Population Structure in the Mediterranean basin: a Y chromosome perspective
Cristian Capelli C.1,2, Nicola Redhead N.1, Valentino Romano V.3, Francesco Calì F.4;, Gerard Lefranc G.5, Valerie Delague V.6., Andre Megarbane A.6, Alex E. Felice A.E. 7; , Vincenzo L. Pascali V.L.2; Pavlos I. ,Neophytou P.I 8, Zena Poulli Z.9, , Andrea Novelletto A.10, Patrizia Malaspina P.11, Luciano Terrenato L.11, Marc Fellous M. 11 2 , Mark G. Thomas, M.G.1, David B. Goldstein1 .D.B.1
1University College of London, London, UK
2 Istituto di Medicina Legale,Università Cattolica del Sacro Cuore, Rome, Italy
3 Department of Biopathology and Biomedical Methodologies, University of Palermo, Palermo, Italy
10Università della Calabria, Italy
11Università di Tor Vergata, Rome, Italy
9Cyprus Research Center (KYNEM), Nicosia, Cyprus
5Laboratoire d’Immunogenetique Moleculaire, Università Montpellier II, Montpellier Cedex ,
France4 Oasi Institute for Research on mental Retardation and Brain Aging (IRCCS), Troina, Italy 5
Laboratoire d’Immunogenetique Moleculaire, Università Montpellier II, Montpellier Cedex , France
6Unité de Génétique Médicale, Faculté de Médecine, Université Saint-Joseph, Beyrouth, Liban
4Oasi Institute for Research on mental Retardation and Brain Aging (IRCCS), Troina, Italy 12Human Genetics, Université Paris, Paris, France
7Laboratory of Molecular Genetics, Departmnet of Pathology, University of Malta, Malta. 8Mendel Center for Biomedical Sciences, Eglomi, Nicosia, Cyprus
9
Cyprus Research Center (KYNEM), Nicosia, Cyprus
10
Università della Calabria, Italy
11
Università di Tor Vergata, Rome, Italy
12
Human Genetics, Université Paris, Paris, France
Keywords: Mediterranean, Y chromosome, population genetic structure, STRs, UEPs..
Corresponding author:
Cristian Capelli, Genetic Identity Europe, Promega Corporation , Madison WI, USA Current address:
Promega Italia, Via Decembrio 28, 20137 Milano email: cristian.capelli@promega.com.
phone: +39 0773 458535 fax: +39 0773 458535
The opinions expressed in this article by C.Capelli do not necessarily reflect those of Promega Corporation
Abstract
The Mediterranean region has been characterised by a number of pre-historical and historical events whose genetic legacy is still a matter of debate. The Neolithic revolution, Greek and Phoenician colonisations , and the Roman and Arab conquests are all thought to have shaped the current
distribution of genetic variation along the coasts of the Mediterranean basin, but the details are largely unknown. Here we study the distribution of Y chromosome genetic variation in 23 Mediterranean populations, (11 firstly described here and 12 from the literature), in order to investigate the degree of population structure shaped by those events. Our analyses identify three main clusters in the
Mediterranean that can be labelled as North Africa, Mediterranean, and Arab. This pattern most likely reflects population movements during the pre-classical and classical periods, and during the later Arab expansions, that have not been obscured by more recent population contacts.
INTRODUCTIONntroduction.
Southern Greece, Sicily, South Coastal Spain were peopled well before 10-12000 years before present (yBP) . By 9000 yBP agricultural development occurred in the Near East and the new technology spread throughout Europe in the next millennia (Cunliffe, 2001). The demographic consequences of such event are still matter of debate among both geneticists (Barbujani et al, 1998; Chikhi et al, 1998; Richards et al, 2000; Simoni et al, 2000; Semino et al 2000; Rosser et al, 2000; Torroni et al, 2001; Chikhi et al, 2002; Richards et al, 2002) and archaelogistsarchaeologists (Ammerman and Cavalli-Sforza, 1984; Zvelebil and Zvelebil, 1988REFS). More recently this issue has been extensively addressed by Barbujani and Goldstein and Barbujani (2004) who suggested that in the frame of hypothesis testing, actual available data supports a Neolithic Demic Diffusion (NDD) scenario. In historical time Greeks started a series of colony foundations toward the central and west
Mediterranean basin (South Italy, Spain and coastal France) and this was paralleled by Phoenician and later Carthaginian settlement, Cartage itself being founded by the Phoenicians (Cunliffe, 2001). A new political reality emerged with the Roman Empire, which at its peak dominated the entire Mediterranean coasts. The last major expansion event was the Arab conquest, starting from the Arabian Peninsula, moving trough the Near East and finally reaching North Africa, the Iberian Peninsula, and Sicily (Finley, 1968; Ricci, 1984; Abun-Nasr, 1987; Hitti, 1990; Dussaud, 1995REFS).
Previous Y chromosome investigations suggested haplogroup (hg) J as a marker for the Neolithic dispersion (Semino et al, 1996; 2001) and Malaspina et al (2001) pointed to Greek colonisation for the dispersion of a subset of these chromosomes. A recent study of Y chromosome variation in
Mediterranean populations showed the distinctiveness of North Africans compared to the rest of the Mediterranean, but failed to find any heterogeneity among other Mediterranean populations (Quintana-Murci et al, 2003). Using a more formal inferential framework, Chikhi et al (2002) estimated the degree of population admixture in Europe when considering as source populations Near Easterners and Basques (Semino et al, 2000). The investigation revealed a higher Near Eastern contribution in
Mediterranean populations than continental European samples.
Here we explicitly assess Mediterranean genetic structure by analysing Y chromosome distribution in 11 different populations with a battery of both fast and slow evolving markers (Figure. 1). A total of 656 Y chromosomes were typed for 6 Y linked STRs and 16 Unique Events Polymorphisms (UEPs). Additionally, we include in our analyses Y chromosome data already available for another 12
populations (Bosch et al, 2000, 2001; Nebel et al, 2000, 2001;Semino et al, 2001; Malaspina et al, 2001, Wilson et al, 2001). Data analyses revealed significant structure in the Mediterranean Y chromosome gene pool, a result confirmed by a reanalysis of published mtDNA and autosomal markers.
Methods
ATERIALS AND METHODS
Samples
Geographic distribution of sampled populations is described in figure 1. The Sicilians, a subset of Sardinians and Tunisian samples origin waswere already described (Romano et al, 2003; Ciminelli et al, 1995; Comas et al, 2000; Plaza et al, 2003). Sample sizes are as in table 1.
Y chromosome genotypings
Y-STRs were genotyped as described in Thomas et al, 1999 and included DYS388, DYS393, DYS392, DYS19, DYS390 and DYS391 loci. The genealogical relationship between the selected markers is shown in figure 1, following the Y chromosome Consortium nomenclature (2002). UEPs were
genotyped using monoplex and multiplex and monoplex reactions. YAP, SRY 10831, SY81 and SRY 4064 were genotyped following published protocols (Thomas et al, 1999). RPS4Y polymorphism was genotyped as described in Capelli et al, 2001. Tat and 12f2 markers were scored as indicated in Rosser et al, (2000). All other markers were genotyped as described below. PCR was carried out in a final volume of 10 l. The reaction contained 1X buffer (HT Biotech, Cambridge), 200 M dNTPs, and 0.13 units of Taq polymerase enzyme (HT Biotech, Cambridge), as well as 9.3 nM TaqStart Antybody (Clontech). The cycling conditions were 94oC for 5 minutes, and then 35 cycles at 95oC for 40 sec, 59°C/58oC/55°C for 40 sec and 40 sec at 72oC, with a final incubation at 72oC for 10 minutes. For M173/M17/M172/M170/M9/92R7/ multiplex, the final concentration of MgCl2 was 2.2 mM . Primers and Endonuclease list are shown in table 2. Restriction reaction were performed following supplier information ( New England Biolabs, Beverly, Mass.? )
The PCR mix preparation was performed following suggestions described in Thomas et al, 1999. Appropriate allelic control DNAs where included to confirm successful restriction reaction conditions. The digested products were run on a 377 ABI instrument (Applied BioSystems, Foster City, CA). Two
chromosome found in Cyprus, ancestral at M89 and YAP markers, were considered hg A. Among the Djerba chromosomes, three were found not to be derived at any of the following markers: M9, 12f2, M170. Taking in consideration their phylogenetic position, and assignment to haplogroups E3b (1 chromosome) and FxIJK (2 chromosomes) was done by haplotype comparison w.ith fully genotyped available samples . For hgs analysis, chromosomes were clustered in 8 groups following genealogical information: E; Yx A,D,E, J, K; PxR1a1; J*xJ2; J2; A; KxP, Na3; R1a1.
Statistical analysis
Geographic structuring of variation was assessed using AMOVA as implemented in the Arlequin software (Schneider et al, 2000). Principal Components (PC) analysis was performed on haplogroup frequencies by using POPSTR software (Henry Harpending, pers comm.). Admixture estimations were calculated by LEA and ADMIX software (Chikhi et al, 2001; Bertorelle and Excoffier, 1998;
Dupanloup and Bertorelle, 2001) using hg information (that is binary markers only) and considering the E3b North African modal type as separated by the rest of the E3b group. Selected autosomal data from Rosemberg et al, 2003 was investigated by the use of the STRUCTURE program (Pritchard et al, 2000). Each STRUCTURE run was performed twice with a burn-in and run length of 200,000 each. Results and DiscussionsESULTS AND DISCUSSION
Mediterranean population structure .
We analysed 16 biallelic markers (a.k.a WHAT IS AKA??otherwise known as Unique Event Polymorphisms - UEPs) identifying haplogroups (hgs) (Fig.ure 2), and 6 Y linked microsatellites (Thomas et al, 1999), defining haplotypes (hts).(Table 1). To include data on Ashkenazi, Sephardic Jews, Kurdish Jews, and Muslim Kurds, Palestinians and Bedouins (Nebel et al, 2001), Syrians and Turkish (Semino et al, 2000) and a United Arab Emirates sample (UAE, Malaspina et al, 2001), PC analyses (Fig.figure 3) were performed with a lower level of resolution, collapsing the 14 observed haplogroups into 8 haplogroups, as described in material and methods section. We also included data from three North African populations, namely Saharawis, Moroccan Berbers and Moroccan Arabs (Bosch et al, 1999, 2001). PC results were mainly influenced by hgs DE (-0.465; loading factor) and J2 (+0.223) on axis 1, while P*xR1a1, DE and J*xJ2 were the most important on axis 2 (-0.161/-0.163,
+0.351). The PC plot suggests the presence of three main groups (Fig.Figure 3): 1) North Africa, 2) Near East/Arabs (including Muslim Lebanese and Ashkenazi Jews) and 3) a general Mediterranean, grouping, including Christian, but not Muslim Lebanese. Kurdish samples were not clearly associated with any of these three. Population differentiation test was performed using an analogue of the Fisher Exact Test as implemented in the Arlequin software (Schneider et al, 2000) on hgs frequencies, using the same 8 hgs tested for PC analysis. The pattern of population similarities paralleled the one
displayed by PC analysis, with populations in the same cluster being mostly not significantly different from each other (P>0.05, data not shown). Interestingly, among the Jewish communities, only the Kurdish and the Sephardic Jews were found not to be significantly different from each other (P=0.07). Population relationships were also investigated by the use of microsatellite variation, including Syrian and Turkish data (Wilson et al, 2001). Data for the same 6 microsatellites was not available for the UAE group so a Yemenite sample was included as a representative of the Arabian Peninsula (Thomas et al, 2000). Analysis of the distribution of molecular variation on STRs haplotypes (performed using Arlequin software, Schneider et al, (2000)) was also consistent with the three group clustering
suggested by PC analysis, with minor variations. The clustering scheme with the lowest intragroup and highest intergroup diversity (st, 1.42% and 11.06% respectively) was one grouping Ashkenazi, Kurdish Jews and Muslim Kurds with the Mediterranean group. Moving the latter two to the Arab cluster lowered the intergroup variation to 7.36% while increasing the intragroup diversity to 3.09%. The exchange of populations between North African and Arab groupings had similar effects (not shown). Following these results, we considered the three population clusters suggested by PC analysis, including Ashkenazi, Kurdish Jews and Muslim Kurds in the Mediterranean cluster and the Djerban Jews in the Arab cluster.
We also tested an ethnic/geographic clustering system, grouping the four Jewish, the Arab/Near eastern, the Mediterranean and the North African populations. Despite the fact that increasing the number of cluster (4) should increase any measure of vVariation (Cavalli-Sforza, Menozzi, Piazza, 1994), intergroup variation decreased to 6.08%, while intragroup diversity increased to 2.64%. This suggests that the scheme suggested by the PC analyses better reflects the pattern of variation thant does an “ethnic” grouping that would cluster, for example, all Jewish and all Arab populations.
We also evaluated the degree of differentiation shown by Mediterranean populations by performing PC analysis on previously published mtDNA haplogroup data (Richards et al, 2002; Thomas et al, 2002; Plaza et al, 2003). In general agreement with the Y chromosome results, a Mediterranean, an Arab and a North African cluster were apparent (Fig.Figure 3b). Mediterraneans and North Africans were closer
to each other than to Arabic populations (Bedouins and Yemenite), a result interpreted as a signature of female mediated gene flow across the Mediterranean basin (Plaza et al, 2003). Near Eastern Arab populations (Palestinians, Jordanians and Syrians) did not cluster with the Arabians and were instead closer to Mediterranean populations. This result is in contrast with the Y chromosome data, where Arabian and non-Arabian Arabs grouped together (Fig.Figure 3a). Sex mediated differential contacts between the Arabian peninsula and the Near East could be responsible for the different observed pattern. Only Bedouins seem to have had extensive contacts with Arabians, as in both mtDNA and Y chromosome analyses they cluster together.
Recently Rosenberg et al (2003) published an investigation of World-wide populations genotyped at almost 400 microsatellite loci. They assessed population differentiation using the clustering scheme implemented in the STRUCTURE software (Pritchard et al, 2000). Using the same approach we focused our attention on samples present in their dataset that are comparable to ours, namely Sardinians and Italians, Mozabites from North Africa, Bedouins and Palestinians. Several Run were performed, with likelihood values overlapping for number of cluster K>= 4 (data not shown). In all cases at least three different groups were present: group 1 clustered the majority (over 70%) of Italians and
Sardinians, and a small part of Bedouins and Palestinians; group 2 was represented by almost 90% of North Africans and group 3 contained majority of Palestinians and a subset of Bedouins. Additional groups were composed by subsequent subdivision of the Bedouin sample. Clusters 1, 2 and 3 broadly mirrored Mediterranean, North African and Arab Y chromosome and mtDNA groupings. Additional groups, composed almost exclusively representedcomposed by Bedouins, were also observed. These
additional clusters groups most lkmmost likely reflect specific gene flow or drift occurring in Bedouins.
Richards et al, (2003) found genetic evidence of female gene flow from Sub-Sahara Africa into Near East Arab populations resulting from the slave trade. When we included in the STRUCTURE analysis the available Sub-Saharan samples from Rosemberg et al (2003), the three African populations (Bantu-speaking Kenians, Yoruba and Mandenka) strongly clustered together, with a minor portion (not above 10%)of North African and Bedouins. Assuming correct identification of source populations, this suggests minor Sub-Saharan contribution to current Near East Arab populations.
Near East, Jewish communities and Arabians: evidence of Arab male genetic contribution to Levantine populations.
frequencies, above 30% in all populations in the Arab group. Nebel et al (2002) suggested this group (H71 in their nomenclature) as a possible marker of the Arab expansion in the Southern Levant and North Africa. The authors found a genealogically related haplotype mainly restricted to Arab
populations or arabised ones (GMH in Nebel et al, 2001), virtually absent from Jewish groups and the North Mediterranean coast (this study and Nebel et al, 2001). The same type has also been identified in various North African groups (this study and Bosch et al, 1999; 2001) and it is modal in both Syria and in Yemen (Thomas et al, 2000). J*xJ2 hg frequency is an important influence on the distribution of populations on PC plot axis 2, the axis along which Arab and Arabian populations tend to cluster.
These populations also show high frequencies for the GMH and its one microsatellite mutational step neighbours. J*xJ2 and GMH appear then to be non randomly distributed across populations and together may represent a signature for Arabian influence. Interestingly, considering the two Lebanese samples, the Muslims had GMH and its one microsatellite mutation step cluster at frequencies of 4.6% and 14% respectively, while, on the contrary, the Christians displayed only the GMH (2.5%)., with h Hg J*xJ2 frequencies in Muslim and Christian Lebanese were of 31% and 9%, respectively.
Nebel et al ( 2002) suggested a “working model” with two main waves of contacts between the Near East and the Arabian peninsula. An earlier Near East expansion toward Arabian Peninsula during Neolithic time would be identified by types shared also with Jewish communities, while Arabian and Near East uniquely shared types could be instead related to a more recent population movement, following the dispersion of nomadic tribes out of the Arabian peninsula (Nebel et al, 2002).
The different pattern shown by mtDNA (figure 4) suggests that Arab introgression had different effects in different groups with sex-biased gene flow. Arabian male Significant admixture withof Near East populations with Arabian groups could explain the independent grouping of those from Mediterranean populations as shown by Y chromosome data. The different pattern shown by mtDNA (Fig. 3b) with non-arabian arabs clustering with Mediterraneans, suggests that Arab introgression had different effects in different groups possibly due to sex-biased gene flow.
This scenario has important implications also on the investigation of the origin Jewish communities. Genetic variation in Jewish populations has been investigated in several recent papers using different genetic systems (e.g. Hammer et al, 2000; Nebel et al,2001; Thomas et al, 2002; Behar et al, 2003) . Basing their analysis on Y chromosome variation, Hammer et al (2000) recently found similarity between Near Eastern and Jewish communities, and suggested a common Near Eastern origin for all these groups. We have focused on Mediterranean and Near Eastern populations and highlight a significant separation between “Arabian” Near Easterners and Jewish populations. Both PC and
AMOVA analyses suggested instead a higher affinity of the latter to Mediterranean populations, with the exception of Djerban Jews who are different from the geographically close North African
populations and more similar to Arab populations. This is confirmed by the analysis of a larger Djerban Jew sample (Leonardi et al, submitted), as suggested by historical records (REF).
. These results contrasts with those of Hammer et al (2000). However, the main differences between the two investigations is are the specific focus on Mediterranean populations and the additional level of resolution within hg J offered by the inclusion of the M172 marker and microsatellite data. Hg J frequencies are in fact similar across Jewish communities and Near Easterners, while J2 and J*xJ2 hgs frequencies highlight important differences. Hg J*xJ2 is always more frequent (sometime even as much as twice) than J2 in the “Arabian” Near Eastern populations, while J2 is more frequent than J*xJ2 in the Jewish populations. The inclusionaddition of genetically different worldwide populations as Sub Saharan African, Europeans and North Africans in the MDS analysis by Hammer et al (2000) probably favoured the clustering of probably forced to cluster populations broadly similar populations as Near
Eeasterners and Jews, Mediterranean, as suggested by PC analysis performed with a similar set of populations (data not shown). .due toClustering of Jews and Near East populations is driven bytheir
high hg J frequencies (between 28% and 84%). All the Europeans included in their analysis had low hg J frequencies except the only two Mediterranean samples: Italy and Greece, which were in fact the closest to Near Eastern/Jews in their MDS analysis. The heterogeneity we observed between the Jewish groups included here and the Near East populations might be related to independent genetic histories and European admixture (Thomas et al, 2002; Nebel et al, 2002; Behar et al, 2003), and to male specific Arabic gene flow into Arab Near East populations.
Mediterranean grouping: the sea as a bridge to gene flow.
The clustering elements for the Mediterranean group were hg J2, whose frequency ranged between 9% and 29% and hg P*xR1a1, between 9% and 33%. J chromosomes (hg 9 in Rosser et al 2001) displayed a clear East to West frequency cline across Europe, more pronounced when focusing on hg J2,
indicating the Near East as a possible centre of dispersion (Semino et al, 2000; Rosser et al, 2001). The hg J distribution has been interpreted as supporting a model of demic diffusion of early farmers westward into Europe (Semino et al, 1996; 2000; Rosser et al, 2001) and eastward from south-western Iran into India (Quintana-Murci, et al, 2001). Hg J microsatellite diversity between the East and West Mediterranean groups was not significantly different (data not shown). This is not unexpected
following the various historical events that characterised most of Mediterranean history and that resulted in several superimposed population movements. , probably due to the extensive population movement that occurred across the Mediterranean basin. Semino et al, (2004) suggested that multiple dispersal events from the Near East during Neolithic and Post Neolithic have shaped the distribution of hg J. Malaspina et al (2001) for example pointed to suggested a subset of hg J2 (Network 1.2) as a possible marker of the westward Greek dispersion. The three most common Network 1.2 types are part of the Mediterranean J2 modal type and its one step mutational neighbours whose frequency is above 16% in East and South West Sicily, areas where Greeks colonization activity was particularly intense. The hg P*xR1a1 frequencies were significantly higher in the Mediterranean group than Near East and North African groups (Mann-Whitney test, p<0.05). Within the Mediterranean group hg P*xR1a1 frequencies are similar, but investigation of haplotypes reveal differential distributions for AMH+1 chromosomes (Wilson et al 2001, Capelli et al 2003). All west Mediterranean populations have frequencies above 12% (except East Sicily at 6%), but in the eastern Mediterranean it is never above 5%. AMH+1 hts and M26 derived hts (hg I1b2) have been indicated as possible markers of the paleolithic inhabitants of Europe (Wilson et al, 2001; Capelli et al, 2003REF). I1b2 types are the most common chromosomes in Sardinia but are almost absent from the rest of Europe, except for few hts in Sicily, South Italy, Iberia and British isles (this study, Semino et al, 2000 and Capelli et al, 2003). Using previously published data (Semino et al, 2000) Chicki et al (2003) found systematically higher Near Eastern contribution in Mediterranean than continental European populations by admixture analysis. Using the same approach, we found median values ranging between 0.22 and 0.74. Our results confirmed the significant contribution of Near Eastern types to the Mediterranean area, but suggested that Neolithic wave did not have an homogenous effect in the region. If we cluster western
Mediterranean populations according to the degree of Neolithic impact, as attested in the archeological record (Sardinia, North-West Sicily, Malta vs. South Italy, South-West and East Sicily; Cunliffe, 2001), the two groups have significantly different Neolithic contribution (the former group less than the latter, median values, Mann-Whitney test, p<0.05).
The North African uniqueness: the sea as a barrier to gene flow.
North African populations have E3b frequencies above 50% (Table 1 and Bosch et al, 2001), while this hg is not above 29% in other Mediterranean and European samples (Table 1, Semino et al, 2000; Rosser et al, 2000). E3b is a subset of Ex3a. In our complete dataset of Mediterranean Y chromosomes
only 1 of the 117 E3xa chromosomestypes was not included in E3b hg, so we consider an acceptable reasonable approximation to assume that the majority of European E3xa chromosomes are E3b. Inspection of the distribution of E3b haplotypes revealesreveals a clear difference between North African and European populations. Between 27 and 31% of the North African chromosomes are represented by a single haplotype (12-13-11-13-24- 9, loci order as in Methods). This haplotype is modal in all the North African populations considered here, being the modal type in each of them..Its The frequency of this type drops dramatically to an average of 3% by crossing the Mediterranean basin into South Europe. The E3b modal type in the European population is represented by the 12-13-11-13-24-10 ht, whose frequency is between12% and 3% but virtually absent from North Africa (0-3%) (this study and Bosch et al, 1999, 2001). The E3b North African types are mostly derived at the M81 marker (not included in our UEP panel). Investigation of Bosch et al dataset (2000, 2001) suggests an almost complete association of the E3b DYS391 allele 9 with the derived state at M81. Seventy eight out 80 chromosomes with this allele were derived at the M81 marker. Within E3b group, aAllele 9 has a
relative frequenfrequencycy in West Mediterranean populations of 17%, while the 10 allele is at 73%. The differential distribution of the two modal types and of DYS391 allele 9 seems to suggest different dispersion patterns, with the large majority of the E3b chromosome in Europe having an alternative origin than North Africa. Semino et al (2002) have indicated that the majority of the European E3b chromosomes are M78 derived. The Near East E3b modal type is identical to the modal one in West Mediterranenan. E3xa microsatellite diversity is higher in the East (Palestinians, Bedouins, Ashkenazi, Sephardic, Syrians, Lebanese, Cypriots) than central west Mediterranean (0.41 vs. 0.31, Variance of the Repeat Scores, VRS). a result compatible with Near East as a centre of dispersion for the European E3xa types, as recently suggested by Semino et al, 2004.
North African gene flow into South Europe has been suggested by mtDNA analysis (Plaza et al, 2003). In order to estimate the North African male genetic introgression on the northern shores of the
Mediterranean basin, we use a likelihood and a least-square frequency composition approaches, as implemented in the LEA and ADMIX softwares (Chikhi et al, 2001; Bertorelle and Excoffier, 1998; Dupanloup and Bertorelle, 2001). We selected Moroccan Berbers/Basques (Bosch et al 1999, 2001) and Tunisian/Southern Italians respectively as possible representatives of the source populations for the Iberian and Sicilian samples. The median likelihood estimations ranged between 0.15 and 0.271, while the ADMIX values were between 0.004-0.21. The two alternative approaches supported a scenario with limited genetic contribution of North African population, in agreement with their independent
The centre of origin of the “North African” M81 derived lineage is unclear. This marker has been assayed in few populations and so far and, with the exception of North Africa, it has been found only in Mali (Underhill et al 2000, Semino et al, 2002; Cruciani et al 2002; Arredi et al, 2004). The M81 derived haplogroup microsatellite diversity in the North African populations (Bosch et al, 2000; 2001) is very low (0.14 VRS)( see also Arredi et al, 2004), suggesting a recent origin or an extreme founder effect/bottleneck associated with the M81 mutation dispersion. Arredi et al suggested that E3b1 hg pattern of distribution and associated clinal diversity are compatible with a Neolithic origin in the Middle East. Alternatively, Nebel et al, (2002) suggested the distribution of J*xJ2 haplogroup and related haplotypes (GMH, see above) in North Africa and the Near East as compatable with Arabian conquest. . An alternative compatible hypothesis would be compatible with the North African conquest by Arabs, whose influences are suggested by the distribution of J*xJ2 haplogroup (the most common group excluding E3b, see also Nebel et al, 2002) and related haplotypes (GMH, see above). Additional sampling in the North Africa, the Near East and the Arabian peninsula would help in clarifying this issue.
Conclusions
The significant genetic structuring of populations facing the Mediterranean basin into three groupings, Near Eastern Arabs, Mediterranean and North Africans, is related to the demographic processes that have occurred since the first peopling of the area. The distribution of Neolithic technologies was probably paralleled by demographic expansion in the Mediterranean basin, and subsequent westward migration by Phoenicians and Greeks contributed to distribution of Y chromosome types of most likely Near East origin. The Arab conquest in particular appears to have had a dramatic influence on the East and South Mediterranean coasts, with differential sex -related gene flow playing a major role in the distribution of genetic variation.
The identified genetic structure raises important issues not only for historical but also for medical genetics. Differential distribution of Malaria resistance variants among Mediterranean populations is well known (REF) and though in part to be the results of local selection pressure (Tishkoff et al, 2001;Verrelli et al,2002)Tishkoff et al, 2001). The presence of structure as identified by multiple genetic systems suggests that other polymorphisms might be not randomly distributed as the results of the indicated demographic phenomena. In particular variants involved in the response to drug
the CYP2D6 and the PKU genes, show significant differences across European and Mediterranean populations (Bradford, 2002; Cali’ et al, 1997). More detailed sampling and investigation focused on the area will be critical for extensive evaluation of the degree of populations structuring present and the demographic processes that have shaped them.
Acknowledgements
We would like to thank the following people: Julia Abernethy and Fiona Gratrix helped in genotypings; Almut Nebel and Elena Bosch kindly provided data in electronic format; Prof. SantaCruz provided a subset of the Sardinian samples; Jim Wilson and Martin Richards commented an earlier version of the manuscript; Henry Harpending gave permission to use POPSTR software. G.L. would like to
additionally thank Nabiha Salem and Eliane Choueiry. V.L.P. was supported by a grant PRIN-MIUR 2002 (N.2002063871); A.N. by grant PRIN-MIUR 2002 and 2003. D.B.G. is a Royal Society/Wolfson Research Merit Award holder.
Legends to Figures and Tables
Figure 1
Geographic origin of the investigated samples . Figure2
Genealogical relationships of the selected UEPs. Nomenclature as suggested by YCC (2002). Figure 3
a)Y chromosome hgs Principal Components plot. Figure 4
b)MtDNA hgs Principal Components plot.
Table 1
Population Y hg frequencies (in brackets absolute number of chromosomes). No hg D and N3 chromosomes were found.
Table 2
References
Abun-Nasr JM (1987) A history of the Maghrib in the Islamic Period. Cambridge University Press, Cambridge
Ammerman A. and Cavalli-Sforza LL (1984) The Neolithic transition and the genetics of human populations in Europe. Princeton , New Jersey: Princeton University Press.
Arredi B, Poloni ES, Paracchini S, Zerjal T, Fathallah DM, Makrelouf M, Pascali VL, Novelletto A, Tyler-Smith C(2004) A Predominantly Neolithic Origin for Y-Chromosomal DNA Variation in North Africa.Am J Hum Genet 75:338-345
Barbujani G, Bertorelle G, Chikhi L (1998) Evidence for Paleolithic and Neolithic gene flow in Europe.
Am J Hum Genet 62: 488-492.
Barbujani G, Goldstein DB (2004) Africans and Asians abroad: genetic diversity in Europe. Annu Rev Genomics Hum Genet 5:119-150.
Bertorelle G, Excoffier L (1998) Inferring admixture proportions from molecular data. Mol Biol Evol 15: 1298-1311.
Behar DM, Thomas MG, Skorecki K, Hammer MF, Bulygina E, Rosengarten D, Jones AL, Held K, Moses V, Goldstein D, Bradman N, Weale ME (2003) Multiple origins of Ashkenazi Levites: Y chromosome evidence for both Near Eastern and European ancestries. Am J Hum Genet 73: 768-779.
Bosch E, Calafell F, Comas D, Oefner PJ, Underhill PA, Bertranpetit J (2001) High-resolution analysis of human Y-chromosome variation shows a sharp discontinuity and limited gene flow between northwestern Africa and the Iberian Peninsula. Am J Hum Genet 68:1019-1029
Bosch E, Calafell F, Perez-Lezaun A, Comas D, Izaabel H, Akhayat O, Sefiani A, Hariti G, Dugoujon JM, Bertranpetit J. Y chromosome STR haplotypes in four populations from northwest Africa. Int J Legal Med. 2000;114(1-2):36-40
Bradford LD (2002) CYP2D6 allele frequency in European Caucasians, Asians, Africans and their descendants. Pharmacogenomics 3:229-243.
Burn AR (1990) The Penguin History of Greece. Penguin Books, London, pp 83-103
Cali F, Dianzani I, Desviat LR, Perez B, Ugarte M, Ozguc M, Seyrantepe V, Shiloh Y, Giannattasio S, Carducci C, Bosco P, De Leo G, Piazza A, Romano V (1997) The STR252-IVS10nt546-VNTR7 phenylalanine hydroxylase minihaplotype in five Mediterranean samples. Hum Genet.100:350-355.
Capelli C, Wilson JF, Richards M, Stumpf MP, Gratrix F, Oppenheimer S, Underhill P, Pascali VL, Ko TM, Goldstein DB (2001) A predominantly indigenous paternal heritage for the Austronesian-speaking peoples of insular Southeast Asia and Oceania. Am J Hum Genet 68: 432-443..
Capelli C, Redhead N, Abernethy JK, Gratrix F, Wilson JF, Moen T, Hervig T, Richards M, Stumpf MP, Underhill PA, Bradshaw P, Shaha A, Thomas MG, Bradman N, Goldstein DB (2003) A Y chromosome census of the British Isles. Curr Biol 13: 979-984.
Cavalli-Sforza LL, Menozzi P, Piazza A (1994) The History and the Geography of Human Genes. Princeton University Press, Princeton, pp 113-114
Chikhi L, Destro-Bisol G, Bertorelle G, Pascali V, Barbujani G (1998) Clines of nuclear DNA markers suggest a largely neolithic ancestry of the European gene pool. Proc Natl Acad Sci U S A 95: 9053-9058.
Chikhi L, Bruford MW, Beaumont MA (2001) Estimation of admixture proportions: a likelihood-based approach using Markov chain Monte Carlo. Genetics 158:1347-1362
Chikhi L, Nichols RA, Barbujani G, Beaumont MA (2002) Y genetic data support the Neolithic demic diffusion model. Proc Natl Acad Sci U S A 99: 11008-11013
Ciminelli BM, Pompei F, Malaspina P, Hammer M, Persichetti F, Pignatti PF, Palena A, Anagnou N, Guanti G, Jodice C, Terrenato L, Novelletto A (1995) Recurrent simple tandem repeat mutations during human Y-chromosome radiation in Caucasian subpopulations. J Mol Evol 41:966-973
Comas D, Calafell F, Benchemsi N, Helal A, Lefranc G, Stoneking M, Batzer MA, Bertranpetit J, Sajantila A (2000) Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits. Hum Genet 107:312-319
Cruciani F, Santolamazza P, Shen P, Macaulay V, Moral P, Olckers A, Modiano D, Holmes S, Destro-Bisol G, Coia V, Wallace DC, Oefner PJ, Torroni A, Cavalli-Sforza LL, Scozzari R, Underhill PA (2002) A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes. Am J Hum Genet 70: 1197-1214.
Cunliffe B. (2001) The Oxford illustrated history of Prehistoric Europe. Oxford University Press, Oxford.
Dupanloup I, Bertorelle G (2001) Inferring admixture proportions from molecular data: extension to any number of parental populations. Mol Biol Evol 18: 672-675.
Dussaud R (1955) La penetration des Arabes en Syrie avant l‘-Islam. P Geuthner, Paris
Finley ML (1968) A History of Sicily: Ancient Sicily to the Arab Conquest. London, Viking Press.
Goldstein DB, Ruiz Linares A, Cavalli-Sforza LL, Feldman MW (1995) An evaluation of genetic distances for use with microsatellite loci. Genetics 139: 463-471.
Hammer MF, Redd AJ, Wood ET, Bonner MR, Jarjanazi H, Karafet T, Santachiara-Benerecetti S, Oppenheim A, Jobling MA, Jenkins T, Ostrer H, Bonne-Tamir B (2000) Jewish and Middle Eastern
non-Jewish populations share a common pool of Y-chromosome biallelic haplotypes. Proc Natl Acad Sci U S A 97:6769-6774.
Hitti (1990) The Arabs: a short history. Gateway Editions, Washington, DC.
Malaspina P, Tsopanomichalou M, Duman T, Stefan M, Silvestri A, Rinaldi B, Garcia O, Giparaki M, Plata E, Kozlov AI, Barbujani G, Vernesi C, Papola F, Ciavarella G, Kovatchev D, Kerimova MG, Anagnou N, Gavrila L, Veneziano L, Akar N, Loutradis A, Michalodimitrakis EN, Terrenato L, Novelletto A (2001) A multistep process for the dispersal of a Y chromosomal lineage in the Mediterranean area. Ann Hum Genet 65: 339-349
Nebel A, Landau-Tasseron E, Filon D, Oppenheim A, Faerman M (2002) Genetic evidence for the expansion of Arabian tribes into the Southern Levant and North Africa. Am J Hum Genet 70:1594-1596.
Nebel A, Filon D, Brinkmann B, Majumder PP, Faerman M, Oppenheim A (2001) The Y chromosome pool of Jews as part of the genetic landscape of the Middle East. Am J Hum Genet 69: 1095-1112.
Nebel A, Filon D, Weiss DA, Weale M, Faerman M, Oppenheim A, Thomas MG (2000) High-resolution Y chromosome haplotypes of Israeli and Palestinian Arabs reveal geographic substructure and substantial overlap with haplotypes of Jews. Hum Genet 107: 630-641
Plaza S, Calafell F, Helal A, Bouzerna N, Lefranc G, Bertranpetit J, Comas D (2003) Joining the pillars of Hercules: mtDNA sequences show multidirectional gene flow in the western Mediterranean. Ann Hum Genet 67:312-328
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics155: 945-959
Quintana-Murci L, Krausz C, Zerjal T, Sayar SH, Hammer MF, Mehdi SQ, Ayub Q, Qamar R, Mohyuddin A, Radhakrishna U, Jobling MA, Tyler-Smith C, McElreavey K (2001) Y-chromosome lineages trace diffusion of people and languages in southwestern Asia. Am J Hum Genet 68: 537-542
Quintana-Murci L, Veitia R, Fellous M, Semino O, Poloni ES (2003) Genetic structure of Mediterranean populations revealed by Y-chromosome haplotype analysis. Am J Phys Anthropol 121:157-171
Ricci L (1984) L’expansion de l’arabie meridionale. In: Chelhod J (ed) L’Arabie du Sud. Vol 1. Maisonneuve et Larose, Paris, pp 239–248
Martin Richards M, Rengo C, Cruciani F,Gratrix F, Wilson JF, Scozzari R, Macaulay V, Torroni A (2003) Extensive Female-Mediated Gene Flow from Sub-Saharan Africa into Near Eastern Arab Populations. Am J Hum Genet 72: 1058-1064.
Richards M, Macaulay V, Torroni A, Bandelt HJ (2002) In search of geographical patterns in European mitochondrial DNA. Am J Hum Genet 71:1168-1174.
Richards M, Macaulay V, Hickey E, Vega E, Sykes B, Guida V, Rengo C, Sellitto D, Cruciani F, Kivisild T, Villems R, Thomas M, Rychkov S, Rychkov O, Rychkov Y, Golge M, Dimitrov D, Hill E, Bradley D, Romano V, Cali F, Vona G, Demaine A, Papiha S, Triantaphyllidis C, Stefanescu G, Hatina J, Belledi M, Di Rienzo A, Novelletto A, Oppenheim A, Norby S, Al-Zaheri N, Santachiara-Benerecetti S, Scozzari R, Torroni A, Bandelt HJ (2000) Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet 67:1251-1276
Romano V, Cali F, Ragalmuto A, D'Anna RP, Flugy A, De Leo G, Giambalvo O, Lisa A, Fiorani O, Di Gaetano C, Salerno A, Tamouza R, Charron D, Zei G, Matullo G, Piazza A (2003) Autosomal microsatellite and mtDNA genetic analysis in Sicily (Italy).Ann Hum Genet 67:42-53.
Rosser ZH, Zerjal T, Hurles ME, Adojaan M, Alavantic D, Amorim A, Amos W, Armenteros M, Arroyo E, Barbujani G, Beckman G, Beckman L, Bertranpetit J, Bosch E, Bradley DG, Brede G, Cooper G, Corte-Real HB, de Knijff P, Decorte R, Dubrova YE, Evgrafov O, Gilissen A, Glisic S, Golge M, Hill EW, Jeziorowska A, Kalaydjieva L, Kayser M, Kivisild T, Kravchenko SA, Krumina A, Kucinskas V, Lavinha J, Livshits LA, Malaspina P, Maria S, McElreavey K, Meitinger TA, Mikelsaar AV, Mitchell RJ, Nafa K, Nicholson J, Norby S, Pandya A, Parik J, Patsalis PC, Pereira L, Peterlin B,
Pielberg G, Prata MJ, Previdere C, Roewer L, Rootsi S, Rubinsztein DC, Saillard J, Santos FR, Stefanescu G, Sykes BC, Tolun A, Villems R, Tyler-Smith C, Jobling MA (2000) Y-chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language. Am J Hum Genet 67:1526-1543
Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW (2002) Genetic structure of human populations. Science 298 :2381-2385.
Schneider, S., Roessli, D., and Excoffier, L. (2000) ARLEQUIN ver. 2.000: A software for Population Genetic Data Analysis Genetics and Biometery Laboratory, University of Geneva, Geneva.
Semino O, Passarino G, Brega A, Fellous M, Santachiara-Benerecetti AS (1996) A view of the neolithic demic diffusion in Europe through two Y chromosome-specific markers. Am J Hum Genet 59:964-968
Semino O, Passarino G, Oefner PJ, Lin AA, Arbuzova S, Beckman LE, De Benedictis G, Francalacci P, Kouvatsi A, Limborska S, Marcikiae M, Mika A, Mika B, Primorac D, Santachiara-Benerecetti AS, Cavalli-Sforza LL, Underhill PA (2000) The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective. Science 290:1155-1159
Semino O, Santachiara-Benerecetti AS, Falaschi F, Cavalli-Sforza LL, Underhill PA (2002) Ethiopians and Khoisan share the deepest clades of the human Y-chromosome phylogeny. Am J Hum Genet 70:265-268
Semino O, Magri C, Benuzzi G, Lin AA, Al-Zahery N, Battaglia V, Maccioni L, Triantaphyllidis C, Shen P, Oefner PJ, Zhivotovsky LA, King R, Torroni A, Cavalli-Sforza LL, Underhill PA, Santachiara-Benerecetti AS (2004) Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area. Am J Hum Genet 74:1023-1034.
Simoni L, Calafell F, Pettener D, Bertranpetit J, Barbujani G (2000) Geographic patterns of mtDNA diversity in Europe. Am J Hum Genet 66:262-278
Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics139:457-462
Thomas MG, Bradman N, Flinn HM (1999) High throughput analysis of 10 microsatellite and 11 diallelic polymorphisms on the human Y-chromosome. Hum Genet 105: 577-581
Thomas MG, Parfitt T, Weiss DA, Skorecki K, Wilson JF, le Roux M, Bradman N, Goldstein DB (2000) Y chromosomes travelling south: the cohen modal haplotype and the origins of the Lemba--the "Black Jews of Southern Africa".Am J Hum Genet 66:674-686
Thomas MG, Weale ME, Jones AL, Richards M, Smith A, Redhead N, Torroni A, Scozzari R, Gratrix F, Tarekegn A, Wilson JF, Capelli C, Bradman N, Goldstein DB (2002) Founding Mothers of Jewish Communities: Geographically Separated Jewish Groups Were Independently Founded by Very Few Female Ancestors. Am J Hum Genet 70:1411–1420
Tishkoff SA, Varkonyi R, Cahinhinan N, Abbes S, Argyropoulos G, Destro-Bisol G, Drousiotou A, Dangerfield B, Lefranc G, Loiselet J, Piro A, Stoneking M, Tagarelli A, Tagarelli G, Touma EH, Williams SM, Clark AG (2001) Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science 293:455-462
Torroni A, Bandelt HJ, Macaulay V, Richards M, Cruciani F, Rengo C, Martinez-Cabrera V, Villems R, Kivisild T, Metspalu E, Parik J, Tolk HV, Tambets K, Forster P, Karger B, Francalacci P, Rudan P, Janicijevic B, Rickards O, Savontaus ML, Huoponen K, Laitinen V, Koivumaki S, Sykes B, Hickey E, Novelletto A, Moral P, Sellitto D, Coppa A, Al-Zaheri N, Santachiara-Benerecetti AS, Semino O, Scozzari R (2001) A signal, from human mtDNA, of postglacial recolonization in Europe. Am J Hum Genet 69:844-852.
Underhill PA, Shen P, Lin AA, Jin L, Passarino G, Yang WH, Kauffman E, Bonne-Tamir B, Bertranpetit J, Francalacci P, Ibrahim M, Jenkins T, Kidd JR, Mehdi SQ, Seielstad MT, Wells RS, Piazza A, Davis RW, Feldman MW, Cavalli-Sforza LL, Oefner PJ (2000) Y chromosome sequence variation and the history of human populations. Nat Genet 26 :358-361
Wilson JF, Weiss DA, Richards M, Thomas MG, Bradman N, Goldstein DB (2001) Genetic evidence for different male and female roles during cultural transitions in the British Isles. Proc Natl Acad Sci U S A 98:5078-5083
Y Chromosome Consortium (2002) A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res 12:339-348
Verrelli BC, McDonald JH, Argyropoulos G, Destro-Bisol G, Froment A, Drousiotou A, Lefranc G, Helal AN, Loiselet J, Tishkoff SA (2002) Evidence for balancing selection from nucleotide sequence analyses of human G6PD. Am J Hum Genet 71:1112-1128
Zvelebil M and Zvelebil KV (1988) Agricultural transition and Indo-European dispersals. Antiquity 62: 574-583
