The genetic legacy of religious diversity and intolerance: paternal lineages of Christians, Jews and Muslims in the Iberian Peninsula Susan M. Adams1*, Elena Bosch1*†, Patricia L. Balaresque1, Stéphane J. Ballereau1, Andrew C. Lee1, Eduardo Arroyo2, Ana M. López-Parra2, Mercedes Aler3, Marina S. Gisbert Grifo3, Maria Brion4, Angel Carracedo4, João Lavinha5, Begoña Martínez-Jarreta6 , Lluis Quintana-Murci7, Antònia Picornell8, Misericordia Ramon8, Karl Skorecki9,10, Doron M. Behar9, Francesc Calafell11 and Mark A. Jobling1 1

Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK

2

Laboratorio de Genética Forense y Genética de Poblaciones, Dep. Toxicología y Legislación

Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid, 28040-Madrid, Spain 3

Unidad Docente de Medicina Legal, Sección de Biología Forense, Facultad de Medicina,

Universidad de Valencia, Spain 5

Centro de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Av. Padre Cruz,

Lisboa, Portugal 4

Instituto de Medicina Legal, Universidade de Santiago, Fundación de Medicina Xenómica- Hospital

Clínico Universitario, 15706 Santiago de Compostela, Spain 6 7 8 9

Unidad Docente de Medicina Legal y Forense, Universidad de Zaragoza, Zaragoza, Spain Unit of Human Evolutionary Genetics, CNRS URA3012, Institut Pasteur, Paris, France Laboratori de Genètica, IUNICS i Dep. Biologia, Universitat de les Illes Balears, Spain Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa 31096, Israel

10

Rappaport Faculty of Medicine and Research Institute, Technion, Israel Institute of Technology,

Haifa, Israel 11

Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i de la Salut,

Universitat Pompeu Fabra, Barcelona, Spain * These two authors contributed equally to the work. †

current address: Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències

Experimentals i de la Salut, Universitat Pompeu Fabra, Spain Address for correspondence and reprints: Prof Mark A. Jobling, Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK Tel.: +44 (0)116 252 3427. Fax: +44 (0)116 252 3378. Email: [email protected] Keywords: Y chromosome; Iberian Peninsula; North Africa; Sephardic Jews; admixture; population history Running head: North African and Sephardic Jewish admixture in Iberia

1

Abstract Most studies of European genetic diversity have focused on large-scale variation and interpretations based on events in prehistory, but migrations and invasions in historical times may also have had profound effects on the genetic landscape. The Iberian peninsula provides a suitable region to examine the demographic impact of such recent events, since its complex recent history has involved the long-term residence of two very different populations with distinct geographical origins, and their own particular cultural and religious characteristics – North African Muslims, and Sephardic Jews. To address this question we analysed Y chromosome haplotypes, which provide the necessary phylogeographic resolution, in 1140 males from the Iberian Peninsula and Balearic Islands. Admixture analysis based on binary and Y-STR haplotypes indicates a high mean proportion of ancestry from North African (10.6%) and Sephardic Jewish (19.8%) sources. Despite alternative possible sources for lineages ascribed a Sephardic Jewish origin, these proportions attest to a high level of religious conversion (whether voluntary or enforced), driven by historical episodes of social and religious intolerance, that ultimately led to the integration of descendants. In agreement with the historical record, analysis of haplotype sharing and diversity within specific haplogroups suggests that the Sephardic Jewish component is the more ancient. The geographical distribution of North African ancestry in the peninsula does not reflect the initial colonization and subsequent withdrawal, and is likely to result from later enforced population movement - more marked in some regions that others – plus the effects of genetic drift.

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Introduction The genetic diversity of human populations in Europe has been the subject of intense scrutiny since the first ‘classical’ markers became available1. Most studies have focused on the identification of large-scale variation, and its interpretation in terms of major events in prehistory, such as expansions from glacial refugia in the Paleolithic2; 3; 4 ; 5, and the spread of agriculture from the Near East in the Neolithic6-13. This approach seems reasonable, since early events when populations were small are likely to have had major effects that could persist to the present day. However, Europe has also been subject to migrations and invasions within historical times that may have played an important role in shaping current patterns of diversity14, and may contribute to confusion over more ancient population movement. Although evidence of the cultural impact of historical events can be gleaned from sources such as archaeology, place-names and linguistic elements, there is often debate about the weight of their corresponding demographic impact. Genetic analysis of modern populations can offer a more direct approach to recognizing the impact of migrations and invasions in historical times, especially when source populations for migrations are clearly differentiated from recipient populations. The Iberian peninsula is of particular interest in this context, since it has a complex recent history over the last two millennia involving the long-term residence of two very different populations with very distinct geographical origins, and their own particular cultural and religious characteristics – North African Muslims, and Sephardic Jews15. North Africa and the Iberian peninsula are separated by a mere 15km of water at the Gibraltar Strait, making the region a potential migration route between Africa and Europe. Historically documented contact began dramatically in 711 CE, when a Berber army under Arab leadership crossed from Morocco, winning a key battle the following year16. Within only four years the invaders had conquered the entire peninsula, with the exception of the northern Basque country, Cantabria, Galicia, Asturias and most of the Pyrenees in the north, which remained largely unoccupied17. Arab and Berber forces then remained in control for more than five centuries, with a gradual withdrawal towards Andalusia in the south, and a final expulsion in 1492. Today, signs of this lengthy Islamic occupation are abundantly obvious in the place-names, language, archaeology18, architecture and other cultural traits of Spain and Portugal, but its demographic impact is less clear.

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The established population of the Iberian peninsula prior to 711 CE has been estimated at 7-8 million people, ruled over by about 200,000 Germanic Visigoths19, who had entered from the north in the sixth century. Though the initial invading North African force was between 10,000 and 15,000 strong, the scale of subsequent migration and settlement is uncertain, with some claiming numbers in the hundreds of thousands20. Islamization of the populace following the invasion was certainly rapid, but it has been argued that this reflects an exponential social process of religious conversion, rather than substantial immigration21; a sizeable proportion of the indigenous population (the so-called Mozarabs) was allowed to retain its Christian practices due to the religious tolerance of the Muslim rulers22. There is also doubt about the extent of intermarriage between indigenous people and settlers in the early phase20. Following the overthrow of Islamic rule in most of the peninsula, a period of tolerant coexistence (convivencia) ensued in the twelfth and thirteenth centuries, but after 1492 (1496 in Portugal) religious intolerance forced Spanish Muslims to either convert to Christianity (as so-called moriscos), or to leave23. After the fifteenth century, moriscos were on occasion relocated across Spain, and, finally, in 1609-1616, over 200,000 were expelled, mostly from Valencia. The people encountered by the Islamic invaders in the eighth century were not a religiously and culturally uniform group, but included among the Catholic Christian majority a substantial minority of Jewish people. They and their descendants are known as Sephardic Jews, from Sepharad, the Hebrew word for Spain. The Jewish presence was very long established, with some evidence that it predated the Christian era; many Jews, however, are thought to have arrived during the Roman period, either voluntarily, or as slaves brought from the Middle East after the defeat of Judea in 70 CE24. The later arrival of others was due to their displacement by the Islamic invasion of their homelands in the Near East. Under the final years of Visigothic rule, the Jews suffered the first of a long series of persecutions including forced religious conversion. During the convivencia, their population size in Spain has been estimated to be around 100,00025; in the late 14th century, a wave of pogroms affected the main Jewish quarters in Iberian cities, particularly Barcelona and Girona. By the time of the expulsions of the late fifteenth century, one estimate26 gives a Spanish Jewish population of 400,000, of which some 160,000 were expelled, largely settling around the Mediterranean, while the remainder underwent conversion to Christianity, living as so-called conversos (in Spain) or cristãos novos (in Portugal).

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Previous genetic studies of the Iberian peninsula include analyses of classical marker frequencies27-30, autosomal Alu insertion polymorphisms31, mitochondrial DNA variation32; 33, and Ychromosomal haplotypes34-39. In general these surveys have paid little attention to the issue of admixture, though studies that include North African populations all identify a marked genetic boundary coinciding with the Gibraltar Strait30-32;

34;

36

. The Y chromosome provides the

phylogeographic resolution that might allow the disentangling of past admixture events40, and studies34; 36; 38; 41; 42 have focused on haplogroup E3b2 (also known as E-M81), common in North Africa and found at an average frequency of 5.6% in the peninsula38, which, adjusting for its frequency in North Africa itself, would correspond to a contribution of 8-9%. While these studies indicate the presence of some North African lineages in the Iberian peninsula, they have taken ad hoc approaches to quantifying this, and have almost entirely41 neglected to address the possible contribution of Sephardic Jews. Here we take a formal admixture approach to reveal a remarkably high level of North African and Sephardic Jewish ancestry in a large sample of Y chromosomes from the Iberian Peninsula and Balearic Islands. We use the power of combined binary marker and short tandem repeat (STR) haplotyping to illuminate the relative time-depths of these contributions, and show that the geographical patterns of ancestry fail to fit simple expectations from historical accounts, suggesting the influence of religious conversions of both Muslims and Jews and the subsequent dispersal and drift of their Y-chromosomal lineages.

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Materials and Methods Subjects A total of 1140 DNA samples isolated from males from the Iberian Peninsula and the Balearic Islands were analyzed; below, we refer to these samples as ‘Iberian’, for brevity. All samples were collected with appropriate ethical approval and informed consent. Individuals were assigned to geographical locations based on place of birth of paternal grandfather, and then grouped based on traditional regions. Andalusia was divided into Western and Eastern (including Murcia) parts; Castilla y Leon was divided into NE and NW Castile; and a set of individuals from the Pyrenees, including some from north of the Spain-France border, were pooled as ‘Gascony’. Samples from Portugal were divided into two sets, north and south of the Mondego river.

Y-chromosome haplotyping Binary markers (Figure 1) on the non-recombining region of the Y chromosome were typed in hierarchical multiplexes43, using the SNaPshot minisequencing procedure (Applied Biosystems) and an ABI3100 Genetic Analyzer (Applied Biosystems). All samples were initially analyzed with multiplex I43 (containing the markers M9, M69, M89, M145, M170, M172, M201 and 12f2). Samples derived for M9 (haplogroup [hg] K) were analyzed with multiplex II43 (containing M17, M45, M173, M207, P25 and SRY10831). Two individuals that were derived for M45 but ancestral for M207 (hgP*[xR]) were analyzed with the markers MEH2 and M3 and could thus be assigned to hgQ*(xQ3). Samples derived for M173 but ancestral for SRY10831.2 and M17 (hgR1*[xR1a]) were further analyzed with the novel multiplex IV containing the markers M65, M153, M222, M269 and SRY-2627. Ten individuals carry reversions of the marker P25 through gene conversion44, and the allelic state of this marker in these chromosomes is therefore ignored for the purposes of this study. Samples derived for M145 within multiplex I (in hgDE) were further analyzed with multiplex III43 (containing M33, M35, M75, M78, M81, M96, M123 and P2), and the marker M2 also analyzed where appropriate. Previously unreported primers were designed based on published information about polymorphic sites45. Note that hgR2 (R-M124) is reported in Figure 1 since it was detected in the Sephardic Jewish sample (Supplementary Table 1), but was not typed in the Iberian samples since all chromosomes derived for M207 (hgR) were also derived for M173 (hgR1).

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Nomenclature of haplogroups is according to the Y Chromosome Consortium45, using updated names40, and is given in Figure 1. We employ shorthand names as follows: E3b* refers to E3b*(xE3b1, E3b2, E3b3), also known as E-M35* (xM78, M81, M123); and R1b3* refers to R1b3*(xR1b3b, R1b3d, R1b3f, R1b3g), also known as R-M269* (xM65, M153, SRY-2627, M222). Nineteen Y-chromosomal STRs (DYS19, DYS385a/b, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS434, DYS435, DYS436, DYS437, DYS438, DYS439, DYS460, DYS461, DYS462) were typed in three multiplexes as described46 on an ABI3100 Genetic Analyzer (Applied Biosystems). Allele nomenclature is as reported46, and DYS385a and b were omitted from statistical analyses.

Comparative data Comparative data for North African populations were obtained from the literature34; 47. For Moroccan and Saharawi data34 haplogroups were made comparable with those determined here by considering previously published data on the marker 12f248, and by typing the hgG-defining marker M201 on chromosomes belonging to hgF*(xH,I,J,K). Haplogroup G was also undetermined in the published Algerian and Tunisian data47, so this was predicted from Y-STR haplotypes using a published method49. We used the Bayesian and support vector machine (SVM) approaches, with our Iberian sample as training set, and based on the 14 Y-STRs (the list above, omitting DYS385a/b, and DYS460-462) shared with the published data47. A single Algerian chromosome among the 10 hgF*(xH,I,J,K) cases was predicted to belong to hgG with high confidence (100% [Bayesian] and 96% [SVM]); this low level of the haplogroup in North Africa is consistent with the Moroccan and Saharawi samples, and with an independently published set of Algerian data50. In comparisons among Iberian samples typed here, 17 Y-STRs were considered; when comparisons were done with published data on North African samples34;

47

, the number of Y-STRs was reduced to eight for

compatibility with the published data, after adjusting allele nomenclature for DYS389I47. Comparative data for Sephardic Jewish populations were extracted from a large collection of Y haplotypes assembled by D.M.B. and K.S.. The term Sephardic Jews is used here in its narrow sense51, referring to Jewish men deriving from originally Ladino-speaking communities that emanated directly from the Iberian Exile. Included males noted in their informed consents that they, their father and paternal grandfather are Sephardic Jews from the specified community. A sample of

7

174 males was compiled (Supplementary Table 1), made up of self-defined Sephardic Jewish males either from the Iberian Peninsula itself, or from countries that received major migrations of Sephardic Jews after the expulsion of 1492-1496, as follows: Belmonte, Portugal (16); Bulgaria (49); Djerba (13); Greece (2); Spain (3); Turkey (91). Countries that received exiles from the Iberian peninsula, but themselves had substantial pre-existing Jewish communities (Italy and the North African countries) were not included. Haplogroups were equivalent to those typed in the Iberian Peninsula samples, except that sublineages of hgR1b3 were not defined. In haplogroup comparisons, therefore, all of these sublineages were combined into hgR1b3 (also known as R-M269) itself. Data on eight Y-STRs were available, allowing comparison with Iberian and North African data.

Data analysis In many cases, sample sizes for analyses using haplogroups are larger than those used for the same populations for Y-STR-based analyses. For the Moroccan sample (total n=147), this is because only a subset (n=104) was typed for Y-STRs. For the remainder, small reductions in sample sizes are due to the removal of chromosomes carrying STR allele duplications, or ‘partial’ alleles, which cannot readily be accommodated in STR-based analyses. Summary statistics (Nei’s estimator of gene diversity, population-pairwise FST [for haplogroups] and RST [for Y-STR haplotypes]) were calculated using Arlequin52. Multi-dimensional scaling based on FST and RST matrices was carried out using PROXSCAL in SPSS 14.0. Relationships between Y-STR haplotypes within specific haplogroups were displayed using reduced median networks53 constructed within Network 4.500 using intra-haplogroup variance-based weighting as described54. Chromosomes carrying Y-STR allele duplications, or partial alleles, were omitted before analysis. Admixture proportions were estimated using mY statistics implemented in Admix 2.055. This coalescent-based estimator takes into account allele frequencies as well as molecular information 56. All potential parental populations are expected to be sampled and constant in size, and the effects of genetic drift or gene flow since the admixture event are considered negligible11. We have used three parental populations: Basques (n=115), Moroccans34 (n=104) and Sephardic Jews (n=174). Molecular distances between haplotypes were calculated using binary markers and microsatellites, weighted

8

respectively at 100 and 1 to reflect their differences in mutation rates. Standard errors were calculated on the basis of 10,000 bootstraps. Average square difference (ASD) was calculated as described57.

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Results A total of 30 binary markers were typed in a set of 1140 Y chromosomes belonging to 18 populations from the Iberian Peninsula and the Balearic Islands (Figure 1). Of the 31 possible haplogroups defined by these markers, 20 were observed, but seven were represented by only one or two individuals. Thirteen haplogroups (each present at about one percent or greater overall) thus account for the vast majority of chromosomes, and one haplogroup, R1b3*, is by far the most common (55%). When all chromosomes derived for the marker M269 are considered (R1b3* plus its sublineages R1b3b, d and f), this figure approaches 66%. To provide a context in which to consider the issue of a North African genetic contribution, haplogroup frequency data were compiled for four North African populations: Moroccans and Saharawi34, plus Algerians and Tunisians47 (Figure 1). The most common haplogroup among North African populations is E3b2, representing 54% of the total of 361 chromosomes. To consider the contribution to the modern Iberian Peninsula of Sephardic Jewish populations, a set of 174 Y haplotypes was compiled from self-defined Sephardic males with ancestry in Mediterranean countries (see Materials and Methods). This sample does not carry one predominant haplogroup, but instead shows >15% frequencies of three haplogroups, J2, J*(xJ2), and G. Haplogroup frequencies in these Iberian, North African and Sephardic Jewish populations are displayed graphically in Figure 2. The dramatic difference in haplogroup frequencies across the Gibraltar Strait34 is the most striking feature. A representation of these haplogroup frequency data in the form of a multi-dimensional scaling (MDS) plot based on a pairwise FST matrix (Figure 3a) displays this distinction clearly, with the Iberian populations forming a clear cluster, the four North African populations separated clearly from them in the first dimension, and the Sephardic Jewish sample occupying an intermediate position. The Iberian populations most strongly differentiated from the non-Iberians are the Basques and the Gascons. Ascertainment bias of the SNPs used to define haplogroups is a potential problem in Ychromosomal diversity analysis (particularly since some Y-SNPs typed here were actually ascertained in Basques58; 59), and can be addressed by considering pairwise RST estimates based on Y-STRs. Most of the Iberian samples had been previously typed with a set of 19 Y-STRs46; this typing was extended to the full set of samples (Supplementary Table 1). Inclusion of published data on the North African

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samples allowed a comparison over eight shared loci, which were also comparable in the Sephardic Jewish sample. The MDS plot based on these data (Figure 3b) shows a similar pattern to that based on haplogroup frequencies, suggesting that ascertainment bias is not a major issue here. Removal of the North African and Sephardic Jewish samples allows the distribution of Iberian populations to be seen more clearly (Figures 3c, d). Once more, the patterns based on haplogroup frequencies and Y-STR haplotypes (here based on 17 loci, with DYS385a,b removed) are broadly similar. In each case the Basques are distinct from all other Iberian populations (and statistically significantly different, as judged by pairwise population differentiation tests), with the exception of the Gascons when haplogroup frequencies are considered. To formally assess the impact of North African and Sephardic Jewish contributions on the indigenous population, we carried out admixture analysis, employing the mY estimator55 and treating the study populations as hybrids of three parental populations. We chose the Basques as the Iberian parental sample: this is justified on the basis of a relative absence of Muslim occupation of the Basque region17, and supported by the genetic distinctiveness of the Basque and neighboring Gascon samples (Figure 3). As the North African parental sample, we chose the Moroccans, based on historical evidence that entry to the Iberian peninsula was via the Strait of Gibraltar17, and that the invading armies were largely native to Morocco. The third parental population was the Sephardic Jewish sample. Mean ancestry proportions and their standard deviations for each population are represented schematically in Figure 4 (and see Supplementary Table 2). Considering the peninsula as a single population, the analysis unsurprisingly finds that the highest mean proportion of ancestry corresponds to the Basque parental population; however, this level is only 69.6%, leaving a remarkably high overall mean proportion of North African and Jewish ancestry comprising the remainder. Mean North African admixture is 10.6% with wide geographical variation (Figure 4, Supplementary Table 2), ranging from zero in Gascony, to 21.7% in Northwest Castile. Mean Sephardic Jewish admixture is 19.8%, varying from zero in Minorca to 36.3% in South Portugal (the value in Asturias is unlikely to be reliable because of small sample size). To examine admixture in more detail, we can compare Y-STR haplotypes within prominent lineages shared between the Iberian samples and the North African and Sephardic Jewish samples. A reduced median network representing the 8-locus haplotypes within hgE3b2, the predominant

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haplogroup in North Africa, is shown in Figure 5a. The network is star-like, with a major core haplotype shared by 48 North African, 27 Iberian, and the sole example of a Sephardic Jewish haplotype. In total, twelve of the 51 haplotypes are shared between North Africans and Iberians, but, but Iberians show a lower diversity (average squared difference, ASD = 2.85) than North Africans (ASD = 9.13). This is consistent with a history of migration of North Africans to Iberia, and introgression of hgE3b2 haplotypes, representing a subset of the North African diversity, into the indigenous population. A reciprocal example is provided by hgG (Figure 5b), frequent in the Sephardic Jewish sample. In this case, only two North African chromosomes belong to this haplogroup, but 7/48 haplotypes are shared betweens Sephardic Jewish and Iberian chromosomes, and the respective ASD values are similar, at 14.00 and 15.10. The high degree of haplotype sharing indicates introgression of Sephardic Jews into the indigenous Iberian population, but the similarity in haplotype diversity suggests that this was relatively ancient. Supporting a contribution of Sephardic Jewish patrilines to the Iberian population, we also observed shared STR haplotypes between the two within haplogroups E3b1, J*, J2 and K* (data not shown; Supplementary Table 1). The mean proportion of identical haplotypes shared between the Sephardic Jewish sample and the Iberian samples is 3.6%, while the corresponding proportion for the Moroccan sample is 2.8%.

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Discussion The Iberian peninsula is often regarded as a source for northward post-glacial expansions2; 3; 5 and a sphere of Neolithic influence from the Near East38. Our study suggests that its recent history has also had a profound influence on its diversity of Y-chromosomal lineages. Historical accounts should allow us to account for this, but are sometimes written long after the incidents they describe, are usually scarce, and are always recorded with a particular audience in mind, and therefore subject to bias17. The marked genetic differentiation between the contributing populations in this case allows an attempt to disentangle their influence; such recognition may be more difficult when source populations for migrations or invasions are only slightly differentiated from recipient populations, as in the case of the Anglo-Saxon60 or Viking61 contributions to the British Isles, for example. Our admixture approach has identified high mean levels of North African and Sephardic Jewish patrilineal ancestry in modern populations of the Iberian Peninsula and Balearic Islands. We find a mean of 10.6% North African ancestry, somewhat higher than previous ad hoc estimates38, and a mean of 19.8% Sephardic Jewish ancestry, a figure that cannot be readily compared with any other study. These findings attest to a high level of religious conversion (whether voluntary or enforced) driven by historical episodes of religious intolerance, that ultimately led to the integration of descendants. Some archaeological evidence has been claimed to support prehistoric African influence in the Iberian peninsula62, and a single mitochondrial DNA (mtDNA) haplotype of North African origin found among Iberian Bronze Age cattle ancient DNA samples from northern Spain63 has been taken to support this. However, we observe low diversity of the prominent North African lineage hgE3b2 in Iberian populations, which argues against a prehistoric origin for the majority of chromosomes in this lineage, being more compatible with their arrival in more recent times. North Africans entered the Iberian peninsula from the south, and apparently spent the least time in the north, being finally expelled from Andalusia over 700 years after their arrival. We might therefore expect a south-north gradient of North African ancestry proportions. However (and in agreement with studies of independent samples36;

41; 64

), we find no evidence of this. Indeed, the

highest mainland proportions of North African ancestry (>20%) are found in Galicia and Northwest Castile, with much lower proportions in Andalusia. The most striking division in North African ancestry proportions is from the western half of the peninsula, where it is relatively high, to the

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eastern half, where it is relatively low (Figure 4). This distribution could reflect genetic drift, and the history of enforced relocations and expulsion of moriscos. The entire large community of moriscos of Granada was relocated northward and westward following the war of 1567-7123. In addition, the final expulsion of moriscos ordered by Philip III and carried out from 1609 was highly effective in some regions of Spain, including Valencia and Western Andalucia, but less so in Galicia and Extremadura, where the population was more dispersed and integrated. Jewish communities were already longestablished by 711 CE, and widespread, so we might expect the level of Sephardic ancestry to also be widespread and undifferentiated. With the exception of the far northeast (NE Castile, Gascony and Catalonia), this is indeed true for the mainland. It is important to consider factors that might act to elevate the apparent proportions of Sephardic Jewish ancestry that we estimate, since these values are surprisingly high. Choice of parental populations in admixture analysis can have a major effect on the outcome, and among the parental populations in our analysis the Sephardic Jewish population has a different status compared to the two others: while Basque and Moroccan samples are drawn from sizeable populations that have maintained their existence in situ, with a probable low level of admixture with the other parentals, the Sephardic Jewish sample is taken from a comparatively small group of self-defined individuals whose ancestors have lived in various parts of the Iberian Peninsula, and were themselves probably subject to some degree of admixture with Iberians. This potential past admixture would have the effect of increasing the perceived level of Sephardic Jewish ancestry compared to the actual proportion. The presence of the typically western European lineage hgR1b3 at a frequency of 11% in the Sephardic Jewish sample might be a signal of such introgression. To examine this, we constructed a network of hgR1b3 Y-STR haplotypes in Iberian, Sephardic Jewish and Moroccan samples (Figure 6). Twelve of the 20 Sephardic Jewish R1b3 haplotypes are shared with Iberian examples, suggesting that they will indeed affect the admixture proportions. However, 8/20 are unique, and five of these are peripheral in the network. They will have little impact on the admixture proportions, and likely reflect R1b3 chromosomes of Middle Eastern origin. It therefore seems that, overall, the ancestry proportions are likely to be only slightly affected by Iberian admixture into the Sephardic Jewish sample. An additional factor that could lead to overestimation of Sephardic Jewish ancestry proportions is the effect of other influences on the Iberian Peninsula from the eastern Mediterranean

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that might have imported lineages such as G, K* and J. These fall into two different time periods: the Neolithic, beginning 10 KYA, the demographic effects of which are a matter for heated debate1, and the colonizing behaviors of the Greeks and Phoenicians65 in the last three millennia. Effects in the second case are expected to be most marked in the eastern part of our sample area, but despite this the apparent Sephardic Jewish ancestry proportions remain substantial in the west (Figure 4). The confounding effects of earlier population movement are likely to be particularly strong for Ibiza, Majorca and Minorca, whose island nature makes them more susceptible to influence by immigration and subsequent drift than inland sites. For example, history records that Ibiza, with a high apparent Sephardic Jewish ancestry proportion in our study, had an insignificant Jewish population compared to its neighbors66, yet had previously been an important Phoenician colony. Likewise, Minorca is recorded as having a substantial Jewish population66, yet here shows no Sephardic Jewish ancestry. Our study has focused on the Y chromosome, but can we say anything about whether admixture has been predominantly male-mediated? Some mtDNA studies32; 33 find evidence of the characteristic North African haplogroup U6 within the Iberian peninsula. While its overall absolute frequency is low (2.4%33), it signals a possible current North African ancestry proportion of 8-9% because it is not a common lineage in North Africa itself. If this figure is reliable, it is not dissimilar from the level of paternal ancestry that we find. This might suggest that initial admixture involved movement of approximately equal numbers of males and females; however, because of drift through differential reproductive success of males and females carrying different lineages, current relative proportions are an unreliable guide to proportions in the past. Comparable mtDNA data reflecting Sephardic Jewish contributions to the various areas of Iberia are not available, but sequence data on hypervariable regions I and II in a sample of 31 Sephardic Jews from Turkey has shown that their sequences and haplogroup frequencies are similar to those of Iberian populations67, suggesting that admixture may be difficult to detect. Interestingly, analysis of European genome-wide SNP data68 shows the western half of the Iberian peninsula to display the highest mean heterozygosity values in the continent, an observation that might reflect its history of admixture of populations from very different sources. In this study we have demonstrated the dramatic impact of recent events on the genetic landscape of an important part of the European continent. Immigration events from the Middle East and North Africa over the last two millennia, followed by introgression driven by religious

15

conversion and intermarriage, seem likely to have contributed a substantial proportion of the patrilineal ancestry of modern populations of Spain, Portugal and the Balearic Islands. In studies that seek to trace the imprint of key events in the earlier prehistory of Europe, the impacts of such recent episodes of gene flow and integration must be taken into account.

16

Acknowledgements We thank all DNA donors, and Santos Alonso, Jaume Bertranpetit, Helena Côrte-Real, Adolfo López de Munain and Carlos Polanco for provision of samples. We also thank Dolors Bramon (University of Barcelona) for historical advice, and two anonymous reviewers for helpful comments. M.A.J. was supported by a Wellcome Trust Senior Fellowship in Basic Biomedical Science (grant no. 057559), and S.M.A., E.B., P.L.B., S.J.B. and A.C.L. by the Wellcome Trust.

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Figure Legends

Figure 1: Y-chromosomal haplogroups in Iberian, North African and Sephardic Jewish samples. Binary marker phylogeny of the Y chromosome, showing mutations on the branches of the tree, and shorthand haplogroup names40 immediately beneath; haplogroups unobserved in any sample are indicated by dashed branches on the tree. Below the phylogeny are given the percentages of chromosomes carrying the observed haplogroup. n: sample size. h: Nei’s unbiased estimator of gene diversity. Data on North African populations are from the literature: - a34; b47, with haplogroup prediction for hgG. c - sub-haplogroups of R1b3 were not typed in the Sephardic Jewish sample.

Figure 2: Haplogroup distributions in Iberian, North African and Sephardic Jewish populations. Haplogroup profiles of samples from the Iberian peninsula and Balearic Islands, published North African samples34; 47, and a Sephardic Jewish sample. Sectors in pie-charts are colored according to haplogroup in the schematic tree to the right, and sector areas are proportional to haplogroup frequency. Sample names, abbreviations, and sizes (within pie-charts) are indicated. Subhaplogroups of R1b3 were not typed in the Sephardic Jewish sample.

Figure 3: Multidimensional scaling (MDS) plots illustrating the relationships among Iberian, North African and Sephardic Jewish populations. a) MDS based on population pairwise FST values from haplogroup data, including Iberian, North African and Sephardic Jewish samples. All haplogroups carrying the derived allele at M269 are pooled into hgR1b3 for the purposes of this analysis. Abbreviations of population names are as in Figure 1. b) MDS based on population pairwise RST values from 8-locus Y-STR data, including Iberian, North African and Sephardic Jewish samples. c)

MDS based on population pairwise FST values from haplogroup data, including only Iberian samples. Abbreviations of population names are as in Figure 1.

d) MDS based on population pairwise RST values from 17-locus Y-STR data, including only Iberian samples.

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Figure 4: Iberian, North African and Sephardic Jewish admixture proportions among Iberian peninsula samples. Mean North African, Sephardic Jewish and Iberian admixture proportions among Iberian samples, based on the mY estimator and Moroccan, Sephardic Jewish and Basque parental populations, are represented on a map as shaded bars on bar charts. Error bars indicate standard deviations, and three-letter codes indicate populations as given in Figure 1.

Figure 5: Diversity of Y-STR haplotypes belonging to haplogroups E3b2 and G. a) Reduced median network53 containing the 8-locus Y-STR (DYS19, DYS388, DYS389I, DYS389II-I, DYS390, DYS391, DYS392, DYS393) haplotypes of 170 hgE3b2 chromosomes. North African haplotypes include those from Moroccan, Algerian, Tunisian and Saharawi samples. Circles represent haplotypes, with area proportional to frequency and colored according to population as shown in the key. b) Analogous network for 82 chromosomes within hgG.

Figure 6: Diversity of Y-STR haplotypes belonging to haplogroup R1b3. Reduced median network53 containing the 8-locus Y-STR (DYS19, DYS389I, DYS389II-I, DYS390, DYS391, DYS392, DYS393, DYS439) haplotypes of 767 hgR1b3 chromosomes, from Iberian populations and the Sephardic Jewish and Moroccan parental samples used in admixture analysis. Circles represent haplotypes, with area proportional to frequency and colored according to population as shown in the key. For Iberian data, hgs R1b3b, d, f and g have been combined into hgR1b3 since these sublineages were not distinguished in the Sephardic Jewish sample.

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8 2 20 nac na na (5) (1) (11)

4 (2)

h 0.804 ±0.049 0.598 ±0.056 0.742± 0.048 0.779 ±0.082 0.576 ±0.049 0.586 ±0.071 0.503 ±0.111 0.656 ±0.051 0.608 ±0.052 0.743 ±0.057 0.701 ±0.049 0.576 ±0.096 0.760 ±0.053 0.774 ±0.041 0.686 ±0.058 0.691 ±0.058 0.634 ±0.085 0.744 ±0.051

0.591 ±0.046 0.725 ±0.063 0.731 ±0.028 0.406 ±0.101

0.849 ±0.013c

Basque Country BAS

Galicia GAL

20 Asturias AST

88

100 60

Gascony GAS

116 24 31

NW Castile NWC

34

NE Castile NEC

Aragon ARA

N Portugal NPO

52 78

Extremadura EXT

Castilla la Mancha CLM

S Portugal SPO

62

54

E Andalusia EAN

Adams et al., Figure 2

E3a E3b* E3b1 E3b2 E3b3 F*(xG-K) G I

Algeria ALG

147 29

E1

J(xJ2) J2 K*(xP)

46

Saharawi SAH

Majorca MAJ

W Andalusia WAN

Morocco MOR

Sephardic Jewish SJ

37

Ibiza IBZ

95

73

73

Minorca MIN

Catalonia CAT

Valencia VAL

63

174

80

139

Tunisia TUN

Q*x(Q3) R1* R1a1 R1b* R1b3* R1b3b R1b3d R1b3f R2

FST (hg data)

a)

S-stress 1.4%

0.3

SJ

SAH

BAS

TUN

0 GAS

ALG MOR

-0.3

0

-1

1

2

RST (8-locus Y-STR data)

b)

S-stress 1.3% SAH

0.4 ALG

BAS

TUN

0 GAS

MOR

-0.4 SJ 0

-1

1

2

FST (hg data)

c)

S-stress 6.4%

0.8 CAT

ARA

0.4 GAS MIN

BAS

0

WAN

MAJ

EXT

VAL

EAN

AST

NPO GAL

CLM

-0.4

SPO

NWC

NEC

IBZ -0.8 -1.5

-1

0

-0.5

0.5

1

2

RST (17-locus Y-STR data)

d)

S-stress 4.3%

0.6 0.4

MAJ GAS

CAT

WAN

EAN NEC

0 BAS

NWC

MIN

EXT

GAL CLM

NPO

VAL

SPO

ARA

AST

-0.4 IBZ -0.8 -1.5

Adams et al., Figure 3

-1

-0.5

0

0.5

1

1.5

AST

GAS

GAL CAT

NEC NWC ARA NPO

MIN MAJ

CLM VAL

EXT

IBZ

SPO

EAN

0

Adams et al., Figure 4

Iberian

50

North African

% ancestry

100

Sephardic Jewish

WAN

n=1 Iberian North African Sephardic Jewish

a) hgE3b2

Adams et al., Figure 5

b) hgG

n=1 Iberian Moroccan Sephardic Jewish

hgR1b3

Adams et al., Figure 6

DYS437

DYS438

DYS461

DYS462

DYS385

10 11 11 13 10 10 11 12 10 11 10 12 10 12 10 12 10 12 11 12 10 11 10 12 10 13 10 11 10 12 10 12 9 13 11 10 9 11 11 12 9 11 10 12 9 12 11 10 9 12 11 11 9 9 10 11 11 10 11 11 12 12 10 12 12 12 10 12 12 11 11 12 12 12 11 12 12 11 10 12 12 13 11 12 12 13 11 12 12 10,12 11 12 12 11 11 12 11 11 11 12 12 12 11 13 12 12 11 12 12 12 11 12 12 13 10 12 12 11 10 13 12 12 11 12 12 11 11 12 12 12 11 13 12 12 11 12

12 12 12 12 12 12 13 12 10 11 11 11 12 12 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

14,14 13,14 13,14 12,12 16,16 14,14 12,12 12,13 13,17 12,17 12,17 14,17 16,17 14,15 11,14 11,14 12,14 11,14 10,13 11,14 11,14 11,11 12,15 11,14 11,14 10,15 11,13 11,14 11,14 11,14 14,14 11,15 11,14 11,14

Asturias IP1008 AST IP1015 AST IP1002 AST IP1019 AST IP716 AST IP995 AST IP992 AST IP997 AST IP1020 AST IP1023 AST IP991 AST IP303 AST IP680 AST IP989 AST IP993 AST IP999 AST IP1011 AST IP1016 AST IP1018 AST IP1021 AST

E3b* E3b* E3b1 G I I J2 J2 J2 K(XP) R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3*

13 13 13 15 17 15 14 15 14 15 14 15 14 14 14 14 14 14 14 14

12 12 12 13 13 14 15 15 15 12 12 12 12 12 12 12 12 12 12 12

12 14 13 12 13 12 13 12 12 12 13 13 13 13 13 13 13 13 14 12

18 17 17 17 15 16 17 16 16 15 16 16 16 16 16 16 16 16 16 16

24 24 25 22 23 22 23 24 23 24 24 23 24 24 24 24 24 24 22 23

10 10 10 10 10 10 10 10 11 10 10 11 12 11 11 10 10 10 10 11

10 11 11 11 11 11 11 11 11 14 13 13 13 13 13 13 13 13 13 14

13 12 14 14 13 13 12 13 13 13 12 13 13 13 13 13 13 13 13 13

11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

14 14 14 15 15 16 15 16 15 14 15 15 15 15 15 15 14 15 14 15

10 11 10 10 10 10 9 9 10 9 12 12 12 12 12 12 12 12 12 12

12 12 11 11 11 11 11 11 12 11 11 12 12 11 12 12 12 13 12 12

10 10 11 10 10 11 9 11 10 10 11 11 11 10 10 10 11 11 13 11

12 13 11 11 11 12 13 10 12 11 12 13 12 13 12 12 12 12 12 13

11 12 13 12 12 12 11 11 11 13 11 11 11 11 11 11 11 11 11 11

16,16 16,19 16,17 14,15 12,12 13,15 13,17 13,17 14,16 13,15 12,14 11,13 11,14 11,15 11,14 11,14 11,14 11,15 11,14 11,14

Basque Country IP1 BAS IP11 BAS IP20 BAS IP25 BAS IP36 BAS IP884 BAS IP902 BAS IP904 BAS IP935 BAS

E3b2 I I I I I I I I

13 15 13 17 17 16 17 17 17

12 13 14 13 13 13 13 13 13

14 13 12 15 13 13 13 13 14

16 16 16 15 15 15 15 15 15

24 25 22 23 24 23 23 23 23

9 10 10 10 9 10 10 11 10

11 11 11 11 11 11 11 11 11

13 13 13 13 13 13 13 13 13

11 11 12 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12

14 15 16 15 14 15 14 14 15

10 10 10 10 10 10 10 10 10

10 11 11 12 13 11 13 13 12

11 11 11 10 10 10 10 10 10

12 11 12 11 12 11 11 11 11

12 12 12 12 12 12 13 13 12

13,14 12,16 13,16 12,12 12,12 12,12 12,12 12,13 12,12

DYS460

DYS436

14 14 16 15 15 15 15 15 16 15 15 16 15 14 14 14 15 15 15 15 15 15 15 15 15 14 15 14 14 15 15 15 15 15

DYS439

DYS435

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

DYS434

13 17 22 9 11 14 11 11 14 16 24 9 11 13 11 11 12 16 22 10 11 13 11 11 14 15 25 9 11 13 11 11 14 17 23 10 12 14 11 11 12 17 22 10 11 13 11 11 13 15 24 10 11 13 11 11 14 15 25 9 11 13 11 11 12 18 24 10 11 12 11 11 13 16 23 11 11 13 11 11 13 15 23 11 11 12 11 10 12 17 23 10 11 12 11 11 14 17 23 10 13 14 11 11 12 15 23 10 14 13 11 11 13 18 25 11 11 13 11 11 13 16 24 11 13 13 11 11 13 17 24 11 13 14 11 11 14 16 24 11 13 13 11 11 14 17 24 10 13 13 11 11 14 16 23 11 13 13 11 11 13 16 24 11 13 13 11 11 14 16 23 10 13 13 11 11 13 16,17 24 11 13 13 11 11 13 16 24 11 13 14 11 11 12 16 24 11 13 13 11 11 13 16 23 10 13 13 11 11 13 16 23 11 13 13 11 11 13 16 23 10 13 13 11 11 13 16 24 10 13 13 11 11 13 16 23 11 13 13 11 11 13 15 23 11 13 13 11 11 13 17 24 11 13 13 11 11 13 17 24 11 13 14 11 11 13 16 23 11 13 13 11 11

DYS393

12 12 14 13 13 14 13 13 15 15 16 15 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

DYS392

15 13 14 17 15 14 17 17 15 14 14 15 13 16 15 14 12 14 14 14 14 14 14 14 14 15 14 14 14 15 14 14 14 14

DYS391

E3b* E3b2 I I I I I I J2 J2 J2 J2 K(XP) K(xP) R1a1 R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3d R1b3f R1b3f R1b3f R1b3f R1b3f

DYS390

DYS389I

ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA ARA

389 II-Ii

DYS388

Aragon IP685 IP314 IP292 IP534 IP575 IP577 IP580 IP586 IP537 IP571 IP574 IP584 IP521 IP572 IP579 IP369 IP533 IP573 IP576 IP581 IP582 IP583 IP585 IP599 IP789 IP808 IP812 IP864 IP359 IP535 IP536 IP578 IP730 IP835

Hg

Popn

DYS19

1

Name

Adams et al., Supplementary Table 1: Haplotype data

Adams et al., Supplementary Table 1: Haplotype data

IP936 IP905 IP889 IP908 IP910 IP906 IP3 IP4 IP6 IP7 IP8 IP10 IP12 IP15 IP16 IP18 IP19 IP21 IP22 IP23 IP24 IP26 IP27 IP29 IP31 IP32 IP33 IP34 IP37 IP38 IP39 IP40 IP44 IP45 IP46 IP48 IP49 IP527 IP531 IP532 IP877 IP878 IP880 IP881 IP882 IP883 IP885 IP887 IP890 IP891 IP892 IP893 IP894 IP897 IP898 IP899 IP900 IP901 IP903 IP907 IP909 IP911 IP925 IP927 IP928 IP929 IP931 IP932 IP933 IP934 IP937 IP938

BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS

I J(xJ2) J2 J2 J2 Q(xQ3) R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3*

17 14 14 15 16 13 14 14 14 14 14 14 14 14 14 15 14 14 14 14 14 14 14 14 13 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14

13 13 15 17 16 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

12 14 12 12 13 14 13 12 12 13 13 14 13 14 13 13 14 13 13 13 14 13 12 14 13 13 11 13 13 12 13 13 13 14 14 14 13 14 13 13 12 14 14 14 13 13 13 13 13 13 15 14 14 12 13 14 13 13 14 13 14 14 14 13 14 14 13 13 14 14 13 13

15 16 17 17 16 18 16 16 16 16 16 16 16 17 16 17 16 15 16 16 16 16 16 16 16 16 16 16 17 16 16 15 16 16 16 16 16 16 16 16 16 16 16 16 16 16 17 16 16 17 16 15 16 16 16 16 16 16 17 15 15 17 16 16 17 17 16 16 18 16 16 16

23 23 23 23 23 24 24 24 24 24 24 23 25 24 24 23 24 23 24 24 23 24 24 24 25 24 24 23 24 24 24 24 24 24 24 23 24 24 24 25 23 24 24 24 24 23 24 24 25 24 24 23 23 23 24 23 24 25 24 24 24 24 24 24 24 23 25 24 24 24 24 25

10 10 10 10 9 10 11 11 11 10 11 11 10 10 10 11 11 11 11 11 11 11 11 11 10 11 10 10 11 11 12 10 11 11 10 10 11 11 11 10 11 10 11 11 11 11 11 11 11 11 11 11 11 11 10 10 11 10 11 11 11 11 11 10 11 11 10 11 10 10 11 10

11 11 12 11 11 14 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 12 13 13 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13

13 12 11 12 12 13 13 13 13 13 13 14 12 13 13 13 13 15 13 13 13 13 13 13 12 13 13 13 13 13 13 13 13 13 13 13 13 13 13 12 14 13 13 13 13 13 13 13 13 13 12 13 13 14 13 13 13 13 13 12 14 13 13 13 13 13 12 13 13 13 13 12

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 12 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11

12 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

15 14 14 15 14 13 15 15 15 15 15 14 15 14 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 14 15 15 15 14 14 15 14 15 15 15 15 15 15 15 14 14 14 15 15 15 15 14 15 14 15 15 15 14 14 15 15 15 14 15 15

2

10 10 9 9 9 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

11 11 11 11 12 12 11 12 11 11 12 13 13 12 12 12 11 11 12 12 13 12 12 12 14 12 12 13 12 12 12 11 12 11 11 12 11 11 12 13 13 11 13 11 13 12 11 13 11 11 11 12 12 13 12 13 11 12 12 12 12 12 11 12 13 12 13 12 12 12 11 13

10 11 10 11 10 10 11 11 11 12 11 11 11 10 11 10 11 11 11 11 10 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 10 11 11 10 10 11 10 11 11 11 12 11 10 10 11 10 11 11 10 10 11 10 12 11 11 10 10 10 11 10 10 11 11

11 13 11 13 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 11 12 12 12 12 12 13 12 12 12 12 12 13 12 13 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

12 13 11 11 10 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12,12 12,18 13,21 12,16 13,15 15,16 12,14 11,14 11,14 11,13 11,14 11,14 11,13 11,14 11,14 11,14 11,14 11,14 11,14 12,14 11,11 10,14 11,14 11,13 11,13 12,14 11,14 11,11 11,14 11,14 11,14 11,15 11,14 11,15 11,14 11,11 11,14 11,14 11,14 11,13 12,14 11,13 11,14 11,14 11,14 11,14 11,14 11,15 11,12 11,14 11,14 12,14 11,11 11,14 11,14 11,11 12,14 11,14 12,14 11,14 12,14 11,14 11,14 12,14 11,14 11,14 11,13 11,14 11,14 11,14 11,14 11,13

Adams et al., Supplementary Table 1: Haplotype data

IP939 IP940 IP941 IP942 IP945 IP946 IP947 IP47 IP50 IP2 IP9 IP13 IP17 IP28 IP30 IP35 IP42 IP526 IP879 IP886 IP888 IP895 IP896 IP944 IP5 IP14 IP41 IP43 IP82 IP83 IP529 IP530 IP926 IP930 IP943

3

BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS BAS

R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3b R1b3b R1b3d R1b3d R1b3d R1b3d R1b3d R1b3d R1b3d R1b3d R1b3d R1b3d R1b3d R1b3d R1b3d R1b3d R1b3d R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f

14 14 14 12 14 14 14 15 15 14 14 14 14 14 14 14 14 14 14 14 14 14 13 14 14 14 14 14 14 14 14 14 14 14 14

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

14 13 14 13 14 14 14 14 14 14 13 13 13 13 13 13 14 13 13 13 13 14 13 13 14 13 14 14 13 13 14 14 13 13 14

16 16 16 17 16 18 17 16 16 16 16 16 16 16 16 16 16 17 16 16 16 16 17 16 16 16 16 16 16 16 16 16 16 16 16

24 24 24 24 23 24 24 23 23 24 24 24 23 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24

11 11 11 11 11 10 11 10 10 11 11 11 10 11 11 10 11 9 10 10 10 10 10 11 10 10 10 11 10 10 11 11 10 12 11

13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13

13 13 13 13 14 13 13 13 13 13 13 14 14 13 13 13 13 13 13 13 13 13 13 14 13 13 13 13 13 13 13 13 13 13 13

11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11 12 14 12 11 12 15 12 11 12 15 12 11 12 15 12 11 12 14 12 11 12 14 12 11 12 14 12 11 12 15 12 11 12 15 12 11 12 14 12 11 12 14 12 11 12 14 12 11 12 14 12 11 12 15 12 11 12 14 12 11 12 14 12 11 12 14 12 11 12 14 12 11 12 14 12 11 12 14 12 11 12 14 12 11 10,12 14 13 11 12 14 11 11 12 14 12 11 12 15 12 11 12 15 12 11 12 15 12 11 12 15 12 11 12 15 12 11 12 15 12 11 12 15 12 11 12 15 12 11 12 15 12 11 12 15 12 11 12 15 12

11 12 11 11 14 11 12 13 13 11 12 13 12 12 12 12 11 12 12 12 12 12 12 12 13 12 13 13 12 12 12 13 12 11 13

10 10 11 11 11 10 10 11 11 10 10 10 10 10 10 10 10 10 10 10 10 11 10 10 10 11 10 10 11 10 10 10 11 11 10

12 12 12 12 12 12 13 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 12 11

11,14 11,14 11,14 11,14 11,14 11,14 11,15 11,11 11,11 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,13 11,14 12,13 11,13 11,14 11,14 11,14 11,14 11,14 11,14 11,14

Catalonia IP73 CAT IP53 CAT IP548 CAT IP59 CAT IP67 CAT IP525 CAT IP555 CAT IP567 CAT IP546 CAT IP557 CAT IP55 CAT IP64 CAT IP543 CAT IP570 CAT IP588 CAT IP52 CAT IP54 CAT IP56 CAT IP57 CAT IP58 CAT IP60 CAT IP61 CAT IP62 CAT IP63 CAT IP65 CAT IP66 CAT IP68 CAT IP70 CAT IP72 CAT IP74 CAT IP76 CAT IP77 CAT IP78 CAT IP79 CAT IP518 CAT

E3b1 E3b2 E3b3 G G G G G I I J2 J2 J2 J2 J2 R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3*

13 13 15 15 15 15 15 15 15 17 14 15 14 14 16 14 15 14 14 14 14 14 14 15 14 14 14 14 14 14 14 14 14 14 14

12 12 12 13 12 13 12 13 13 13 15 15 15 16 16 12 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12

13 14 13 12 12 12 12 12 13 14 13 13 14 13 13 13 13 13 14 13 13 13 13 13 13 14 13 13 13 13 14 12 14 13 13

17 16 18 17 18 17 16 16 16 15 18 18 17 16 16 16 16 16 16 16 16 16 16 16 16 16 16 17 16 16 17 16 17 16 17

24 24 23 22 22 22 21 22 26 25 25 23 23 23 23 24 24 24 24 24 24 24 24 24 24 24 23 24 24 23 24 26 24 25 24

10 9 10 10 10 11 10 10 10 9 10 9 11 10 9 10 10 11 11 11 11 11 11 10 12 11 11 10 11 11 11 10 11 11 10

11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 13 13 13 13 13 13 13 13 13 14 13 14 13 12 13 12 13 13 13 14

13 13 14 14 13 15 13 13 13 13 12 13 12 12 12 13 13 13 13 13 13 13 13 13 14 13 14 13 12 13 13 13 13 13 13

11 11 11 11 11 11 12 11 11 11 11 11 10 11 11 12 11 11 11 11 11 11 11 11 11 11 11 11 10 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 10 12 12 12 11 11 11 11 12 11 12 11 11 11 13 13 11 11 12 12 13 12 11 12 13 12 11 12 12 12 12 11 12 12

11 11 10 10 11 10 9 10 10 10 12 10 9 11 10 11 10 11 10 11 11 11 11 10 11 10 10 11 11 11 12 10 12 11 10

12 13 12 11 10 11 11 11 11 12 11 13 12 10 13 12 12 12 13 12 12 12 12 12 12 12 12 12 11 12 12 12 12 12 12

12 12 11 12 12 12 12 12 12 12 10 11 11 11 10 11 11 11 11 11 11 11 11 11 11 11 11 12 11 12 11 11 11 11 11

16,18 13,15 15,17 14,15 12,14 15,15 12,14 14,14 12,16 12,12 14,18 12,13 12,14 13,17 13,16 11,14 11,15 11,14 11,14 11,14 12,14 11,13 11,15 11,15 12,14 11,15 11,14 11,14 12,14 11,14 11,14 11,14 11,14 11,15 12,14

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

14 14 14 16 16 16 16 16 15 15 14 15 15 14 14 15 15 15 15 15 16 15 15 15 15 14 15 14 14 15 14 15 15 15 15

10 10 11 10 10 10 10 10 10 10 9 9 9 10 9 12 13 12 11 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 13

Adams et al., Supplementary Table 1: Haplotype data

IP519 IP520 IP523 IP524 IP643 IP834 IP539 IP541 IP542 IP545 IP547 IP549 IP550 IP551 IP553 IP554 IP559 IP560 IP561 IP564 IP565 IP566 IP568 IP590 IP591 IP592 IP600 IP552 IP51 IP69 IP71 IP75 IP80 IP81 IP538 IP540 IP544 IP556 IP558 IP562 IP563 IP569 IP589 IP603 IP604

CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT

Castilla La Mancha IP381 CLM IP676 CLM IP250 CLM IP267 CLM IP333 CLM IP492 CLM IP706 CLM IP742 CLM IP264 CLM IP638 CLM IP335 CLM IP336 CLM IP345 CLM IP347 CLM IP263 CLM IP677 CLM IP379 CLM IP280 CLM IP293 CLM IP300 CLM IP302 CLM IP304 CLM IP305 CLM IP307 CLM IP308 CLM

4

R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3d R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f

14 14 14 14 14 14 14 14 14 14 14 15 14 15 14 14 14 12 15 14 14 14 14 14 14 14 14 14 14 14 14 14 15 14 14 14 14 14 14 14 14 14 14 14 14

12 12 12 12 14 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

13 13 14 14 14 13 13 14 14 13 13 14 13 14 12 12 13 13 13 13 13 13 12 14 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13 12 13 13 13 14 13

17 16 16 16 16 16 17 16 16 16 16 17 16 16 16 16 18 17 16 16 16 16 16 16 17 16 16 17 16 16 16 16 17 16 18 16 16 16 16 16 16 16 16 16 16

24 24 24 24 23 24 24 24 24 24 25 24 24 24 24 25 25 24 23 24 25 24 25 24 24 23 24 23 24 24 24 24 24 24 24 24 24 24 24 24 24 23 25 24 24

10 11 12 11 11 10 11 11 11 11 10 11 10 11 11 11 11 10 10 11 10 11 11 10 10 10 10 11 11 10 11 10 11 10 12 11 11 10 11 11 11 11 11 11 11

13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 12 13 12 13 13 13 13 13 13

13 13 13 13 13 13 12 14 13 12 12 12 13 13 13 13 13 13 13 12 13 13 13 13 13 13 13 13 13 13 13 13 13 14 13 13 13 13 14 13 13 13 13 13 13

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

15 14 14 14 14 15 15 14 15 15 15 15 15 14 15 15 15 15 15 15 15 15 15 15 15 15 14 14 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

12 12 12 12 12 12 12 12 12 12 12 13 12 14 12 12 12 12 12 12 12 12 12 12 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

12 12 12 12 12 12 12 11 11 12 12 12 13 12 12 12 12 13 12 12 12 13 12 11 12 11 12 11 12 11 12 12 12 12 12 13 12 12 11 13 12 14 12 11 11

11 11 10 9 9 11 11 10 11 11 11 11 10 10 11 11 11 11 11 12 10 11 11 10 11 11 10 11 11 11 11 11 11 11 12 12 12 11 11 10 12 11 11 11 11

12 12 12 12 12 12 11 12 12 11 12 11 12 12 12 12 12 12 12 11 13 12 12 12 12 12 12 12 12 12 12 12 13 13 12 12 13 12 11 13 12 12 12 12 12

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11,15 11,14 11,15 11,13 11,14 11,15 11,14 11,14 12,14 11,14 11,14 11,14 11,15 11,14 11,15 11,15 11,14 11,15 11,14 11,11 11,15 11,14 11,15 11,15 11,14 11,13 11,14 11,13 11,14 11,15 12,15 12,16 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,15 11,14 11,14 11,14 11,14 11,15

E3b1 E3b2 G G G G G G I J(xJ2) J2 J2 J2 J2 K(xP) K(xP) R1a1 R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3*

14 13 15 15 15 16 15 15 16 14 15 13 14 15 15 14 15 14 14 13 14 14 14 14 14

12 12 12 13 12 12 12 12 13 16 15 15 14 17 12 12 12 12 12 12 12 12 12 12 12

12 14 12 12 12 13 12 12 13 13 13 14 14 13 13 13 13 13 13 14 12 14 13 14 14

17 16 16 17 17 16 17 17 15 18 18 19 17 18 16 16 18 16 16 16 16 17 15 18 16

24 24 22 23 23 22 23 23 23 23 23 23 24 21 23 24 25 25 24 24 23 24 24 24 23

10 9 10 10 10 10 10 10 10 11 10 11 10 10 11 11 11 11 10 13 11 11 11 11 10

11 11 11 11 11 11 11 11 11 11 11 11 11 11 13 13 11 13 13 13 13 13 13 13 13

13 13 13 14 14 14 13 14 13 12 12 12 12 12 13 13 14 13 13 14 13 13 13 13 13

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11

11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

14 14 16 16 15 15 16 16 15 14 15 15 15 15 14 15 14 15 15 14 15 14 15 15 15

10 10 10 10 10 10 10 10 10 10 9 9 9 9 9 12 11 12 12 12 12 9 12 12 12

11 10 11 13 10 13 12 12 11 13 11 10 12 10 11 12 10 11 12 11 12 13 13 13 13

11 10 11 10 11 11 11 10 10 11 10 11 10 10 11 11 8 11 10 10 10 10 10 11 11

12 13 11 11 10 8 11 12 11 11 13 12 12 13 11 12 11 12 12 12 12 12 12 11 12

12 12 13 12 12 12 12 12 12 11 11 11 11 11 14 11 11 11 11 11 11 11 11 11 11

16,17 13,14 15,15 14,14 14,14 14,15 14,15 14,14 12,12 13,17 13,13 14,17 13,13 14,15 14,16 11,14 11,14 11,14 11,14 11,14 11,15 11,14 11,14 11,14 11,11

Adams et al., Supplementary Table 1: Haplotype data

IP318 IP323 IP324 IP325 IP338 IP348 IP351 IP361 IP362 IP367 IP368 IP370 IP372 IP375 IP376 IP466 IP487 IP488 IP490 IP496 IP661 IP667 IP698 IP703 IP721 IP766 IP790 IP800 IP826 IP854 IP863 IP873 IP312 IP717 IP320 IP628 IP635 IP648

CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM

East Andalusia IP758 EAN IP463 EAN IP734 EAN IP231 EAN IP277 EAN IP326 EAN IP842 EAN IP484 EAN IP502 EAN IP503 EAN IP727 EAN IP753 EAN IP756 EAN IP684 EAN IP724 EAN IP736 EAN IP273 EAN IP278 EAN IP481 EAN IP498 EAN IP779 EAN IP794 EAN IP827 EAN IP831 EAN IP848 EAN IP506 EAN IP235 EAN IP238 EAN IP252 EAN IP254 EAN IP255 EAN IP257 EAN

5

R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3d R1b3d R1b3f R1b3f R1b3f R1b3f

14 14 14 14 14 14 14 15 15 14 14 14 15 14 14 15 14 15 14 15 14 15 14 15 14 14 14 14 14 14 14 14 14 14 14 14 14 14

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

14 16 24 10 12 13 11 11 13 15 24 11 13 13 11 11 14 16 23 10 13 13 11 11 14 17 24 11 12 13 11 11 13 16 24 10 13 13 11 11 13 16 24 10 13 12 11 11 12 16 24 10 14 13 11 11 14 16 24 10 13 13 11 11 13 16 24 11 13 12 11 11 13 17 25 11 13 13 12 11 13 17 24 10 13 13 11 11 13 18 24 11 13 13 11 11 13 16 23 11 13 13 11 11 14 17 24 11 13 13 11 11 12 16 23 11 13 13 11 11 13 16 24 11 13 13 11 11 13 16 24 11 13 13 11 11 13 16 23 11 13 13 11 11 14 16 24 11 13 13 11 11 13 16 24 11 15 13 11 11 13 16,17 24 11 13 13 11 11 12 16 24 11 13 13 11 11 13 16 24 11 13 13 11 11 13 16 23 11 13 13 11 11 13 16 24 11 13 13 11 11 13 16 25 11 13 14 11 11 13 16 24 11 13 13 11 11 13 16 23 10 13 13 11 11 13 16 23 11 13 13 11 11 14 16 24 10 13 13 11 11 14 16 24 10 13 13 11 11 14 16 24 12 13 13 11 11 13 16 24 10 13 13 11 11 13 17 24 11 13 12 12 11 14 16 23 11 13 13 11 11 13 16 24 11 13 13 11 11 13 17 25 11 13 13 11 11 13 16 24 11 13 13 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

14 15 15 14 15 15 14 15 15 15 15 15 15 14 15 15 14 15 14 15 15 14 14 15 15 14 15 14 15 15 14 14 14 14 15 15 15 15

13 13 10 12 11 13 11 12 12 13 11 12 12 13 10 12 12 12 11 12 12 12 11 12 12 12 10 13 12 13 11 12 12 13 10 11 12 12 11 12 12 12 11 12 12 11 11 12 12 12 11 12 12 11 10 12 12 12 10 13 12 13 10 12 12 13 11 13 12 12 10 12 12 12 10 12 13 11 12 12 12 10,13 11 13 12 12 10 12 12 13 10 11 12 13 11 12 12 11 12 13 12 12 10 11 12 13 10 12 12 12 10 12 12 12 10 12 12 12 11 12 12 12 10 13 12 12 10 12 12 13 10 12 12 12 11 13 12 13 11 12 12 12 12 13 12 12 10 12 12 11 10 12

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11,12 11,14 11,11 11,14 10,14 11,14 11,14 11,14 11,14 12,14 11,14 11,14 11,14 11,15 11,14 11,14 11,14 11,15 12,14 13,14 12,14 11,15 11,13 11,14 11,14 12,15 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14

E3b1 E3b2 E3b2 E3b3 G G G I I I I I I J(xJ2) J(XJ2) J(xJ2) J2 J2 J2 J2 J2 J2 J2 J2 J2 R1a1 R1b3* R1b3* R1b3* R1b3* R1b3* R1b3*

13 13 13 13 15 15 15 16 17 14 17 16 17 14 14 14 14 14 15 15 14 14 14 15 15 15 14 14 14 14 14 14

12 12 12 12 13 12 12 13 13 12 13 13 13 15 14 16 15 15 15 15 15 15 14 14 14 12 13 12 12 12 12 12

12 14 14 13 13 12 12 13 14 13 13 12 14 13 14 13 13 13 13 13 12 13 13 13 14 13 13 13 12 14 13 14

12 12 12 12 12 12 12 12 12 12 12 12 12 12 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

14 14 14 14 16 16 16 15 15 14 15 15 15 14 14 14 15 16 15 14 16 16 15 14 15 14 15 15 15 14 14 14

10 10 10 11 10 10 10 10 10 10 10 8 10 10 10 10 9 7 9 9 9 7 9 9 9 11 13 12 12 12 12 12

12 12 12 12 12 11 12 12 12 12 12 12 12 11 12 11 11 11 11 10 11 11 11 10 11 11 11 11 10 11 11 11

17,19 13,14 13,14 16,19 15,15 14,14 12,15 12,12 12,12 15,16 12,12 15,15 12,12 14,18 12,12 12,18 14,18 14,14 13,18 13,16 13,16 14,14 15,16 13,18 13,18 11,15 11,14 9,14 11,15 11,15 11,13 11,14

16 16 16 17 17 17 17 15 15 17 15 16 15 18 16 16 17 16 16 16 16 16 17 16 15 17 16 15 16 17 16 16

24 24 24 24 22 23 22 23 25 23 23 23 25 22 23 24 23 23 23 23 24 23 25 23 22 25 23 24 24 24 24 24

10 9 10 10 10 10 10 10 9 10 10 10 9 10 10 10 11 9 10 9 11 9 10 9 10 11 11 11 12 11 11 11

11 11 11 11 11 11 11 11 11 12 11 11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 13 13 13 13 13 14

13 13 13 14 13 13 14 13 13 14 13 14 13 12 13 12 12 13 12 12 12 13 12 12 12 13 13 13 13 13 13 13

11 11 11 11 11 11 11 11 11 11 11 11 11 11 10 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11 10 10 12 11 11 13 11 12 11 11 11 11 12 11 11 12 11 11 12 12 11 12 12 11 11 12 8 13 12 12 12

9 11 11 10 10 10 11 10 10 11 10 11 10 11 11 11 11 10 10 11 11 10 11 10 10 11 10 10 11 11 11 11

12 13 13 13 11 11 11 11 12 12 11 12 12 11 12 11 12 13 13 12 13 13 14 13 12 11 12 12 12 13 12 12

Adams et al., Supplementary Table 1: Haplotype data

IP258 IP286 IP311 IP322 IP332 IP344 IP349 IP358 IP365 IP383 IP460 IP479 IP480 IP482 IP485 IP491 IP497 IP499 IP500 IP504 IP505 IP507 IP508 IP510 IP511 IP651 IP653 IP671 IP679 IP691 IP710 IP720 IP722 IP729 IP731 IP745 IP746 IP751 IP764 IP770 IP778 IP781 IP785 IP796 IP798 IP801 IP819 IP820 IP823 IP832 IP838 IP844 IP847 IP297 IP723 IP743 IP476 IP665 IP712 IP761 IP772 IP858 IP875

EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN EAN

Extremadura IP256 EXT IP262 EXT IP719 EXT IP868 EXT IP244 EXT IP245 EXT IP352 EXT

6

R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3d R1b3d R1b3d R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f

15 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 15 14 14 14 14 14 14 14 14 14 14 14 12 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

13 12 14 12 14 13 14 13 13 13 14 14 13 13 14 13 13 13 13 13 13 13 13 13 14 13 13 13 13 14 14 13 14 12 13 13 12 13 14 15 13 14 13 14 14 13 13 13 13 13 13 13 13 13 13 13 14 13 13 14 13 13 14

16 16 16 15 16 16 17 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 17 16 17 16 17 16 17 16 16 15 19 16 16 16 16 16 15 16 16 16 16 16 17 16 16 16 16 16 16 16 16 16 16 16 16 17 16 16 16 18 16

24 23 24 23 24 24 24 24 25 24 24 23 24 24 25 24 24 24 24 25 23 24 24 24 23 23 23 24 24 24 25 24 25 24 24 24 24 24 24 23 24 24 23 24 24 24 23 24 23 24 23 24 24 23 24 24 24 24 24 23 24 24 24

11 11 11 11 10 11 11 11 11 11 11 10 11 11 11 11 11 11 10 11 10 11 11 11 10 10 10 10 11 11 11 11 11 11 11 11 10 10 11 11 11 11 11 11 11 11 11 12 11 10 11 10 11 10 10 10 11 10 11 11 11 11 10

13 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 14 13 14 13 13 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 12 13 13 13 13 13 12

13 13 13 12 13 12 13 13 12 12 13 13 13 13 13 13 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 12 13 13 13 13 13 13 13 13 13 13 13 13 13

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

14 15 15 15 15 15 15 15 15 15 14 14 14 15 15 15 15 15 14 15 15 15 15 15 15 15 14 14 15 14 15 15 15 14 15 14 15 15 16 15 15 15 15 14 15 15 15 15 14 15 14 15 15 14 14 14 15 15 15 14 15 16 15

12 12 12 12 12 12 12 12 12 12 9 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 10 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

11 13 12 14 11 12 11 11 11 12 11 13 12 12 12 12 12 12 12 12 12 11 13 12 12 11 13 11 12 12 11 12 11 12 12 12 12 13 11 12 11 10 12 12 11 11 11 12 11 13 11 11 12 12 12 12 13 13 12 13 13 12 13

11 11 11 11 11 11 11 11 8 11 10 11 10 10 11 11 11 10 11 10 10 11 11 11 10 11 11 10 10 10 11 11 10 10 11 11 11 10 11 11 11 11 11 10 11 11 11 11 11 10 11 11 11 10 10 10 11 11 11 11 11 11 11

12 12 12 11 12 12 12 12 11 12 12 12 12 12 11 12 13 12 12 12 12 12 13 12 12 12 12 11 12 12 12 11 12 12 12 12 12 11 12 11 11 12 12 13 12 12 12 12 12 12 12 13 13 12 11 11 12 12 12 12 12 12 12

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12,15 11,14 11,15 11,14 11,14 11,14 11,14 12,14 11,14 11,14 11,14 11,14 11,14 11,15 11,14 11,14 11,14 11,14 11,14 11,14 13,14 11,15 15,15 11,15 11,11 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,15 11,14 11,14 11,13 11,14 11,16 11,14 11,14 11,14 11,14 11,14 11,14 11,13 10,15 11,13 11,14 11,14 11,14 11,15 11,15 11,14 11,14 11,14 11,14

E3b1 E3b1 E3b1 E3b1 E3b2 E3b2 E3b2

13 14 13 13 13 13 13

13 12 12 12 12 13 13

13 13 13 12 13 13 13

17 17 17 17 16 16 16

24 25 24 24 25 24 24

10 10 10 10 9 9 9

11 11 11 11 11 11 11

13 13 13 13 13 13 13

11 11 11 11 11 11 11

11 11 11 11 11 11 11

12 12 12 12 12 12 12

14 14 14 14 14 14 14

10 10 10 9 10 10 10

12 12 13 10 10 10 10

9 11 10 10 11 11 11

12 12 12 13 13 13 13

12 12 12 13 12 12 12

16,18 17,18 17,17 16,17 14,14 13,14 13,14

Adams et al., Supplementary Table 1: Haplotype data

7

IP750 IP330 IP339 IP478 IP769 IP265 IP268 IP299 IP857 IP874 IP281 IP329 IP773 IP784 IP795 IP817 IP371 IP755 IP815 IP233 IP237 IP242 IP261 IP346 IP357 IP366 IP477 IP483 IP494 IP501 IP739 IP744 IP760 IP771 IP807 IP811 IP816 IP818 IP822 IP829 IP836 IP846 IP856 IP861 IP803

EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT EXT

E3b2 E3b3 F* G G I I I I I J2 J2 J2 J2 J2 J2 K(xP) K(xP) K(xP) R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3f

13 13 14 15 15 16 14 14 15 14 15 16 15 15 14 14 13 15 14 15 15 13 14 14 14 15 14 15 15 14 14 14 14 12 12 14 14 14 14 14 14 15 14 14 14

12 12 13 13 12 13 15 14 13 14 16 16 15 16 15 15 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 14 12 12 12 12 12 12 12 12 12

15 13 14 12 12 13 12 12 12 12 13 13 12 13 13 13 13 13 13 13 13 13 13 13 14 13 13 13 14 13 14 13 14 13 13 14 13 14 14 13 13 13 13 13 14

17 16 16 18 17 15 17 16 17 16 17 17 15 17 16 17 16 17 16 16 16 17 15 16 17 18 16 16 16 16 16 16 16 17 17 16 16 17 16 16 16 16 16 16 16

24 24 23 22 23 26 22 23 23 23 23 23 23 23 23 23 23 25 23 23 24 22 23 24 24 24 24 23 24 23 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24

9 9 10 10 10 9 10 10 10 10 10 11 10 10 9 10 10 10 10 11 11 10 10 11 11 13 10 11 10 11 11 11 10 10 10 10 10 11 11 11 10 10 11 11 9

11 11 11 11 12 11 11 11 12 11 11 11 11 11 11 11 13 14 15 13 13 13 13 13 13 13 13 13 13 13 14 13 13 13 14 13 13 13 13 13 13 13 13 13 13

13 13 12 14 14 13 14 13 15 13 12 12 13 12 13 12 13 13 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 12 13 13

11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

14 14 14 16 16 15 16 16 15 16 14 15 16 14 16 14 15 14 14 15 15 15 15 15 15 15 16 15 14 15 15 15 14 15 15 15 14 14 14 15 15 14 15 15 15

10 10 10 10 9 10 10 10 10 10 9 9 9 9 7 9 9 9 8 10 12 12 12 13 12 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

10 10 11 13 11 11 11 12 11 11 11 14 12 11 11 11 13 11 11 12 12 12 11 11 12 12 12 12 13 12 12 14 12 12 12 11 12 12 12 13 13 12 12 11 13

11 11 11 11 11 10 10 10 11 10 10 10 12 10 10 10 10 10 11 11 11 11 12 11 10 11 10 11 10 11 11 11 10 11 11 11 10 10 10 11 11 11 10 11 10

14 14 13 11 11 12 12 12 12 12 12 13 10 12 13 13 11 11 12 12 12 12 12 12 12 12 12 12 12 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

12 12 12 12 12 12 12 12 12 13 10 11 11 10 11 12 12 12 12 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11

13,14 13,14 13,14 12,14 14,14 12,12 13,14 14,14 14,15 14,14 13,18 12,18 18,18 13,18 14,14 13,16 14,16 14,16 15,17 11,14 11,15 12,14 11,14 11,15 12,14 11,15 11,13 11,14 11,13 11,14 11,14 11,14 11,14 11,15 11,15 11,14 11,14 11,14 10,13 11,14 12,14 11,13 11,14 11,14 11,14

Galicia IP409 IP234 IP397 IP416 IP683 IP765 IP777 IP387 IP399 IP413 IP419 IP725 IP740 IP799 IP855 IP294 IP400 IP406 IP699 IP718 IP276 IP282 IP386 IP404 IP411

GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL

E3b* E3b1 E3b1 E3b1 E3b1 E3b1 E3b1 E3b2 E3b2 E3b2 E3b2 E3b2 E3b2 E3b2 E3b2 G G G G G I I I I I

13 13 13 13 13 13 14 13 13 13 13 13 13 13 13 15 15 17 15 16 14 14 16 15 14

12 12 12 12 12 12 12 12 12 12 13 12 12 12 12 13 12 13 12 12 14 14 13 13 14

13 13 13 13 14 13 13 13 14 14 14 14 14 14 14 12 12 13 12 12 12 12 13 14 12

16 17 17 17 17 17 18 16 16 17 16 16 16 16 16 16 16 17 18 17 16 16 16 18 16

24 23 23 24 23 23 24 24 24 25 24 23 24 23 23 22 21 22 23 21 23 22 23 23 23

10 10 10 10 10 10 10 9 9 9 9 9 9 10 9 10 10 10 10 10 10 10 11 11 10

11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 12 12 11

12 13 13 13 13 13 13 14 13 13 13 13 13 13 13 14 14 14 15 15 13 13 14 14 13

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 14 12 12 12 12 12

14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 16 16 16 16 16 16 16 15 15 16

11 10 10 10 10 10 10 10 10 10 10 10 10 10 10 11 10 11 10 10 10 10 10 10 10

12 12 12 12 12 11 12 10 10 10 11 10 11 10 10 11 12 11 11 11 13 12 11 11 11

10 11 11 9 11 9 11 11 12 11 11 11 12 11 10 9 10 11 11 10 10 10 11 11 10

13 11 11 12 11 12 12 12 13 13 13 13 13 12 13 11 11 11 12 11 12 12 12 12 12

12 13 13 12 12 12 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 11 12 12

16,18 15,16 16,16 16,18 15,16 18,18 17,19 13,14 12,15 13,15 14,14 13,14 13,14 13,14 13,14 14,14 13,15 14,14 13,14 13,16 13,15 13,15 12,16 15,15 13,15

Adams et al., Supplementary Table 1: Haplotype data

IP422 IP673 IP747 IP809 IP266 IP295 IP389 IP423 IP802 IP833 IP872 IP414 IP85 IP227 IP229 IP259 IP270 IP287 IP289 IP317 IP354 IP384 IP385 IP388 IP391 IP392 IP393 IP394 IP395 IP396 IP398 IP401 IP402 IP403 IP407 IP408 IP410 IP415 IP417 IP420 IP421 IP668 IP669 IP694 IP695 IP702 IP704 IP705 IP714 IP715 IP733 IP748 IP763 IP806 IP845 IP865 IP867 IP871 IP390 IP824 IP405 IP412 IP708

8

GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL GAL

I I I I J(xJ2) J2 J2 J2 J2 J2 J2 K(xP) R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3d R1b3d R1b3f R1b3f R1b3f

16 15 14 14 14 14 14 15 15 15 15 15 14 14 14 14 14 14 14 14 14 14 15 14 13 14 14 14 14 14 14 14 14 15 14 14 14 15 14 14 15 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 15 14 14 14 14 14

13 13 14 13 16 15 16 15 16 16 15 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

13 13 12 13 13 13 12 12 13 13 12 12 13 13 13 13 13 13 12 13 13 13 13 13 13 13 13 13 13 13 13 13 14 13 12 13 13 13 12 13 13 13 13 14 13 15 14 13 13 14 13 13 14 12 13 13 13 13 13 13 12 13 13

16 17 17 19 17 17 16 16 16 16 16 15 16 16 16 16 16 16 16 16 14 17 16 16 16 15 16 17 16 16 14 16 15 16 15 16 16 16 16 16 16 16 16 17 16 16 16 17 16 17 16 16 16 16 15 16 15 16 17 16 16 16 16

23 24 23 25 23 22 23 24 23 22 26 24 25 23 24 24 24 24 23 25 24 23 24 24 25 23 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 23 24 24 24 24 23 24 24 23 23 24 24 24 22 25 25 24 24 25 24 24 23

11 10 10 11 10 10 10 10 9 10 10 10 11 10 11 11 11 11 11 11 11 10 10 11 11 12 11 11 11 11 11 11 11 10 10 10 11 11 10 11 10 12 11 10 10 11 11 11 10 11 10 11 11 11 10 11 10 11 11 11 11 11 11

12 12 11 11 11 11 11 11 11 11 11 14 13 13 13 13 13 14 13 14 13 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 14 13 13 13 14 13 13 13 14 13 13 13 13 13 13 13

14 15 13 13 12 12 12 13 13 12 12 13 13 13 12 13 13 13 13 13 14 13 13 14 13 13 13 13 13 12 13 15 13 14 13 13 13 13 13 13 13 13 12 14 13 13 13 13 13 13 13 13 13 12 13 13 14 13 13 13 13 13 13

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 10 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

15 15 16 15 14 15 14 16 14 15 16 14 15 15 15 15 15 14 15 15 15 14 15 15 15 15 15 15 15 15 15 14 15 15 15 15 15 14 15 15 15 15 15 15 15 15 15 15 15 14 15 14 15 15 15 15 15 14 14 14 15 15 15

10 10 10 10 10 9 9 9 9 9 9 9 12 12 12 12 12 12 12 12 11 12 12 12 12 12 12 12 12 12 13 12 12 12 11 13 13 13 12 12 12 12 12 12 11 13 12 12 12 12 12 12 12 12 11 12 12 12 12 12 12 12 12

11 11 11 11 11 10 11 11 12 11 11 11 12 12 12 12 11 12 11 12 12 13 12 12 13 11 13 12 11 12 13 12 13 11 11 13 13 12 12 12 12 13 12 14 12 14 12 13 11 13 12 12 12 12 11 12 13 12 12 11 13 11 12

11 11 10 10 11 10 11 11 10 10 11 10 11 11 11 11 10 11 10 10 11 11 11 10 11 10 10 10 10 10 10 10 12 11 10 10 10 10 11 10 11 11 10 11 11 10 10 10 11 10 11 11 10 11 11 10 10 11 11 11 11 11 12

12 12 12 11 11 12 13 10 13 13 10 11 12 11 11 12 13 12 12 12 12 12 12 11 12 11 12 12 12 11 12 11 13 12 12 12 12 12 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 10 12 12 12 12 12

11 12 12 12 11 11 11 11 10 11 11 13 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 10 11 11 11 11 11 11 11 11 11 11 11 11 11 12 12 11 11 11 11 11 11 11 11 11 11 11 11 12 11

12,16 14,15 13,15 12,15 13,16 14,14 13,16 13,17 13,16 14,15 15,18 13,15 12,14 11,13 11,13 11,14 11,15 11,16 11,14 11,14 11,14 11,14 11,15 11,11 12,14 10,14 11,14 11,15 12,14 11,14 11,14 12,15 11,13 11,14 11,16 11,16 11,14 12,14 11,14 11,14 11,15 12,12 11,12,14 11,13 11,14 11,13 11,14 11,17 11,15 11,14 11,15 11,16 11,14 12,14 11,16 11,14 11,14 11,13 11,15 11,14 11,14 11,14 11,14

Gascony IP921 GAS IP587 GAS IP593 GAS IP594 GAS IP595 GAS IP596 GAS IP601 GAS

J2 R1b3* R1b3* R1b3* R1b3* R1b3* R1b3*

15 14 14 14 14 14 14

15 12 12 12 12 12 12

12 12 14 14 14 12 13

16 16 16 16 16 16 16

24 23 24 24 24 24 24

10 11 11 11 11 10 10

11 13 13 13 13 13 13

12 13 13 13 13 13 13

11 11 11 11 11 11 11

11 11 11 11 11 11 11

12 12 12 12 12 12 12

16 15 15 15 15 15 14

9 12 12 12 12 12 12

12 11 12 12 12 12 12

11 11 11 11 11 11 10

10 13 12 12 12 12 12

11 11 11 11 11 11 11

14,16 12,15 11,14 11,14 11,14 11,15 10,14

Adams et al., Supplementary Table 1: Haplotype data

IP605 IP913 IP914 IP915 IP919 IP920 IP922 IP923 IP924 IP912 IP916 IP917 IP918 IP84 IP597 IP598 IP602

GAS GAS GAS GAS GAS GAS GAS GAS GAS GAS GAS GAS GAS GAS GAS GAS GAS

9

R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3d R1b3d R1b3d R1b3d R1b3f R1b3f R1b3f R1b3f

14 14 14 14 14 15 14 14 15 14 14 14 14 14 14 14 14

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

13 14 13 13 14 13 14 12 13 13 13 13 14 13 13 13 13

16 16 16 16 16 17 16 16 16 16 16 16 16 15 15 16 15

24 24 24 24 24 24 22 24 24 24 24 24 24 24 24 24 23

11 11 10 11 10 11 10 11 11 10 10 11 11 10 11 11 11

13 13 13 13 13 13 13 13 12 13 13 13 13 13 13 13 13

13 13 13 14 13 13 13 13 13 13 13 13 14 13 13 13 13

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

14 14 15 14 14 14 15 15 15 14 14 14 14 15 15 15 15

12 12 12 12 12 11 12 12 12 12 12 12 12 12 12 12 12

11 12 11 12 12 11 12 12 12 12 12 12 11 12 13 12 14

10 10 11 11 11 10 11 10 11 11 10 10 10 11 11 11 10

12 12 12 12 12 12 13 12 13 12 12 12 12 12 12 12 12

12 11 11 11 11 11 11 11 10 11 11 11 11 11 11 11 11

11,14 11,14 11,14 11,13 12,14 11,13 11,11 12,14 11,14 11,14 11,14 12,14 11,14 11,15 11,14 11,14 11,14

Northeast Castille IP341 NEC IP342 NEC IP364 NEC IP788 NEC IP428 NEC IP447 NEC IP427 NEC IP86 NEC IP319 NEC IP321 NEC IP378 NEC IP424 NEC IP425 NEC IP426 NEC IP429 NEC IP430 NEC IP431 NEC IP432 NEC IP433 NEC IP435 NEC IP436 NEC IP437 NEC IP446 NEC IP681 NEC IP732 NEC IP735 NEC IP775 NEC IP787 NEC IP862 NEC IP434 NEC IP285 NEC

E3b* E3b1 E3b2 G I J2 K(xP) R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3d R1b3f*

14 13 13 15 17 14 15 14 14 15 14 14 14 14 14 15 14 14 14 13 15 14 14 14 14 14 14 14 14 14 15

12 14 12 12 13 15 12 12 12 12 12 12 12 11 12 12 12 12 12 12 12 12 12 12 12 12 12 13 12 12 12

13 13 14 13 13 13 13 13 13 13 13 13 13 13 13 13 12 13 14 13 12 13 13 13 14 13 13 13 14 14 13

17 18 17 17 15 16 16 16 16 16 17 16 18 16 16 16 16 16 16 16 16 16 16 16 16 16 15 16 16 15 16

23 24 24 22 24 24 23 24 23 25 24 23 24 24 25 24 24 24 24 25 25 25 24 24 24 24 23 24 24 23 24

9 11 9 10 9 10 10 11 10 11 11 11 11 11 12 11 11 11 10 12 11 11 11 11 11 11 10 11 12 11 10

11 11 11 11 11 11 15 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13

13 13 13 12 13 12 13 14 13 13 13 13 13 13 13 13 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

14 14 14 16 15 14 14 15 15 15 14 15 15 15 15 15 15 14 14 15 15 15 15 15 15 15 15 15 15 14 15

10 10 10 10 10 9 9 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

12 13 11 10 12 12 10 13 12 11 11 12 13 13 12 11 12 12 13 13 11 12 11 13 13 12 12 12 12 11 12

10 10 11 10 10 10 10 11 11 11 10 10 11 11 10 10 11 10 10 11 11 11 11 10 10 10 10 11 11 10 11

13 11 13 13 12 12 11 12 12 12 12 12 12 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13

12 12 12 12 12 12 13 11 11 11 11 11 11 11 11 12 11 11 12 11 11 11 11 11 11 11 10 12 11 11 11

12,15 15,15 13,14 12,13 12,12 13,15 16,17 11,15 12,14 10,14 11,15 11,14 11,12 12,14 11,15 11,14 11,14 11,14 11,14 11,14 12,14 11,14 12,14 11,14 11,14 11,13 11,14 10,15 11,14 11,14 11,14

North Portugal IP118 NPO IP124 NPO IP113 NPO IP91 NPO IP103 NPO IP138 NPO IP95 NPO IP114 NPO IP143 NPO IP87 NPO IP89 NPO IP94 NPO IP104 NPO IP107 NPO IP127 NPO IP133 NPO IP111 NPO IP93 NPO IP109 NPO IP117 NPO

E1 E1 E3b* E3b1 E3b1 E3b1 E3b2 E3b2 E3b3 G G G G G G G I J(xJ2) J2 J2

17 17 14 13 13 13 13 13 13 15 15 15 16 15 15 15 16 14 15 15

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 13 16 15

12 12 13 13 13 11 13 14 13 12 13 12 12 12 12 11 14 13 13 13

17 17 17 17 16 18 17 16 19 17 16 17 16 17 17 17 16 16 17 16

22 22 25 24 24 25 23 24 24 22 24 22 21 22 22 23 24 24 23 24

9 9 10 10 10 10 9 9 10 10 10 10 11 10 10 11 11 10 10 10

12 12 11 11 11 12 11 11 11 11 13 11 11 11 11 11 12 11 11 11

13 13 14 13 13 13 13 13 13 15 13 13 14 14 13 14 14 13 12 12

11 11 11 11 11 10 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 14 12 12 12 12 12 12 12 11 12 12

15 16 14 14 15 14 14 14 14 16 14 16 16 16 16 16 15 14 15 16

11 10 10 10 10 10 10 10 10 10 12 10 10 10 11 10 8 10 9 9

13 13 11 12 12 11 10 11 14 11 12 12 12 12 14 12 12 13 11 13

10 10 11 10 9 11 11 11 10 10 11 11 10 11 11 10 11 11 10 11

13 13 12 12 12 11 13 12 11 11 12 11 11 11 10 11 12 12 8 10

12 12 13 12 12 12 12 12 10 12 11 12 12 12 12 12 12 12 11 11

14,16 15,16 16,17 16,18 16,18 16,19 13,14 13,14 15,16 13,17 11,14 12,15 15,15 12,16 15,15 13,14 15,15 13,19 13,15 15,17

Adams et al., Supplementary Table 1: Haplotype data

IP136 IP139 IP146 IP128 IP142 IP88 IP92 IP96 IP97 IP98 IP102 IP105 IP106 IP108 IP110 IP112 IP115 IP116 IP120 IP121 IP123 IP125 IP126 IP129 IP130 IP131 IP132 IP135 IP137 IP140 IP145 IP147 IP148 IP100 IP99 IP119 IP122 IP134 IP141 IP144

NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO NPO

Northwest Castille IP439 NWC IP963 NWC IP443 NWC IP450 NWC IP675 NWC IP678 NWC IP749 NWC IP960 NWC IP448 NWC IP451 NWC IP782 NWC IP828 NWC IP952 NWC IP956 NWC IP958 NWC IP971 NWC IP977 NWC IP980 NWC IP373 NWC IP228 NWC IP377 NWC IP454 NWC IP455 NWC IP752 NWC IP876 NWC IP966 NWC IP987 NWC IP967 NWC IP243 NWC IP440 NWC

10

J2 J2 K(xP) R1a1 R1a1 R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3d R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f

15 15 14 15 15 14 14 14 14 14 14 14 14 14 15 13 14 14 14 14 16 14 15 14 14 14 14 15 14 15 14 14 15 14 14 14 14 14 14 14

15 16 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

12 13 13 13 13 13 13 14 13 14 14 13 13 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13 13 13 14 13 13 13 13 13 13 13 13 13

16 16 16 20 17 16 16 16 17 16 16 15 16 16 16 16 17 15 16 16 16 16 16 16 16 16 16 16 16 17 17 16 18 16 16 16 17 17 16 16

24 23 23 26 24 22 24 25 24 24 24 24 23 24 24 23 24 23 25 24 23 24 24 25 24 24 23 24 25 24 24 24 24 24 24 23 23 23 24 24

10 9 10 11 10 10 11 11 11 11 11 11 10 11 10 11 11 12 11 12 11 11 10 11 11 10 11 10 11 11 11 11 11 11 11 11 11 11 11 11

11 11 14 11 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 12 13 13 13 14 13 13 13 13 14 13 13 13 13 13 13 13

13 13 13 13 13 12 13 13 13 12 14 13 13 13 13 13 11 13 13 13 13 13 13 13 13 13 13 13 12 13 13 13 13 13 13 12 13 13 13 14

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

16 14 14 14 15 15 15 15 15 15 15 15 15 15 15 15 14 14 14 15 15 15 15 15 16 14 15 15 15 15 15 15 14 14 15 15 15 15 15 15

9 9 9 11 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 12 12 13 12 12 12 12 12 12 12 11 12 12 12 11 12

11 11 11 10 14 12 11 12 12 12 13 13 12 12 12 12 12 11 12 12 12 11 11 12 12 11 12 11 14 12 13 12 12 12 11 12 12 12 12 11

11 10 10 11 11 11 11 11 10 10 10 11 10 11 11 11 11 10 11 11 10 10 11 12 10 11 11 11 10 11 11 10 11 10 12 11 11 11 11 12

10 13 11 11 12 12 12 13 12 11 12 12 12 12 12 12 12 13 12 12 12 12 12 12 12 12 11 12 12 13 13 13 12 12 13 13 13 13 13 13

11 10 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 10 11 11 11 11 11

13,17 13,16 15,16 11,14 11,14 11,14 11,15 11,14 12,14 11,14 11,14 11,14 11,14 11,15 11,16 11,14 11,15 11,14 12,14 11,14 11,14 11,14 11,14 12,16 11,13 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,13 11,14 11,14 11,14 11,14 11,14 11,14 11,13

E3b* E3b* E3b1 E3b1 E3b1 E3b1 E3b1 E3b1 E3b2 E3b2 E3b2 E3b2 E3b2 E3b2 E3b2 E3b2 E3b2 E3b2 E3b3 G G G G G I I I J(xJ2) J2 J2

15 14 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13 13 13 15 15 15 15 15 17 15 14 13 14 14

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 13 12 12 13 13 14 15 15 15

13 14 13 13 13 13 13 13 14 14 14 14 13 14 14 14 14 14 12 11 12 12 13 13 13 15 12 12 12 13

16 16 17 17 17 17 17 17 16 16 16 16 16 16 16 16 16 16 18 17 16 17 16 17 15 17 16 17 18 17

22 23 24 24 25 24 24 24 24 24 24 24 24 24 24 24 24 24 24 22 22 22 23 22 23 23 22 24 24 23

9 9 10 10 10 10 10 10 9 9 9 9 9 9 9 9 9 9 10 10 10 10 11 11 10 11 11 10 10 10

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11

14 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 14 14 14 14 13 13 14 13 12 12 12

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 10 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 16 16 16 16 15 15 14 16 14 16 15

10 11 11 12 10 11,12 10 13 10 12 9 12 10 12 9 12 10 14 11 12 10 12 9 12 10 12 10 12 10 12 10 12 10 10 11 13 10 10 11 12 10 10 10 13 10 10 11 13 10 10 11 13 10 10 12 13 10 10 11 13 10 10 11 12 10 10 11 13 10 10 11 13 10 12 11 13 10 11 10 12 10 11 10 11 10 11 10 11 10 11 11 12 9 10 10 11 10 12 10 11 10 11 11 12 10 11 10 12 10 12 10 11 11 11 10 13 9 12 10 13

12 12 11 12 12 12 12 12 12 12 12 13 12 12 12 12 12 11 11 12 12 12 12 12 12 12 12 11 11 11

14,15 12,17 15,18 16,18 18,19 16,18 17,17 16,17 13,14 13,15 14,14 13,14 13,14 13,14 13,14 13,14 12,14 13,15 15,19 13,14 14,15 14,14 14,15 14,14 12,12 15,16 12,13 12,17 13,16 13,20

Adams et al., Supplementary Table 1: Haplotype data

IP441 IP449 IP741 IP837 IP860 IP985 IP248 IP309 IP959 IP974 IP232 IP247 IP269 IP284 IP288 IP290 IP306 IP337 IP343 IP353 IP355 IP356 IP360 IP363 IP382 IP438 IP442 IP444 IP445 IP452 IP453 IP687 IP709 IP711 IP767 IP786 IP792 IP804 IP805 IP821 IP830 IP843 IP851 IP866 IP869 IP948 IP949 IP950 IP951 IP953 IP954 IP955 IP961 IP962 IP964 IP965 IP968 IP969 IP970 IP972 IP973 IP975 IP976 IP978 IP979 IP981 IP982 IP986 IP957 IP983

NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC NWC

South Portugal

J2 J2 J2 J2 J2 J2 K(xP) K(xP) R1a1 R1a1 R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3d R1b3f

17 14 14 15 14 16 15 13 16 15 14 14 16 14 14 14 14 14 14 15 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14.5 15 14 13 14 14 14 14 14 14 14 13 13 14 14 14 13 14 14 14 14 14 15 14 14 14 14 16 14 14 14

15 14 14 16 16 15 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 11 12 12 12 12 12 13 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 14 12 12 12 12

12 13 14 13 12 12 14 13 13 14 13 13 13 14 13 13 14 14 12 13 13 13 13 13 13 13 12 13 13 13 12 13 14 13 13 14 13 13 13 13 13 14 13 13 12 14 13 14 13 13 13 15 14 13 14 13 10 12 13 13 14 13 13 13 15 13 12 14 13 12

16 17 18 16 17 16 16 17 19 17 16 16 16 16 16 16 16 17 17 16 15 16 16 16 16 16 16 17 16 16 15 16 16 17 15 16 15 16 16 17 16 15 17 16 16 16 17 16 16 17 16 16 17 16 16 17 16 16 16 16 16 16 16 16 16 17 16 17 16 16

24 24 25 23 23 25 23 23 25 25 24 24 24 25 24 23 24 24 24 24 24 24 23 23 24 24 23 24 23 24 25 23 24 22 25 25 22 24 24 24 24 24 24 24 24 23 24 24 25 24 25 24 24 24 25 24 23 24 24 24 24 24 24 24 24 25 23 24 24 23

10 10 10 9 10 10 10 9 11 10 11 11 11 10 10 10 10 11 11 10 11 11 11 10 11 10 11 11 11 11 10 11 10 11 10 10 10 10 11 11 11 11 10 11 10 11 12 10 10 10 12 11 11 10 11 10 10 11 10 10 10 10 11 11 11 11 10 11 11 11

11 11 11 11 11 11 13 11 11 11 14 13 13 13 13 13 13 13 13 13 13 13 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 11 13 13 13 13 13 12 13 13

12 12 12 12 12 12 13 13 13 12 13 13 13 13 13 13 13 13 13 13 13 13 12 14 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 14 12 13 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

16 15 15 14 15 16 14 14 14 14 14 15 15 15 15 14 15 14 16 15 15 15 15 15 15 15 15 14 14 15 15 15 14 15 16 15 15 15 15 15 15 15 14 14 15 14 15 15 15 15 15 14 14 15 14 15 15 15 15 14 14 14 15 15 14 15 15 14 14 15

11

9 9 9 9 9 9 9 10 11 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 12 12 11 12 12 12 12 13 12 12 11 12 12 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

12 12 11 11 11 11 11 12 10 10 12 12 12 12 12 11 11 12 12 13 13 13 12 12 11 11 12 12 12 12 11 11 11 12 12 12 11 11 11 11 12 12 12 12 11 12 11 12 12 11 13 12 11 12 12 12 12 13 11 12 12 12 13 14 12 13 11 11 12 12

10 11 10 10 12 11 11 10 11 11 10 11 11 11 12 11 11 10 10 11 11 10 11 11 11 11 11 11 11 10 10 11 10 10 10 11 11 11 11 11 10 11 11 10 10 11 10 10 10 10 11 10 10 11 10 11 11 11 11 10 11 11 10 11 10 11 10 10 10 11

10 15 12 13 12 10 11 13 11 12 13 13 12 12 11 12 12 11 12 12 11 12 11 12 12 12 12 12 12 12 11 12 14 12 11 12 12 12 12 12 12 11 12 12 12 12 12 12 12 12 12 12 12 12 12 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12

11 11 11 10 11 11 12 12 11 11 11 11 11 11 11 11 11 11 11 11 10 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12

16,17 15,15 13,15 13,16 13,17 14,16 14,16 12,15 11,15 11,14 11,12,14 12,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,13 11,11 11,14 11,14 11,17 11,14 12,14 11,15 11,14 12,14 11,14 11,13 11,14 12,14 11,14 11,16 13,14 12,14 12,15 11,15 11,14 11,14 11,14 11,14 11,14 11,15 11,14 11,14 11,15 11,14 11,14 11,15 11,14 11,14 11,13 11,14 11,14 11,14 11,14 11,14 14,14 11,15 11,14 12,14 12,14 11,14 11,13 11,14 11,14

Adams et al., Supplementary Table 1: Haplotype data

IP160 IP206 IP210 IP168 IP180 IP198 IP149 IP152 IP162 IP174 IP178 IP201 IP184 IP159 IP177 IP186 IP202 IP205 IP219 IP222 IP158 IP172 IP223 IP167 IP192 IP156 IP157 IP164 IP173 IP179 IP181 IP183 IP187 IP199 IP203 IP213 IP225 IP154 IP163 IP211 IP220 IP226 IP150 IP151 IP153 IP161 IP165 IP166 IP169 IP170 IP171 IP175 IP176 IP182 IP185 IP188 IP189 IP190 IP191 IP193 IP194 IP195 IP196 IP197 IP200 IP204 IP207 IP209 IP212 IP214 IP215 IP216

SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO SPO

E3a E3b* E3b* E3b1 E3b1 E3b1 E3b2 E3b2 E3b2 E3b2 E3b2 E3b2 E3b3 G G G G G G G I I I J(xJ2) J(xJ2) J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 K(XP) K(xP) K(xP) K(xP) R1a1 R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3*

17 13 14 13 13 14 13 13 13 13 13 13 13 15,16 15 15 15 15 15 15 16 16 16 14 14 15 14 14 14 14 15 14 15 15 14 14 14 13 13 13 13 15 14 14 15 14 15 15 14 14 15 14 14 14 14 14 15 14 14 14 14 14 14 15 14 14 14 14 15 14 14 14

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 15 13 13 16 16 16 15 15 15 15 15 15 15 15 15 15 15 12 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 12 12 12 12 12 12

13 13 14 13 13 12 14 14 14 14 13 14 13 14 13 12 12 12 12 14 13 13 13 13 13 13 13 13 13 13 12 12 12 12 14 13 13 14 13 14 14 14 12 13 14 13 13 13 13 12 13 14 13 13 13 14 13 14 15 13 13 13 13 13 13 13 12 13 13 13 14 14

17 19 19 16 17 17 16 16 16 17 16 16 17 16 17 16 16 18 17 16 18 15 15 18 17 16 17 16 17 16 16 16 17 17 17 17 17 16 16 15 15 17 16 16 15 16 15 17 16 16 16 16 16 16 16 16 17 16 16 17 16 16 16 17 16 16 16 18 16 16 17 16

21 24 25 24 23 23 24 23 24 24 24 24 24 22 21 22 22 23 22 22 25 22 23 23 23 23 24 23 22 23 25 25 23 25 23 23 21 22 23 24 24 25 24 25 24 23 24 24 25 24 24 24 23 24 23 24 24 24 24 24 24 25 23 25 23 24 24 25 24 24 24 24

11 10 10 10 10 10 9 9 9 9 9 9 11 10 10 10 9 10 10 10 10 11 10 10 10 9 10 10 10 10 10 10 10 10 10 11 10 10 10 10 10 11 11 10 11 11 11 11 11 11 10 10 11 11 10 11 11 11 11 11 10 11 11 11 11 10 10 11 11 10 11 11

11 11 12 11 11 11 11 11 11 11 11 11 11 11 13 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 13 13 13 13 11 13 13 13 13 13 13 13 12 13 13 13 13 13 12 13 13 12 13 13 13 13 13 13 13 13 13 13 13 13 14

13 12 14 13 13 13 13 13 13 13 13 13 13 14 14 14 14 14 14 14 14 13 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 14 13 13 13 13 13 13 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13 12 13 13 14 13 13 13 15 13 13 13 13

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 10 11 11 11 11 11 11 10 11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 14 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

14 14 14 14 14 14 14 14 14 14 14 14 14 16 16 16 16 16 16 17 15 15 14 14 14 14 16 14 15 15 16 16 15 16 14 15 15 15 15 14 14 14 14 15 15 15 15 15 15 15 15 14 15 15 15 15 15 15 15 15 16 15 15 15 15 15 14 15 14 15 14 15

12

11 10 11 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 11 10 10 10 10 10 10 9 7 9 9 9 9 9 9 9 9 9 9 9 9 9 9 11 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

11 12 13 12 11 11 10 10 10 10 10 10 13 10 13 13 13 12 12 10 13 12 12 11 14 12 12 10 11 12 11 11 12 11 11 10 11 11 11 12 12 10 13 12 12 13 12 12 11 12 12 11 13 12 13 12 12 12 12 13 12 12 11 12 13 12 12 13 12 12 14 12

11 10 10 9 11 10 11 10 11 11 12 11 10 11 11 12 12 11 11 11 10 11 10 11 11 10 11 10 10 11 11 11 10 11 9 11 10 10 11 10 10 11 11 12 10 11 10 10 11 10 11 10 11 11 11 11 10 10 11 10 10 10 11 10 11 11 11 11 11 10 10 12

13 12 17,17 13 12 16,16 12 12 17,18 12 12 16,17 12 12 15,15 12 12 17,19 13 12 13,14 13 12 14,14 13 12 14,14 13 12 14,14 12 11 11,14 13 12 13,14 11 11 16,16 13 12 13,16 11 12 13,16 11 12 12,16 11 12 12,16 11 12 14,15 10 12 15,15 12 12 13,16 11 12 12,15 11 12 12,12 11 13 12,12 12 11 13,19 11 11 13,15 13 10 13,16 13 11 13,15 12 11 14,16 14 11 13,15 12 11 16,16 10 11 14,17 10 11 14,17 10 11 14,17 10 11 13,19 13 11 13,16 12 11 13,15 14 11 13,15 11 12,13 13,13,14 11 13 15,16 12 12 13,15 12 12 13,15 11 11 11,14 14 12 11,14 12 11 11,14 12 11 11,14 12 11 11,14 12 11 11,14 12 12 11,14 11 11 11,13 12 11 11,14 12 11 11,15 12 11 11,14 12 11 12,12 12 11 11,14 12 11 11,14 12 10 11,14 12 11 11,15 13 11 11,15 12 10 11,14 12 11 11,14 13 11 11,13 13 11 11,14 12 10 11,14 12 12 11,14 12 12 11,14 12 11 11,14 12 11 10,14 12 11 11,14 12 11 11,15 12 11 11,14 12 11 12,14 12 11 11,14

Adams et al., Supplementary Table 1: Haplotype data

IP217 IP218 IP221 IP224 IP155 IP208

13

SPO SPO SPO SPO SPO SPO

R1b3* R1b3* R1b3* R1b3* R1b3f R1b3f

14 14 14 14 14 15

12 12 12 12 12 12

13 13 13 13 13 13

16 17 16 16 16 16

24 24 25 24 24 24

11 10 11 10 11 11

14 13 12 13 13 13

14 13 12 13 13 13

11 11 11 11 11 11

11 11 11 11 11 11

12 12 12 12 12 12

15 15 15 15 15 15

12 12 12 12 11 12

12 11 12 11 12 12

11 12 10 11 11 12

13 13 12 12 13 12

11 11 11 11 11 11

11,15 13,13 11,14 8,14 11,15 11,14

Valencia IP474 VAL IP609 VAL IP627 VAL IP629 VAL IP649 VAL IP471 VAL IP611 VAL IP644 VAL IP619 VAL IP459 VAL IP465 VAL IP614 VAL IP623 VAL IP641 VAL IP647 VAL IP658 VAL IP660 VAL IP470 VAL IP630 VAL IP464 VAL IP606 VAL IP612 VAL IP624 VAL IP469 VAL IP631 VAL IP632 VAL IP456 VAL IP637 VAL IP271 VAL IP457 VAL IP458 VAL IP461 VAL IP462 VAL IP467 VAL IP472 VAL IP473 VAL IP475 VAL IP607 VAL IP608 VAL IP610 VAL IP613 VAL IP615 VAL IP616 VAL IP618 VAL IP620 VAL IP621 VAL IP622 VAL IP625 VAL IP626 VAL IP633 VAL IP634 VAL IP636 VAL IP639 VAL IP640 VAL IP642 VAL IP645 VAL IP646 VAL IP650 VAL IP652 VAL IP656 VAL IP657 VAL IP659 VAL IP662 VAL IP663 VAL

E3a E3b1 E3b1 E3b1 E3b1 E3b2 E3b2 E3b2 E3b3 G I I I I I I I J(xJ2) J(xJ2) J2 J2 J2 J2 K(xP) R1a1 R1a1 R1b* R1b* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3*

16 13 13 13 13 14 13 13 13 15 15 14 17 14 14 17 14 14 14 14 13 14 14 14 16 15 16 17 15 14 14 14 14 14 15 14 14 14 14 14 14 14 14 14 14 14 16 14 14 14 14 14 15 16 14 14 14 15 14 14 14 14 14 14

12 12 12 12 12 12 10 12 12 13 13 14 13 14 14 13 14 17 16 15 15 15 15 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

13 13 13 13 13 14 14 14 14 12 13 12 14 12 12 14 12 14 12 14 13 13 14 13 14 13 13 13 12 13 14 14 13 13 13 14 14 13 14 13 12 13 13 13 13 13 14 13 13 13 14 13 13 13 13 14 13 13 13 13 13 13 13 13

18 18 17 18 17 16 16 16 18 16 16 17 15 15 16 16 16 17 18 17 16 16 17 15 18 18 16 15 16 16 17 16 16 16 16 17 16 16 16 16 16 16 16 15 16 16 16 16 16 17 15 15 16 17 16 16 16 16 16 16 17 16 16 17

21 23 24 23 24 24 24 24 23 22 23 23 23 22 22 23 23 23 23 22 22 24 23 23 25 25 25 22 25 24 25 24 23 23 24 24 24 23 24 23 24 24 24 24 24 24 25 24 24 23 24 24 24 23 26 24 24 24 23 24 25 24 24 24

11 10 10 11 10 9 9 9 10 10 11 10 10 10 10 10 10 11 10 10 11 11 10 10 10 11 11 11 11 10 11 11 12 11 10 10 11 10 11 12 10 10 11 11 10 11 10 11 11 11 10 11 10 10 11 11 10 10 10 11 11 11 11 10

11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 12 11 11 11 13 11 11 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 11 13 13 13 13 12 13 13 13 13 13 13 13 14 13 13 13 13

14 14 13 13 13 13 13 13 13 15 14 13 13 13 13 13 13 13 12 12 12 12 12 13 14 13 13 13 13 13 13 14 13 13 13 13 13 13 13 13 13 13 12 14 13 13 13 13 13 13 13 13 13 13 13 13 13 14 13 13 12 13 13 13

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

15 14 14 14 14 14 14 14 14 16 15 16 15 17 16 15 16 14 14 15 15 16 14 14 14 14 14 14 15 15 14 15 14 15 15 14 15 15 15 14 15 14 14 15 15 15 14 15 15 14 15 15 15 15 15 14 15 15 15 15 14 15 14 15

11 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 9 9 9 9 9 11 11 12 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 11 12 12 12 12 12 12 12 12 9 12 12 12 12 12 12 12 12

12 12 11 12 11 10 10 10 12 11 12 11 11 11 11 12 11 10 11 12 11 11 11 11 10 10 12 12 12 12 11 12 13 12 13 12 11 12 12 12 12 13 12 12 12 11 11 12 12 11 11 12 12 13 13 12 12 13 12 13 14 12 12 12

10 11 9 9 9 12 11 11 10 11 10 10 10 11 9 10 10 11 11 11 11 11 9 10 11 12 11 11 10 11 10 10 10 10 11 10 11 10 11 10 11 11 10 11 11 11 11 11 10 11 11 11 11 11 10 10 10 11 11 10 11 11 11 11

13 12 12 11 12 13 13 13 12 11 12 12 11 12 12 12 12 12 11 12 13 14 13 11 11 11 12 12 13 12 13 12 12 12 12 11 12 12 12 12 12 12 12 12 12 12 11 12 11 10 12 12 12 12 12 12 12 12 12 14 13 12 12 12

12 13 13 13 12 12 12 12 11 12 12 12 12 12 12 12 12 12 11 11 11 11 11 13 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

17,17 15,16 15,18 16,17 16,16 13,14 13,14 13,14 15,18 14,15 15,15 13,15 12,12 13,14 13,14 12,12 13,14 11,18 12,17 13,14 13,16 13,17 13,16 13,16 11,14 11,14 13,14 13,14 11,14 11,14 11,14 11,15 11,15 11,14 11,14 11,14 11,14 12,14 11,14 11,14 10,16 11,14 13,14 11,14 11,14 11,15 11,15 11,14 11,14 11,13 12,14 11,14 11,14 11,13 11,15 11,14 12,14 11,14 11,14 11,13 11,14 11,15 11,14 11,14

Adams et al., Supplementary Table 1: Haplotype data

IP693 IP697 IP700 IP707 IP468 IP617 IP655 IP664 IP814

VAL VAL VAL VAL VAL VAL VAL VAL VAL

West Andalusia IP514 WAN IP272 WAN IP513 WAN IP759 WAN IP298 WAN IP515 WAN IP516 WAN IP791 WAN IP813 WAN IP852 WAN IP853 WAN IP674 WAN IP696 WAN IP839 WAN IP374 WAN IP517 WAN IP754 WAN IP783 WAN IP797 WAN IP279 WAN IP296 WAN IP666 WAN IP672 WAN IP690 WAN IP737 WAN IP738 WAN IP774 WAN IP316 WAN IP340 WAN IP246 WAN IP689 WAN IP274 WAN IP350 WAN IP849 WAN IP230 WAN IP236 WAN IP240 WAN IP241 WAN IP249 WAN IP260 WAN IP291 WAN IP301 WAN IP310 WAN IP313 WAN IP315 WAN IP327 WAN IP328 WAN IP331 WAN IP380 WAN IP486 WAN IP489 WAN IP493 WAN IP495 WAN IP512 WAN IP654 WAN IP670 WAN IP686 WAN IP701 WAN IP713 WAN IP726 WAN IP757 WAN

14

R1b3* R1b3* R1b3* R1b3* R1b3d R1b3f R1b3f R1b3f R1b3f

14 14 15 14 14 14 15 14 14

13 12 12 12 12 12 12 12 12

13 14 13 13 14 13 13 13 13

16 17 16 17 16 15 15 16 16

24 25 24 24 24 24 24 24 24

10 11 11 11 11 11 11 11 11

13 13 13 13 13 13 13 12 13

13 13 13 13 13 13 13 14 13

11 11 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11

9 12 12 12 12 12 12 12 12

15 15 15 16 14 15 15 15 15

12 12 12 12 12 12 12 12 12

13 13 13 11 11 13 11 11 12

11 11 11 11 10 11 11 11 11

12 12 12 12 11 12 12 12 12

11 11 11 11 11 11 11 11 11

11,14 12,14 10,15 11,14 10,13 11,15 11,14 10,14 11,14

E3b* E3b1 E3b1 E3b1 E3b2 E3b2 E3b2 E3b2 E3b2 E3b2 E3b2 G G G I I I I J(xJ2) J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 Q(XQ3) R1* R1a1 R1a1 R1a1 R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3*

13 13 13 13 13 13 13 13 13 13 13 15 15 15 16 17 16 15 14 14 15 15 16 15 15 15 15 15 15 13 15 16 16 15 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 15 14 14 14

12 12 12 12 12 12 12 12 12 12 12 13 12 13 13 13 13 13 16 15 15 16 15 16 15 16 16 14 16 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 12 12 12 12 12 12

12 13 13 13 14 14 14 14 14 14 13 13 12 13 13 12 12 13 14 12 12 13 13 13 13 13 13 13 13 14 14 14 13 13 12 14 13 13 13 12 14 13 13 13 13 13 13 12 13 14 12 14 13 13 12 13 13 13 13 13 14

17 17 17 18 16 16 16 16 16 16 16 17 18 17 15 17 15 17 16 17 16 16 16 16 17 16 16 16 16 17 16 17 19 17 16 18 16 16 17 16 17 15 16 16 16 16 16 16 16 16 16 16 16 16 16 16 17 16 16 16 17

24 24 24 24 24 23 24 24 23 24 24 22 23 22 23 25 25 24 23 22 24 23 24 23 23 24 23 23 24 25 24 25 24 25 23 24 24 23 23 24 24 24 25 23 24 24 25 23 24 24 24 24 24 25 24 24 25 23 24 24 24

10 10 10 11 9 9 9 9 10 9 9 10 11 10 10 10 11 10 10 10 10 9 11 11 10 9 9 10 9 10 10 10 11 11 11 11 11 10 10 11 10 11 11 10 10 11 10 11 11 11 11 11 11 10 10 11 11 11 10 11 10

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11 14 13 11 11 11 13 13 13 13 13 13 13 13 13 13 13 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13 13

14 12 13 13 13 13 13 13 13 13 13 15 14 15 13 13 13 14 12 12 12 12 12 12 12 12 12 12 12 12 13 13 13 13 14 14 13 13 13 13 13 13 13 13 13 13 13 13 13 12 13 13 13 13 13 13 13 13 13 13 13

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

15 14 14 14 14 14 14 14 14 14 14 16 16 16 15 15 15 15 14 15 16 15 15 15 15 14 14 15 14 13 14 14 14 14 14 15 15 15 15 15 14 15 15 15 15 15 15 14 15 15 15 14 15 15 15 15 15 15 14 14 14

10 10 10 11 10 10 10 10 10 10 10 11 10 10 10 10 10 10 10 9 10 9 9 9 9 9 9 9 9 9 11 11 11 11 12 12 12 12 12 10 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

10 12 12 11 10 10 9 10 11 11 10 11 11 11 11 12 11 11 11 11 12 12 11 12 12 12 11 14 12 13 11 10 10 11 12 11 12 13 12 13 12 11 11 11 12 12 13 11 12 13 12 11 12 13 12 12 12 12 12 12 13

11 9 10 11 10 11 11 10 11 10 11 10 11 10 10 10 10 13 11 9 11 10 10 11 10 10 11 11 10 11 11 11 12 12 10 11 11 11 10 10 9 10 12 11 11 10 11 11 11 11 11 10 11 11 11 11 11 10 11 11 10

13 12 12 12 13 13 13 13 13 13 13 11 12 11 11 12 12 12 11 14 10 13 13 12 14 12 12 13 12 13 12 11 11 11 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 11 12 13 12 12 12 13 12 12 12 12 12

12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 11 11 11 10 11 11 11 10 8 11 10 12 11 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11

16,18 16,18 16,18 18,18 13,14 13,14 13,15 13,14 13,14 13,14 13,14 14,14 13,15 14,14 12,12 12,16 13,17 15,15 13,15 13,15 12,18 13,16 12,16 13,13 13,17 13,16 13,16 13,15 13,16 15,17 11,13 11,14 11,11 11,14 10,14 11,14 11,14 11,14 12,15 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,11 11,14 11,12 11,14 11,14 11,14 11,14 11,15 11,14 11,14 11,14 11,14 11,16 11,14 11,14

Adams et al., Supplementary Table 1: Haplotype data

IP762 IP768 IP776 IP780 IP825 IP840 IP841 IP850 IP275 IP810 IP283 IP688

15

WAN WAN WAN WAN WAN WAN WAN WAN WAN WAN WAN WAN

R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3d R1b3d R1b3f R1b3f

14 14 15 14 14 14 15 14 14 14 14 14

12 12 12 12 12 12 12 12 12 12 12 12

13 13 13 14 13 14 13 13 13 13 12 13

16 16 16 17 16 15 16 16 16 18 16 16

24 23 24 25 24 24 24 24 24 24 24 24

11 10 11 10 10 10 10 11 10 10 11 11

13 13 13 13 13 13 13 14 13 13 13 13

12 13 13 13 13 13 13 13 13 14 13 13

11 11 11 11 10 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12

14 15 14 14 14 14 15 15 14 14 15 15

12 12 12 12 12 12 12 12 12 12 12 12

12 12 14 12 12 12 12 12 12 12 12 13

10 11 11 11 10 10 10 10 10 11 10 10

12 12 12 12 11 12 12 12 12 12 12 12

11 11 11 12 11 11 11 12 11 11 11 11

11,16 11,16 11,17 11,15 11,15 12,15 11,15 12,15 11,14 11,14 11,15 11,14

IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ IBZ

E3b1 E3b1 E3b3 E3b3 G G G G G G G I J2 J2 K(xP) K(xP) K(xP) K(xP) K(xP) K(xP) K(xP) K(xP) K(xP) R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3d R1b3d R1b3f R1b3f R1b3f R1b3f

13 13 13 13 15 15 15 15 15 15 15 16 14 14 14 14 14 14 14 14 14 14 14 15 14 14 14 14 15 16 14 14 14 15 16 14 15 14 14 14 14 14 14 14 14 14 15 15 15 15 14 14 14 14

12 12 12 12 12 12 13 12 13 12 13 13 15 15 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 13 12 12 12 12 12 12 12 12 12 12 12 12 12

13 13 13 13 12 12 12 12 12 12 12 13 14 14 14 14 14 14 14 14 14 14 14 13 13 13 13 13 13 13 13 13 13 13 13 14 13 13 13 14 14 13 13 13 13 14 13 13 13 13 14 13 13 14

17 17 17 17 16 16 17 16 17 16 17 19 16 17 16 16 16 16 16 16 16 16 16 16 16 16 17 16 16 16 16 17 17 17 16 16 16 16 16 16 16 16 16 16 16 16 16 18 16 16 16 16 16 16

24 24 25 25 22 22 22 22 22 22 22 24 23 23 23 23 23 23 23 23 23 23 23 23 24 24 24 24 23 23 24 24 24 24 23 24 24 24 24 24 24 25 24 24 24 24 23 24 24 24 25 24 24 25

11 11 10 10 10 10 10 10 10 10 10 11 10 10 11 12 11 11 12 12 11 12 11 11 11 10 11 10 11 11 11 11 11 11 10 10 11 11 11 10 10 10 11 11 10 10 10 9 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 15 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13

13 13 14 14 14 14 14 14 14 14 14 13 12 12 13 13 13 13 13 13 13 13 13 13 13 13 10 13 13 13 13 13 13 13 13 13 13 10 13 13 13 13 13 10 13 13 13 13 13 13 13 13 13 13

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

14 14 14 14 16 16 16 16 16 16 16 15 15 16 14 14 14 14 14 14 14 14 14 15 15 14 15 14 15 15 15 14 14 14 15 14 15 14 15 14 14 15 15 15 14 14 15 14 14 14 15 15 15 15

10 10 10 10 10 10 10 10 10 10 10 10 9 9 9 9 9 9 9 9 9 9 9 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12

12 12 12 13 13 13 12 13 12 13 12 13 10 10 11 11 11 11 11 11 11 11 11 12 12 13 12 13 12 12 12 12 12 12 12 12 13 12 13 12 12 12 12 12 13 12 11 11 13 12 12 11 11 12

9 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 11 11 11 11 11 11 11 11 11 11 11 11 10 11 11 11 10 10 11 11 12 11 10 11 10 10 10 11 10 10 11

12 12 12 12 12 12 11 12 11 12 11 11 12 12 11 11 11 11 12 11 11 11 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

12 12 12 12 12 12 12 12 12 12 12 12 11 11 12 12 12 12 12 12 12 12 12 11 11 11 11 11 11 11 12 11 11 11 12 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 11

14,18 14,18 14,17 14,17 14,14 14,14 14,14 14,14 14,14 14,14 13,14 14,15 14,16 14,16 17,17 17,17 17,17 17,17 17,17 17,17 17,17 17,17 17,17 11,14 12,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 12,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14

MAJ MAJ

E3a E3b1

15 12 13 14 12 13

18 21 10 11 14 17 24 10 13 13

11 11

11 11

12 14 11 12 14 10

11 13

11 13 11 12

12 13

16,18 16,19

Ibiza IP1056 IP1077 IP1030 IP1050 IP1025 IP1032 IP1037 IP1045 IP1054 IP1059 IP1060 IP1075 IP1028 IP1042 IP1024 IP1047 IP1049 IP1053 IP1058 IP1064 IP1065 IP1071 IP1073 IP1027 IP1029 IP1031 IP1034 IP1036 IP1038 IP1039 IP1040 IP1041 IP1043 IP1044 IP1046 IP1051 IP1052 IP1057 IP1061 IP1062 IP1063 IP1066 IP1068 IP1069 IP1070 IP1072 IP1074 IP1076 IP1033 IP1035 IP1026 IP1048 IP1055 IP1067

Majorca IP1139 IP1081

Adams et al., Supplementary Table 1: Haplotype data

IP1090 IP1091 IP1121 IP1084 IP1085 IP1088 IP1097 IP1089 IP1093 IP1095 IP1129 IP1137 IP1099 IP1080 IP1092 IP1120 IP1127 IP1134 IP1115 IP1078 IP1079 IP1082 IP1083 IP1086 IP1087 IP1094 IP1098 IP1100 IP1101 IP1102 IP1103 IP1105 IP1106 IP1107 IP1109 IP1110 IP1111 IP1113 IP1116 IP1119 IP1122 IP1123 IP1124 IP1125 IP1126 IP1128 IP1130 IP1131 IP1133 IP1135 IP1136 IP1138 IP1096 IP1104 IP1108 IP1112 IP1114 IP1117 IP1118 IP1132

16

MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ MAJ

E3b1 E3b1 E3b2 G G G G I I I I I J(xJ2) J2 J2 J2 J2 J2 K(xP) R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f R1b3f

13 14 13 15 16 15 15 14 17 14 14 15 14 15 16 16 14 15 14 14 14 14 15 15 14 14 15 14 15 14 14 14 14 14 14 14 15 16 14 14 14 14 15 14 14 16 14 14 13 14 14 14 14 14 14 13 14 14 14 14

12 12 12 12 12 12 13 14 13 14 14 13 17 15 15 15 15 16 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

13 14 14 12 12 12 12 12 15 12 12 12 13 12 13 14 12 13 13 13 13 13 13 13 13 13 13 13 13 14 14 15 12 13 13 13 14 13 13 13 12 13 13 13 13 13 13 13 14 13 13 13 13 13 13 12 13 13 13 13

17 18 16 17 16 16 17 16 15 16 16 16 18 16 16 16 16 16 16 16 16 16 16 16 16 16 16 17 16 16 16 16 18 17 16 16 18 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16

24 24 24 23 21 21 22 23 25 22 23 25 23 23 23 23 23 23 25 24 25 24 23 24 24 24 24 24 24 23 24 23 25 24 24 24 24 23 24 221 24 24 22 24 24 23 24 24 23 24 24 24 24 24 25 24 24 24 24 24

10 10 9 10 11 10 10 10 9 10 10 10 10 10 10 10 10 9 11 10 11 11 11 11 11 11 11 10 10 10 11 11 10 11 11 11 11 10 11 11 10 12 11 11 11 10 11 11 11 11 11 11 10 11 11 11 10 10 10 10

11 11 11 12 11 11 11 11 11 11 11 11 11 11 12 12 11 11 13 13 13 13 13 13 13 13 13 13 14 13 12 14 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 12 12 12 12

13 13 13 12 13 15 14 13 13 13 13 13 12 12 12 12 12 12 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 12 13 13 13 13 13 13 13 14 13 13 13 13 14 14 14 14

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

14 14 14 16 16 15 16 16 15 15 16 15 14 15 14 14 16 14 14 15 15 14 14 15 14 15 14 15 15 15 14 15 14 15 14 15 15 14 15 14 15 14 15 14 15 15 14 14 15 15 14 14 15 15 14 15 15 15 15 15

10 10 10 10 10 10 10 10 10 10 10 10 10 9 9 9 9 9 12 12 12 12 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 13 12 12 12 12 12 13 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12

11 11 10 11 11 11 11 11 12 12 11 11 12 11 12 12 11 11 11 12 12 11 12 12 11 12 12 11 12 13 12 12 12 12 11 11 12 12 11 11 12 12 12 12 11 12 11 11 11 11 12 12 12 13 12 11 11 11 11 11

9 11 11 10 10 10 10 10 11 10 10 10 11 11 10 11 11 10 11 11 10 11 12 12 11 11 11 12 10 11 10 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 11 10 10 11 11 11 11 11 11 11 11

12 12 13 13 11 11 11 12 12 12 12 14 12 10 13 13 10 13 13 12 12 12 13 11 12 12 12 13 12 13 12 12 12 12 12 12 11 14 12 13 12 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

12 12 12 13 12 13 12 12 12 12 12 12 11 11 10 10 11 10 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 11 11 11 12 11 11 11 11 11 11 11

16,17 17,18 13,14 15,15 13,15 13,16 14,14 13,15 12,12 13,14 13,15 13,17 13,17 14,18 13,17 13,17 14,17 13,16 11,14 11,14 11,15 11,14 10,15 11,15 11,14 8,14 11,14 11,14 11,14 11,11 11,14 11,14 11,14 11,14 11,15 11,14 11,14 10,14 13,17 11,14 12,14 11,14 11,14 11,14 13,17 11,14 11,15 11,14 11,14 13,17 12,15 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,14

MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN

E3b1 E3b1 E3b1 E3b1 E3b2 E3b3 E3b3 I J2 R1a1

14 13 14 14 13 13 13 16 16 16

12 12 12 12 12 12 12 13 15 12

13 14 13 13 14 13 13 13 13 14

16 17 16 16 16 18 18 15 19 16

24 22 24 23 24 24 24 23 22 25

10 10 10 11 9 10 10 10 10 11

11 11 11 11 11 11 11 11 11 11

13 11 13 11 13 11 13 11 13 12 13 11 13 11 13 11 12 11 13 12

11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12

14 14 14 14 14 13 13 15 14 14

10 10 10 10 10 10 10 10 9 12

12 12 12 12 10 12 12 13 11 10

10 11 10 10 10 10 10 10 10 10

12 11 12 12 13 12 12 11 13 11

12 13 12 12 12 11 11 12 11 11

17,19 15,15 17,19 17,19 14,14 15,16 14,16 12,12 13,15 11,14

Minorca IP1157 IP1160 IP1168 IP1175 IP1140 IP1152 IP1162 IP1144 IP1149 IP1148

Adams et al., Supplementary Table 1: Haplotype data

IP1141 IP1145 IP1147 IP1150 IP1151 IP1154 IP1155 IP1156 IP1158 IP1159 IP1161 IP1163 IP1164 IP1165 IP1166 IP1167 IP1169 IP1170 IP1171 IP1173 IP1174 IP1176 IP1142 IP1143 IP1146 IP1153 IP1172

MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN MIN

R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3* R1b3d R1b3f R1b3f R1b3f R1b3f

15 14 14 14 14 14 15 15 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

14 13 14 13 13 13 13 13 14 14 13 12 13 13 13 14 13 13 13 13 14 13 13 13 13 13 13

16 16 16 16 16 17 16 16 16 17 16 16 16 17 16 16 16 16 16 17 16 16 16 16 16 16 16

24 24 24 23 24 24 24 23 24 24 24 24 24 24 24 24 23 24 24 24 24 23 25 24 24 24 24

11 11 11 11 10 11 10 11 11 10 11 11 11 11 11 11 11 11 11 10 11 11 11 10 11 11 11

13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 12 13 13 13

13 11 13 11 13 11 12 11 13 11 13 11 13 11 13 11 14 11 13 11 14 11 13 11 10 11 13 11 13 11 14 11 13 11 13 11 13 11 13 11 13 11 13 11 13 11 14 11 13 13 13 12 13 11

Sephardic Jewish sample Sj1 SJ E3a Sj2 SJ E3b* Sj3 SJ E3b* Sj4 SJ E3b1 Sj5 SJ E3b1 Sj6 SJ E3b1 Sj7 SJ E3b1 Sj8 SJ E3b1 Sj9 SJ E3b1 Sj10 SJ E3b2 Sj11 SJ E3b3 Sj12 SJ E3b3 Sj13 SJ E3b3 Sj14 SJ E3b3 Sj15 SJ E3b3 Sj16 SJ E3b3 Sj17 SJ G Sj18 SJ G Sj19 SJ G Sj20 SJ G Sj21 SJ G Sj22 SJ G Sj23 SJ G Sj24 SJ G Sj25 SJ G Sj26 SJ G Sj27 SJ G Sj29 SJ G Sj30 SJ G Sj31 SJ G Sj32 SJ G Sj33 SJ G Sj34 SJ G Sj35 SJ G Sj36 SJ G Sj38 SJ G Sj39 SJ G Sj40 SJ G Sj41 SJ G Sj42 SJ G Sj43 SJ G Sj44 SJ I Sj45 SJ J(xJ2)

13 13 13 13 13 13 13 13 13 13 14 13 13 13 14 13 15 15 16 15 15 15 15 15 15 16 16 16 15 16 16 15 15 15 15 16 15 16 16 15 15 17 14

14 12 12 12 12 12 12 12 12 12 12 13 13 12 12 12 12 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 15

13 13 14 12 12 13 12 13 13 14 13 12 12 14 13 13 12 12 12 12 12 13 12 11 12 12 12 12 12 12 12 12 12 12 12 12 12 13 11 12 12 14 14

16 19 18 17 17 17 18 18 17 16 17 17 17 17 17 17 16 17 16 16 16 17 17 18 17 19 16 16 17 16 16 17 17 17 17 16 17 16 17 17 17 15 17

23 25 23 24 23 24 23 25 24 24 24 24 24 24 24 24 22 22 22 23 22 22 22 23 21 22 23 22 23 22 22 22 22 23 22 22 22 24 23 22 22 23 23

10 10 10 10 10 10 10 10 10 9 9 10 10 9 9 10 10 11 10 11 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 11 11 11 10 11 10 10 11 11 11 11 11 12 11 11 11 12 10 11 11 12 11 11

13 14 12 13 13 13 13 12 13 13 14 13 13 13 14 13 14 14 14 13 13 13 14 14 15 14 14 14 13 14 14 13 14 14 14 13 14 14 14 13 14 13 12

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

17

14 14 15 15 15 15 15 14 14 14 14 15 15 15 14 14 15 14 15 15 14 15 14 15 15 15 15

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 11 12 12 13 12 12 12 12 12 12 12

12 12 11 12 12 13 12 11 12 12 12 12 11 13 12 12 14 12 12 13 12 12 13 11 12 12 11

10 11 12 11 11 10 11 11 10 10 11 11 11 11 11 10 11 11 12 11 11 11 10 11 11 11 10

13 12 12 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 12 12 14 12 13

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11,14 11,14 12,14 11,14 12,15 11,14 12,14 11,14 11,14 11,14 12,14 12,13 11,14 11,14 11,14 11,14 11,14 11,14 11,14 11,13 11,14 11,14 11,14 11,14 11,15 11,15 11,14

Adams et al., Supplementary Table 1: Haplotype data

Sj46 Sj47 Sj48 Sj49 Sj50 Sj51 Sj52 Sj53 Sj54 Sj55 Sj56 Sj57 Sj58 Sj59 Sj60 Sj61 Sj62 Sj63 Sj64 Sj65 Sj66 Sj67 Sj68 Sj69 Sj70 Sj71 Sj72 Sj73 Sj74 Sj75 Sj76 Sj77 Sj78 Sj79 Sj80 Sj81 Sj82 Sj83 Sj84 Sj85 Sj86 Sj87 Sj88 Sj89 Sj90 Sj91 Sj92 Sj93 Sj94 Sj95 Sj96 Sj97 Sj98 Sj99 Sj100 Sj101 Sj102 Sj103 Sj104 Sj105 Sj106 Sj107 Sj108 Sj109 Sj110 Sj111 Sj112 Sj113 Sj114 Sj115 Sj116 Sj117

SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ SJ

J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J(xJ2) J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2 J2

14 14 14 14 14 14 14 14 14 14 14 14 14 15 14 14 14 14 14 14 14 15 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 15 15 15 15 14 15 14 15 15 15 15 17 14 15 16 14 17 15 15 14 14 14 17 14 15 16 14 14 13 15 15 15 16 15

15 15 15 15 15 15 15 15 15 15 16 16 16 17 15 17 16 17 16 16 16 16 16 17 16 13 16 16 16 16 13 17 16 17 16 16 17 16 16 16 16 16 16 16 15 16 16 16 16 15 15 15 13 14 15 17 15 14 14 14 15 14 16 15 15 16 15 15 15 16 15 16

14 14 14 14 14 14 14 14 14 14 13 13 13 14 14 14 13 13 13 13 13 13 13 13 14 13 13 13 13 13 13 13 13 13 13 13 13 14 14 14 13 14 14 14 14 14 14 14 14 13 12 12 14 13 13 13 12 13 13 13 13 13 13 13 14 13 12 12 12 13 13 14

17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 18 18 18 17 17 17 17 16 16 16 17 17 17 18 16 16 17 18 16 17 18 16 16 17 16 16 17 16 17 16 16 17 16 16 15 16 17 17 17 17 19 17 18 17 17 17 16 16 18 16 15 16 17 16 16 16

23 23 23 23 23 23 23 23 23 23 23 24 23 23 23 23 23 23 23 23 24 23 23 23 23 23 23 23 23 23 23 23 23 23 25 23 23 24 24 24 24 24 23 23 24 23 24 24 24 23 24 24 22 24 25 23 23 24 23 24 23 22 23 23 22 23 24 24 24 23 22 23

10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 9 9 9 9 9 10 10 10 10 9 9 9 10 10 11 10 10 9 10 10 10 10 10 10 10 9 9 10 10 10 11 10 9 10 10

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 10 11 13 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 10 12 11 11 11 11 11 12 11 11 11 11 11 11 11 11 11 11 12 11

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 9 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12

18

Adams et al., Supplementary Table 1: Haplotype data

Sj118 SJ J2 14 14 13 16 23 Sj119 SJ J2 15 14 13 16 23 Sj120 SJ J2 13 15 13 15 24 Sj121 SJ J2 14 15 14 16 23 Sj122 SJ J2 16 15 13 15 23 Sj123 SJ J2 16 15 13 16 22 Sj124 SJ J2 14 15 13 17 22 Sj125 SJ J2 13 15 14 19 23 Sj126 SJ K(xP) 15 12 13 17 23 Sj127 SJ K(xP) 14 12 13 17 23 Sj128 SJ K(xP) 13 12 13 15 22 Sj129 SJ K(xP) 15 12 13 16 23 Sj130 SJ K(xP) 14 12 14 15 23 Sj131 SJ K(xP) 14 12 13 18 23 Sj132 SJ K(xP) 15 12 13 17 23 Sj133 SJ K(xP) 13 12 13 16 22 Sj134 SJ K(xP) 13 12 13 15 22 Sj135 SJ K(xP) 14 12 14 16 23 Sj136 SJ K(xP) 15 12 15 15 23 Sj137 SJ Q(xQ3) 13 14 13 15 22 Sj138 SJ Q(xQ3) 13 12 13 16 22 Sj139 SJ Q(xQ3) 13 12 13 15 22 Sj140 SJ Q(xQ3) 13 12 13 14 22 Sj141 SJ R1a 15 12 13 16 24 Sj142 SJ R1a 16 12 13 17 25 Sj143 SJ R1a 16 12 12 18 25 Sj144 SJ R1a 15 12 13 17 25 Sj145 SJ R1a 16 12 13 17 25 Sj146 SJ R1a 16 12 13 17 24 Sj147 SJ R1a 16 12 13 17 25 Sj148 SJ R1a 16 12 13 17 24 Sj149 SJ R1b* 15 12 14 15 24 Sj150 SJ R1b* 16 12 13 16 23 Sj151 SJ R1b3 14 12 13 15 24 Sj152 SJ R1b3 14 12 13 15 24 Sj153 SJ R1b3 14 12 13 15 24 Sj154 SJ R1b3 14 12 13 16 24 Sj155 SJ R1b3 16 12 13 16 24 Sj156 SJ R1b3 14 12 13 16 24 Sj157 SJ R1b3 14 12 13 15 25 Sj158 SJ R1b3 14 12 13 15 24 Sj159 SJ R1b3 14 12 14 16 24 Sj160 SJ R1b3 14 12 12 15 24 Sj161 SJ R1b3 14 12 14 16 22 Sj162 SJ R1b3 14 12 13 15 24 Sj163 SJ R1b3 14 12 13 17 24 Sj164 SJ R1b3 14 12 12 15 24 Sj165 SJ R1b3 14 12 13 15 24 Sj166 SJ R1b3 14 12 13 16 25 Sj167 SJ R1b3 14 12 13 16 24 Sj168 SJ R1b3 14 12 13 16 24 Sj169 SJ R1b3 14 13 12 16 24 Sj170 SJ R1b3 14 12 13 15 25 Sj171 SJ R2 14 12 13 15 23 Sj172 SJ R2 14 12 14 15 23 Sj173 SJ R2 14 12 14 15 23 Sj174 SJ R2 14 12 14 15 23 NB no subtyping of R1b3 available for Sephardic Jewish sample

10 10 10 10 9 10 10 10 11 10 10 11 10 10 11 10 10 10 10 10 10 10 10 11 10 11 10 10 10 10 10 11 10 11 11 11 11 11 10 11 11 11 10 10 10 10 11 10 11 11 11 11 10 10 10 10 10

11 11 11 11 11 12 11 11 13 13 13 13 13 13 13 13 13 14 14 15 15 16 15 11 11 11 11 11 11 11 11 13 13 13 13 13 13 13 14 14 13 13 14 13 14 13 14 14 13 13 13 13 14 10 10 10 10

12 12 12 12 13 12 12 12 13 13 13 13 13 13 13 13 13 12 11 13 13 13 13 13 13 13 12 14 13 13 13 14 13 13 13 13 13 13 13 12 13 13 12 13 12 12 12 12 13 13 13 13 13 14 14 14 14

19

Adams et al., Supplementary Table 2: Ancestry proportions in Iberian populations.

Basque

Moroccan

Sephardic Jewish

Population

mY1 (%)

SD (%)

mY2 (%)

SD (%)

mY3 (%)

SD (%)

Aragon

59.4

11.6

4.8

3.6

35.8

12.0

Andalucia, E

80.1

7.1

2.4

2.7

17.6

7.4

Andalucia, W

59.7

8.1

16.7

5.9

23.6

8.8

Asturias

44.3

15.3

10.5

7.3

45.2

16.2

Castilla la Mancha

81.1

8.3

0.9

2.7

18.0

8.7

Castile, NE

88.3

9.9

9.3

5.7

2.5

9.4

Castile, NW

65.4

6.0

21.7

5.4

12.9

2.7

Catalonia

91.5

7.0

2.3

2.5

6.2

7.1

Extremadura

52.3

9.4

19.0

7.1

28.7

10.4

Galicia

62.3

7.4

20.8

5.6

16.9

7.5

Gascony

110.8

4.7

-2.5

0.7

-8.3

4.7

Portugal, N

64.7

8.8

11.8

5.3

23.6

9.1

Portugal, S

47.6

8.1

16.1

6.1

36.3

9.2

Valencia

72.1

7.7

12.8

5.1

15.1

7.8

Majorca

71.9

8.5

6.6

4.3

21.5

8.7

Minorca

86.0

9.3

21.5

7.8

-7.5

7.3

Ibiza

63.2

9.0

3.8

4.3

33.0

9.7