between Egypt and Crete or Greece. Conversely, the Y-chromosome results do provide data that support population movements from both western and northwestern Anatolia (regions T1 and T8) and Syro-Palestine. One can point to another post-colonization population influx into Crete (1100 BC) this time from Greece, as represented by V13 which occurs at ca. 35% frequency in both Thessaly and the Peloponnese while its frequency on Crete is only 7%, indicating a mainland contribution to the Cretan Y chromosome inventory, albeit no more than 20%. Once again, the genetic data resonates with a major debate in Aegean prehistory; that of the processes involved in the ‘Mycenaeanisation’ of Cretan society towards the end of the Bronze Age. Sometime around the mid 15th century BC, Crete witnessed another series of major sociocultural changes, as evidenced by the adoption of the mainland proto-Greek Linear B script/language, burial practices, iconography and material culture. These cultural transformations have been interpreted by many as indicative of Crete’s invasion by its mainland Mycenaean neighbors (Popham 1994; Warren 1973: p45). The Y chromosome data can be taken as further evidence that some of these later Bronze Age changes in Crete were indeed underwritten by an incursion of mainland populace. One final field of research that our data affects is that of the archaeology of languages. While correlations between genes and languages must be interpreted cautiously, their co-analysis may provide useful insights. The differential phylogenetic pattern of J2a-M410 and J2b-M12 lineages to Crete and southern European respectively are broadly consistent with the model of Renfrew (1998), and with the 212 Annals of Human Genetics (2008) 72,205–214 linguistic analysis of Gray & Atkinson (2003), that claim an early split of the Anatolian languages from the rest of Indo-European languages around 7000BC. In this model the J2a-M410 speakers in Anatolia and Crete may have been speaking Anatolian related languages that may be reflected in the un-deciphered scripts of the 2nd millennium BC: Cretan hieroglyphic and Linear A (Finkelberg 1997, 2001). Alternatively, the J2a-M410 populations may have been speaking a non-Indo-European language with affinities to the Hattic language of central Anatolia (Nichols 2007). Acknowledgements We thank all the donor men who participated in this study. We thank three anonymous reviewers for their valuable suggestions. 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Received: 29 September 2007 Accepted: 7 October 2007  C 2008 The Authors C 2008 University College London Journal compilation