The genetic legacy of religious diversity and intolerance ... · The genetic legacy of religious...

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1 The genetic legacy of religious diversity and intolerance: paternal lineages of Christians, Jews and Muslims in the Iberian Peninsula Susan M. Adams 1 *, Elena Bosch 1 * , Patricia L. Balaresque 1 , Stéphane J. Ballereau 1 , Andrew C. Lee 1 , Eduardo Arroyo 2 , Ana M. López-Parra 2 , Mercedes Aler 3 , Marina S. Gisbert Grifo 3 , Maria Brion 4 , Angel Carracedo 4 , João Lavinha 5 , Begoña Martínez-Jarreta 6 , Lluis Quintana-Murci 7 , Antònia Picornell 8 , Misericordia Ramon 8 , Karl Skorecki 9,10 , Doron M. Behar 9 , Francesc Calafell 11 and Mark A. Jobling 1 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 Unidad Docente de Medicina Legal y Forense, Universidad de Zaragoza, Zaragoza, Spain 7 Unit of Human Evolutionary Genetics, CNRS URA3012, Institut Pasteur, Paris, France 8 Laboratori de Genètica, IUNICS i Dep. Biologia, Universitat de les Illes Balears, Spain 9 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

Transcript of The genetic legacy of religious diversity and intolerance ... · The genetic legacy of religious...

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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 Unidad Docente de Medicina Legal y Forense, Universidad de Zaragoza, Zaragoza, Spain 7 Unit of Human Evolutionary Genetics, CNRS URA3012, Institut Pasteur, Paris, France 8 Laboratori de Genètica, IUNICS i Dep. Biologia, Universitat de les Illes Balears, Spain 9 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

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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 Y-

chromosomal 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

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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

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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 Y-

chromosomal 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 long-

established 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

15

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

16

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.

17

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.

18

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. Sub-

haplogroups 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.

19

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.

20

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17

P25

269

22215365

173

9

172

12f2

69

201

89

1238178

352

P233

96

145

R1b3d

R1b3*

R1a1 R1b3f

R1b3b

R1b*R1*K*(xP)

J2J(xJ2)

IGF*(xG-K)

E3b3

E3b2

E3b1

E3b*E3aE1

SRY-2627

M45

3

MEH2

Q*(xQ3)

AragonARA

- 15338- 3-- - - 612-18 -3 - 3 - -34

Andalusia, EEAN

- 7362- 2-- 3 -936 -1 - 1 - -195

Andalusia, WWAN

- 3348- 101- 4 -1415 14 1 4 - --73

AsturiasAST

- --50- -10- 5 515-10 -5 - - - --20

BasqueCountry, BAS

- 91363- 1-- - -318 1- - - - 2-116

Castilla laMancha, CLM

- 6363- 2-- 10 3622 -2 - 2 - --63

Castile, NENEC

- 3371- 33- 3 33-3 -3 - - - --31

Castile, NWNWC

- 1158- 102- 5 2813 -6 - 2 - -1100

CataloniaCAT

- 21159- 1-- 6 -6-3 -1 - - - -180

ExtremaduraEXT

2 2-48- 8-- 4 612-10 -8 - - - -252

GaliciaGAL

- 3252- 91- 6 17110 -7 - - - --88

GasconyGAS

- 171763- --- - -4-- -- - - - --24

Portugal, NNPO

- 10247- 323 12 2722 -5 - 3 - -260

Portugal, SSPO

- 3-441 83- 9 51534 -4 - 1 - -178

ValenciaVAL

- 51551 4-- 1 15310 -5 - 3 3 -173

n

SRY10831.2

All IberianPeninsula

1(0.1)

84(7)

37(3)

623(55)

3(0.3)

49(4)

11(1)

2(0.2)

57(5)

29(3)

88(8)

14(1)

68(6)

2(0.2)

42(4)

1(0.1)

14(1)

2(0.2)

2(0.2)

11(1)

1140

Moroccoa

MOR1 --37 6261 1 1381 -7 - - - --147

Algeriab

ALG7 --7- 5022 2 -415- -7 - - - -446

Tunisiab

TUN4 1-71 4341 - 1328- -5 - - - -2139

SaharawiaSAH

- ---3 76-3 - --17- -- - - - --29

All N.Africa 11(3)

1(0.3)

-18(5)

13(4)

196(54)

13(4)

5(1)

- 3(1)

10(3)

63(17)

1(0.3)

-21(6)

- - - -5(1)

361

MajorcaMAJ

- 13-532 2-- 6 2828 -5 - - - --62

MinorcaMIN

- 11359- 3-- - -3-3 -11 - 3 - -537

IbizaIBZ

- 7446- --- 13 174-2- -4 - - - -454

0.804±0.0490.598±0.0560.742±0.0480.779±0.0820.576±0.0490.586±0.0710.503±0.1110.656±0.0510.608±0.0520.743±0.0570.701±0.0490.576±0.0960.760±0.0530.774±0.0410.686±0.058

h

0.591±0.0460.725±0.0630.731±0.0280.406±0.101

0.691±0.0580.634±0.085

0.744±0.051

124

R2

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

SephardicJewish, SJ

- nana20(11)

1(1)

1(1)

2(1)

- 27(16)

11(6)

43(25)

38(22)

1(1)

4(2)

6(3)

- 8(5)

2(1)

nac6(3)

174 4(2)

0.849±0.013c

170

Adams et al., Figure 1

75

207

GaliciaGAL

N PortugalNPO

S PortugalSPO

NW CastileNWC

NE CastileNEC

ExtremaduraEXT

Castilla la ManchaCLM

E AndalusiaEAN

WAndalusia

WAN

ValenciaVAL

AragonARA

CataloniaCAT

GasconyGAS

Basque CountryBAS

IbizaIBZ

MajorcaMAJ

MinorcaMIN

MoroccoMOR Algeria

ALG

SaharawiSAH

SephardicJewish

SJ

24

116

100

88

60

78

52

7395

63

73

3480

R1b3d

R1b3*

R1a1

R1b3f

R1b3b

R1b*

R1*

K*(xP)J2J(xJ2)IGF*(xG-K)E3b3E3b2E3b1E3b*E3a

E1

Q*x(Q3)

R2

Adams et al., Figure 2

TunisiaTUN

62

54

37

31

14729

139

174

20Asturias

AST

46

b)

d)

FST (hg data)S-stress 1.4%

RST (8-locus Y-STR data)S-stress 1.3%

BAS

VAL

NWC

GAL

WAN

SPO

EXT AST

NPO

ARACAT

GAS

BASEAN

CLMNEC

IBZ

MAJ

MIN

FST (hg data)S-stress 6.4%

VAL

NWC

GAL

WAN SPO

EXT

ASTNPO ARA

CATGAS

BAS

EAN

CLM

NEC

IBZ

MAJ

MIN

RST (17-locus Y-STR data)S-stress 4.3%

GAS

GAS

Adams et al., Figure 3

-0.3

0.3

-1 1 20

0

-1.5 -1 -0.5 0.5 10

-0.8

-0.4

0.4

0.8

0

2

-1.5 -1 -0.5 0.5 1 1.50-0.8

-0.4

0.4

0.6

0

-0.4

0.4

-1 1 20

0

a)

c)

SAH

TUN

ALG

MOR

SJBAS

MOR

ALG

TUN

SAH

SJ

Adams et al., Figure 4

NEC

IBZ

GAS

Nor

th A

fric

an

Iber

ian

Sep

hard

ic J

ewis

h

0

50

100

% a

nces

try

AST

GAL

NWC

NPO

EXT

SPO

WAN

ARA

CAT

MAJ

VAL

CLM

EAN

MIN

Adams et al., Figure 5

a) hgE3b2 b) hgG

n=1IberianNorth AfricanSephardic Jewish

Adams et al., Figure 6

hgR1b3

n=1IberianMoroccanSephardic Jewish

Adams et al., Supplementary Table 1: Haplotype data 1

Nam

e

Popn Hg

DY

S19

DY

S38

8

DY

S38

9I

389

II-Ii

DY

S39

0

DY

S39

1

DY

S39

2

DY

S39

3

DY

S43

4

DY

S43

5

DY

S43

6

DY

S43

7

DY

S43

8

DY

S43

9

DY

S46

0

DY

S46

1

DY

S46

2

DY

S38

5

AragonIP685 ARA E3b* 15 12 13 17 22 9 11 14 11 11 12 14 10 11 11 13 12 14,14IP314 ARA E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 11 12 12 13,14IP292 ARA I 14 14 12 16 22 10 11 13 11 11 12 16 10 11 10 12 12 13,14IP534 ARA I 17 13 14 15 25 9 11 13 11 11 12 15 10 12 10 12 12 12,12IP575 ARA I 15 13 14 17 23 10 12 14 11 11 12 15 10 12 11 12 12 16,16IP577 ARA I 14 14 12 17 22 10 11 13 11 11 12 15 10 11 10 12 12 14,14IP580 ARA I 17 13 13 15 24 10 11 13 11 11 12 15 10 13 10 11 13 12,12IP586 ARA I 17 13 14 15 25 9 11 13 11 11 12 15 10 12 10 12 12 12,13IP537 ARA J2 15 15 12 18 24 10 11 12 11 11 12 16 9 13 11 10 10 13,17IP571 ARA J2 14 15 13 16 23 11 11 13 11 11 12 15 9 11 11 12 11 12,17IP574 ARA J2 14 16 13 15 23 11 11 12 11 10 12 15 9 11 10 12 11 12,17IP584 ARA J2 15 15 12 17 23 10 11 12 11 11 12 16 9 12 11 10 11 14,17IP521 ARA K(XP) 13 12 14 17 23 10 13 14 11 11 12 15 9 12 11 11 12 16,17IP572 ARA K(xP) 16 12 12 15 23 10 14 13 11 11 12 14 9 9 10 11 12 14,15IP579 ARA R1a1 15 12 13 18 25 11 11 13 11 11 12 14 11 10 11 11 11 11,14IP369 ARA R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 12 10 12 11 11,14IP533 ARA R1b3* 12 12 13 17 24 11 13 14 11 11 12 15 12 12 10 12 11 12,14IP573 ARA R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP576 ARA R1b3* 14 12 14 17 24 10 13 13 11 11 12 15 12 12 11 12 12 10,13IP581 ARA R1b3* 14 12 14 16 23 11 13 13 11 11 12 15 12 11 10 12 11 11,14IP582 ARA R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 13 11 12 11 11,14IP583 ARA R1b3* 14 12 14 16 23 10 13 13 11 11 12 15 12 13 11 12 11 11,11IP585 ARA R1b3* 14 12 13 16,17 24 11 13 13 11 11 12 15 12 10,12 11 12 11 12,15IP599 ARA R1b3* 14 12 13 16 24 11 13 14 11 11 12 15 12 11 11 12 11 11,14IP789 ARA R1b3* 14 12 12 16 24 11 13 13 11 11 12 15 11 11 11 12 11 11,14IP808 ARA R1b3* 15 12 13 16 23 10 13 13 11 11 12 14 12 12 11 13 11 10,15IP812 ARA R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 12 12 11 12 11 11,13IP864 ARA R1b3* 14 12 13 16 23 10 13 13 11 11 12 14 12 12 11 12 11 11,14IP359 ARA R1b3d 14 12 13 16 24 10 13 13 11 11 12 14 12 13 10 12 11 11,14IP535 ARA R1b3f 15 12 13 16 23 11 13 13 11 11 12 15 12 11 10 13 11 11,14IP536 ARA R1b3f 14 12 13 15 23 11 13 13 11 11 12 15 12 12 11 12 11 14,14IP578 ARA R1b3f 14 12 13 17 24 11 13 13 11 11 12 15 12 11 11 12 11 11,15IP730 ARA R1b3f 14 12 13 17 24 11 13 14 11 11 12 15 12 12 11 13 11 11,14IP835 ARA R1b3f 14 12 13 16 23 11 13 13 11 11 12 15 12 12 11 12 11 11,14

AsturiasIP1008 AST E3b* 13 12 12 18 24 10 10 13 11 11 12 14 10 12 10 12 11 16,16IP1015 AST E3b* 13 12 14 17 24 10 11 12 11 11 12 14 11 12 10 13 12 16,19IP1002 AST E3b1 13 12 13 17 25 10 11 14 11 11 12 14 10 11 11 11 13 16,17IP1019 AST G 15 13 12 17 22 10 11 14 11 11 12 15 10 11 10 11 12 14,15IP716 AST I 17 13 13 15 23 10 11 13 11 11 12 15 10 11 10 11 12 12,12IP995 AST I 15 14 12 16 22 10 11 13 11 11 12 16 10 11 11 12 12 13,15IP992 AST J2 14 15 13 17 23 10 11 12 12 11 12 15 9 11 9 13 11 13,17IP997 AST J2 15 15 12 16 24 10 11 13 11 11 12 16 9 11 11 10 11 13,17IP1020 AST J2 14 15 12 16 23 11 11 13 11 11 12 15 10 12 10 12 11 14,16IP1023 AST K(XP) 15 12 12 15 24 10 14 13 11 11 12 14 9 11 10 11 13 13,15IP991 AST R1b3* 14 12 13 16 24 10 13 12 11 11 12 15 12 11 11 12 11 12,14IP303 AST R1b3* 15 12 13 16 23 11 13 13 11 11 12 15 12 12 11 13 11 11,13IP680 AST R1b3* 14 12 13 16 24 12 13 13 11 11 12 15 12 12 11 12 11 11,14IP989 AST R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 10 13 11 11,15IP993 AST R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP999 AST R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 12 10 12 11 11,14IP1011 AST R1b3* 14 12 13 16 24 10 13 13 11 11 12 14 12 12 11 12 11 11,14IP1016 AST R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 13 11 12 11 11,15IP1018 AST R1b3* 14 12 14 16 22 10 13 13 11 11 12 14 12 12 13 12 11 11,14IP1021 AST R1b3* 14 12 12 16 23 11 14 13 11 11 12 15 12 12 11 13 11 11,14

Basque CountryIP1 BAS E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 11 12 12 13,14IP11 BAS I 15 13 13 16 25 10 11 13 11 11 12 15 10 11 11 11 12 12,16IP20 BAS I 13 14 12 16 22 10 11 13 12 11 12 16 10 11 11 12 12 13,16IP25 BAS I 17 13 15 15 23 10 11 13 11 11 12 15 10 12 10 11 12 12,12IP36 BAS I 17 13 13 15 24 9 11 13 11 11 12 14 10 13 10 12 12 12,12IP884 BAS I 16 13 13 15 23 10 11 13 11 11 12 15 10 11 10 11 12 12,12IP902 BAS I 17 13 13 15 23 10 11 13 11 11 12 14 10 13 10 11 13 12,12IP904 BAS I 17 13 13 15 23 11 11 13 11 11 12 14 10 13 10 11 13 12,13IP935 BAS I 17 13 14 15 23 10 11 13 11 11 12 15 10 12 10 11 12 12,12

Adams et al., Supplementary Table 1: Haplotype data 2

IP936 BAS I 17 13 12 15 23 10 11 13 11 11 12 15 10 11 10 11 12 12,12IP905 BAS J(xJ2) 14 13 14 16 23 10 11 12 11 11 11 14 10 11 11 13 13 12,18IP889 BAS J2 14 15 12 17 23 10 12 11 11 11 12 14 9 11 10 11 11 13,21IP908 BAS J2 15 17 12 17 23 10 11 12 11 12 12 15 9 11 11 13 11 12,16IP910 BAS J2 16 16 13 16 23 9 11 12 11 11 12 14 9 12 10 13 10 13,15IP906 BAS Q(xQ3) 13 12 14 18 24 10 14 13 11 11 12 13 11 12 10 12 12 15,16IP3 BAS R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 11 12 11 12,14IP4 BAS R1b3* 14 12 12 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP6 BAS R1b3* 14 12 12 16 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP7 BAS R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 11 12 12 11 11,13IP8 BAS R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP10 BAS R1b3* 14 12 14 16 23 11 13 14 11 11 12 14 12 13 11 12 11 11,14IP12 BAS R1b3* 14 12 13 16 25 10 13 12 11 11 12 15 12 13 11 12 11 11,13IP15 BAS R1b3* 14 12 14 17 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP16 BAS R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP18 BAS R1b3* 15 12 13 17 23 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP19 BAS R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP21 BAS R1b3* 14 12 13 15 23 11 13 15 11 11 12 15 12 11 11 12 11 11,14IP22 BAS R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP23 BAS R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 12,14IP24 BAS R1b3* 14 12 14 16 23 11 13 13 11 11 12 15 12 13 10 13 11 11,11IP26 BAS R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 10,14IP27 BAS R1b3* 14 12 12 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP29 BAS R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,13IP31 BAS R1b3* 13 12 13 16 25 10 13 12 11 11 12 15 12 14 11 12 11 11,13IP32 BAS R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 12,14IP33 BAS R1b3* 14 12 11 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP34 BAS R1b3* 14 12 13 16 23 10 13 13 11 11 12 15 12 13 11 12 11 11,11IP37 BAS R1b3* 14 12 13 17 24 11 13 13 11 11 12 15 12 12 12 12 11 11,14IP38 BAS R1b3* 14 12 12 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP39 BAS R1b3* 14 12 13 16 24 12 13 13 11 11 12 15 12 12 11 12 11 11,14IP40 BAS R1b3* 14 12 13 15 24 10 13 13 11 11 12 15 12 11 11 12 11 11,15IP44 BAS R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP45 BAS R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 11 11 11 12 11,15IP46 BAS R1b3* 14 12 14 16 24 10 13 13 11 11 12 15 12 11 11 12 11 11,14IP48 BAS R1b3* 14 12 14 16 23 10 13 13 11 11 12 15 13 12 11 12 11 11,11IP49 BAS R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 11 11 12 11 11,14IP527 BAS R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP531 BAS R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP532 BAS R1b3* 14 12 13 16 25 10 13 12 11 11 12 15 12 13 10 13 11 11,13IP877 BAS R1b3* 14 12 12 16 23 11 13 14 11 11 12 14 12 13 11 12 11 12,14IP878 BAS R1b3* 14 12 14 16 24 10 13 13 11 11 12 14 12 11 11 12 11 11,13IP880 BAS R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 13 10 12 11 11,14IP881 BAS R1b3* 14 12 14 16 24 11 13 13 11 11 12 14 12 11 10 12 11 11,14IP882 BAS R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 13 11 12 11 11,14IP883 BAS R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 12 12 10 13 11 11,14IP885 BAS R1b3* 14 12 13 17 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP887 BAS R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 13 11 13 11 11,15IP890 BAS R1b3* 14 12 13 16 25 11 13 13 11 11 12 15 12 11 11 11 11 11,12IP891 BAS R1b3* 14 12 13 17 24 11 13 13 11 11 12 15 12 11 12 12 11 11,14IP892 BAS R1b3* 14 12 15 16 24 11 13 12 11 12 12 15 12 11 11 12 11 11,14IP893 BAS R1b3* 14 12 14 15 23 11 13 13 11 12 12 14 12 12 10 12 11 12,14IP894 BAS R1b3* 14 12 14 16 23 11 13 13 11 11 12 14 12 12 10 12 11 11,11IP897 BAS R1b3* 14 12 12 16 23 11 13 14 11 11 12 14 12 13 11 12 11 11,14IP898 BAS R1b3* 14 12 13 16 24 10 12 13 11 11 12 15 12 12 10 12 11 11,14IP899 BAS R1b3* 14 12 14 16 23 10 13 13 11 11 12 15 12 13 11 12 11 11,11IP900 BAS R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 11 12 11 12,14IP901 BAS R1b3* 14 12 13 16 25 10 13 13 11 11 12 15 12 12 10 12 11 11,14IP903 BAS R1b3* 14 12 14 17 24 11 13 13 11 11 12 14 12 12 10 12 11 12,14IP907 BAS R1b3* 14 12 13 15 24 11 14 12 11 11 12 15 12 12 11 12 11 11,14IP909 BAS R1b3* 14 12 14 15 24 11 13 14 11 12 12 14 12 12 10 12 11 12,14IP911 BAS R1b3* 14 12 14 17 24 11 13 13 11 11 12 15 12 12 12 12 11 11,14IP925 BAS R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP927 BAS R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 12,14IP928 BAS R1b3* 14 12 14 17 24 11 13 13 11 11 12 14 12 13 10 12 11 11,14IP929 BAS R1b3* 14 12 14 17 23 11 13 13 11 11 12 14 12 12 10 12 11 11,14IP931 BAS R1b3* 14 12 13 16 25 10 13 12 11 11 12 15 12 13 10 12 11 11,13IP932 BAS R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP933 BAS R1b3* 14 12 14 18 24 10 13 13 11 11 12 15 12 12 10 12 11 11,14IP934 BAS R1b3* 14 12 14 16 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP937 BAS R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP938 BAS R1b3* 14 12 13 16 25 10 13 12 11 11 12 15 12 13 11 12 11 11,13

Adams et al., Supplementary Table 1: Haplotype data 3

IP939 BAS R1b3* 14 12 14 16 24 11 13 13 11 11 12 14 12 11 10 12 11 11,14IP940 BAS R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 10 12 12 11,14IP941 BAS R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP942 BAS R1b3* 12 12 13 17 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP945 BAS R1b3* 14 12 14 16 23 11 13 14 11 11 12 14 12 14 11 12 11 11,14IP946 BAS R1b3* 14 12 14 18 24 10 13 13 11 11 12 14 12 11 10 12 11 11,14IP947 BAS R1b3* 14 12 14 17 24 11 13 13 11 11 12 14 12 12 10 13 11 11,15IP47 BAS R1b3b 15 12 14 16 23 10 13 13 11 11 12 15 12 13 11 12 11 11,11IP50 BAS R1b3b 15 12 14 16 23 10 13 13 11 11 12 15 12 13 11 12 11 11,11IP2 BAS R1b3d 14 12 14 16 24 11 13 13 11 11 12 14 12 11 10 13 11 11,14IP9 BAS R1b3d 14 12 13 16 24 11 13 13 11 11 12 14 12 12 10 12 11 11,14IP13 BAS R1b3d 14 12 13 16 24 11 13 14 11 11 12 14 12 13 10 12 11 11,14IP17 BAS R1b3d 14 12 13 16 23 10 13 14 12 11 12 14 12 12 10 12 11 11,14IP28 BAS R1b3d 14 12 13 16 24 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP30 BAS R1b3d 14 12 13 16 24 11 13 13 11 11 12 14 12 12 10 12 11 11,14IP35 BAS R1b3d 14 12 13 16 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP42 BAS R1b3d 14 12 14 16 24 11 13 13 11 11 12 14 12 11 10 12 11 11,14IP526 BAS R1b3d 14 12 13 17 24 9 13 13 11 11 12 14 12 12 10 12 11 11,14IP879 BAS R1b3d 14 12 13 16 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP886 BAS R1b3d 14 12 13 16 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP888 BAS R1b3d 14 12 13 16 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP895 BAS R1b3d 14 12 14 16 24 10 13 13 11 11 10,12 14 13 12 11 12 11 11,14IP896 BAS R1b3d 13 12 13 17 24 10 13 13 11 11 12 14 11 12 10 12 11 11,14IP944 BAS R1b3d 14 12 13 16 24 11 13 14 11 11 12 14 12 12 10 12 12 11,14IP5 BAS R1b3f 14 12 14 16 24 10 13 13 11 11 12 15 12 13 10 12 11 11,13IP14 BAS R1b3f 14 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP41 BAS R1b3f 14 12 14 16 24 10 13 13 11 11 12 15 12 13 10 12 11 12,13IP43 BAS R1b3f 14 12 14 16 24 11 13 13 11 11 12 15 12 13 10 12 11 11,13IP82 BAS R1b3f 14 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP83 BAS R1b3f 14 12 13 16 24 10 13 13 11 11 12 15 12 12 10 12 11 11,14IP529 BAS R1b3f 14 12 14 16 24 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP530 BAS R1b3f 14 12 14 16 24 11 13 13 11 11 12 15 12 13 10 12 11 11,14IP926 BAS R1b3f 14 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP930 BAS R1b3f 14 12 13 16 24 12 13 13 11 11 12 15 12 11 11 12 12 11,14IP943 BAS R1b3f 14 12 14 16 24 11 13 13 11 11 12 15 12 13 10 12 11 11,14

CataloniaIP73 CAT E3b1 13 12 13 17 24 10 11 13 11 11 12 14 10 12 11 12 12 16,18IP53 CAT E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 11 13 12 13,15IP548 CAT E3b3 15 12 13 18 23 10 11 14 11 11 12 14 11 12 10 12 11 15,17IP59 CAT G 15 13 12 17 22 10 11 14 11 11 12 16 10 12 10 11 12 14,15IP67 CAT G 15 12 12 18 22 10 11 13 11 11 12 16 10 12 11 10 12 12,14IP525 CAT G 15 13 12 17 22 11 11 15 11 11 12 16 10 11 10 11 12 15,15IP555 CAT G 15 12 12 16 21 10 11 13 12 11 12 16 10 11 9 11 12 12,14IP567 CAT G 15 13 12 16 22 10 12 13 11 11 12 16 10 11 10 11 12 14,14IP546 CAT I 15 13 13 16 26 10 11 13 11 11 12 15 10 11 10 11 12 12,16IP557 CAT I 17 13 14 15 25 9 11 13 11 11 12 15 10 12 10 12 12 12,12IP55 CAT J2 14 15 13 18 25 10 11 12 11 11 12 14 9 11 12 11 10 14,18IP64 CAT J2 15 15 13 18 23 9 11 13 11 11 12 15 9 12 10 13 11 12,13IP543 CAT J2 14 15 14 17 23 11 11 12 10 11 12 15 9 11 9 12 11 12,14IP570 CAT J2 14 16 13 16 23 10 11 12 11 11 12 14 10 11 11 10 11 13,17IP588 CAT J2 16 16 13 16 23 9 11 12 11 11 12 14 9 11 10 13 10 13,16IP52 CAT R1b3* 14 12 13 16 24 10 13 13 12 11 12 15 12 13 11 12 11 11,14IP54 CAT R1b3* 15 12 13 16 24 10 13 13 11 11 12 15 13 13 10 12 11 11,15IP56 CAT R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP57 CAT R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 11 11 10 13 11 11,14IP58 CAT R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP60 CAT R1b3* 14 13 13 16 24 11 13 13 11 11 12 16 12 12 11 12 11 12,14IP61 CAT R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 13 13 11 12 11 11,13IP62 CAT R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,15IP63 CAT R1b3* 15 12 13 16 24 10 13 13 11 11 12 15 12 11 10 12 11 11,15IP65 CAT R1b3* 14 12 13 16 24 12 14 14 11 11 12 15 12 12 11 12 11 12,14IP66 CAT R1b3* 14 12 14 16 24 11 13 13 11 11 12 14 12 13 10 12 11 11,15IP68 CAT R1b3* 14 12 13 16 23 11 14 14 11 11 12 15 12 12 10 12 11 11,14IP70 CAT R1b3* 14 12 13 17 24 10 13 13 11 11 12 14 12 11 11 12 12 11,14IP72 CAT R1b3* 14 12 13 16 24 11 12 12 10 11 12 14 12 12 11 11 11 12,14IP74 CAT R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 12 12 11 12 12 11,14IP76 CAT R1b3* 14 12 14 17 24 11 12 13 11 11 12 14 12 12 12 12 11 11,14IP77 CAT R1b3* 14 12 12 16 26 10 13 13 11 11 12 15 12 12 10 12 11 11,14IP78 CAT R1b3* 14 12 14 17 24 11 13 13 11 11 12 15 12 11 12 12 11 11,14IP79 CAT R1b3* 14 12 13 16 25 11 13 13 11 11 12 15 12 12 11 12 11 11,15IP518 CAT R1b3* 14 12 13 17 24 10 14 13 11 11 12 15 13 12 10 12 11 12,14

Adams et al., Supplementary Table 1: Haplotype data 4

IP519 CAT R1b3* 14 12 13 17 24 10 13 13 11 11 12 15 12 12 11 12 11 11,15IP520 CAT R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 12 11 12 11 11,14IP523 CAT R1b3* 14 12 14 16 24 12 13 13 11 11 12 14 12 12 10 12 11 11,15IP524 CAT R1b3* 14 12 14 16 24 11 13 13 11 11 12 14 12 12 9 12 11 11,13IP643 CAT R1b3* 14 14 14 16 23 11 13 13 11 11 12 14 12 12 9 12 11 11,14IP834 CAT R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,15IP539 CAT R1b3* 14 12 13 17 24 11 13 12 11 11 12 15 12 12 11 11 11 11,14IP541 CAT R1b3* 14 12 14 16 24 11 13 14 11 11 12 14 12 11 10 12 11 11,14IP542 CAT R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 11 11 12 11 12,14IP545 CAT R1b3* 14 12 13 16 24 11 13 12 11 11 12 15 12 12 11 11 11 11,14IP547 CAT R1b3* 14 12 13 16 25 10 13 12 11 11 12 15 12 12 11 12 11 11,14IP549 CAT R1b3* 15 12 14 17 24 11 13 12 11 11 12 15 13 12 11 11 11 11,14IP550 CAT R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 13 10 12 11 11,15IP551 CAT R1b3* 15 12 14 16 24 11 13 13 11 11 12 14 14 12 10 12 11 11,14IP553 CAT R1b3* 14 12 12 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,15IP554 CAT R1b3* 14 12 12 16 25 11 13 13 11 11 12 15 12 12 11 12 11 11,15IP559 CAT R1b3* 14 12 13 18 25 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP560 CAT R1b3* 12 12 13 17 24 10 13 13 11 11 12 15 12 13 11 12 11 11,15IP561 CAT R1b3* 15 12 13 16 23 10 13 13 11 11 12 15 12 12 11 12 12 11,14IP564 CAT R1b3* 14 12 13 16 24 11 13 12 11 11 12 15 12 12 12 11 11 11,11IP565 CAT R1b3* 14 12 13 16 25 10 13 13 11 11 11 15 12 12 10 13 11 11,15IP566 CAT R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 13 11 12 11 11,14IP568 CAT R1b3* 14 12 12 16 25 11 13 13 11 11 12 15 12 12 11 12 11 11,15IP590 CAT R1b3* 14 12 14 16 24 10 13 13 11 11 12 15 12 11 10 12 11 11,15IP591 CAT R1b3* 14 12 13 17 24 10 13 13 11 11 12 15 11 12 11 12 11 11,14IP592 CAT R1b3* 14 12 13 16 23 10 13 13 11 11 12 15 12 11 11 12 11 11,13IP600 CAT R1b3* 14 12 14 16 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP552 CAT R1b3d 14 12 13 17 23 11 13 13 11 11 12 14 12 11 11 12 11 11,13IP51 CAT R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP69 CAT R1b3f 14 12 13 16 24 10 13 13 11 11 12 15 12 11 11 12 11 11,15IP71 CAT R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 12,15IP75 CAT R1b3f 14 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 12,16IP80 CAT R1b3f 15 12 13 17 24 11 13 13 11 11 12 15 12 12 11 13 11 11,14IP81 CAT R1b3f 14 12 13 16 24 10 13 14 11 11 12 15 12 12 11 13 11 11,14IP538 CAT R1b3f 14 12 13 18 24 12 13 13 11 12 12 15 12 12 12 12 11 11,14IP540 CAT R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 13 12 12 11 11,14IP544 CAT R1b3f 14 12 13 16 24 11 12 13 11 11 12 15 12 12 12 13 11 11,14IP556 CAT R1b3f 14 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP558 CAT R1b3f 14 12 13 16 24 11 12 14 11 11 12 15 12 11 11 11 11 11,14IP562 CAT R1b3f 14 12 12 16 24 11 13 13 11 11 12 15 12 13 10 13 11 11,15IP563 CAT R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 12 12 12 11 11,14IP569 CAT R1b3f 14 12 13 16 23 11 13 13 11 11 12 15 12 14 11 12 11 11,14IP589 CAT R1b3f 14 12 13 16 25 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP603 CAT R1b3f 14 12 14 16 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP604 CAT R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 11 11 12 11 11,15

Castilla La ManchaIP381 CLM E3b1 14 12 12 17 24 10 11 13 11 11 12 14 10 11 11 12 12 16,17IP676 CLM E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 10 13 12 13,14IP250 CLM G 15 12 12 16 22 10 11 13 11 11 12 16 10 11 11 11 13 15,15IP267 CLM G 15 13 12 17 23 10 11 14 11 11 12 16 10 13 10 11 12 14,14IP333 CLM G 15 12 12 17 23 10 11 14 11 11 12 15 10 10 11 10 12 14,14IP492 CLM G 16 12 13 16 22 10 11 14 11 11 12 15 10 13 11 8 12 14,15IP706 CLM G 15 12 12 17 23 10 11 13 11 11 12 16 10 12 11 11 12 14,15IP742 CLM G 15 12 12 17 23 10 11 14 11 12 12 16 10 12 10 12 12 14,14IP264 CLM I 16 13 13 15 23 10 11 13 11 11 12 15 10 11 10 11 12 12,12IP638 CLM J(xJ2) 14 16 13 18 23 11 11 12 11 11 12 14 10 13 11 11 11 13,17IP335 CLM J2 15 15 13 18 23 10 11 12 11 11 12 15 9 11 10 13 11 13,13IP336 CLM J2 13 15 14 19 23 11 11 12 11 11 12 15 9 10 11 12 11 14,17IP345 CLM J2 14 14 14 17 24 10 11 12 11 11 12 15 9 12 10 12 11 13,13IP347 CLM J2 15 17 13 18 21 10 11 12 11 11 12 15 9 10 10 13 11 14,15IP263 CLM K(xP) 15 12 13 16 23 11 13 13 11 11 12 14 9 11 11 11 14 14,16IP677 CLM K(xP) 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP379 CLM R1a1 15 12 13 18 25 11 11 14 11 11 12 14 11 10 8 11 11 11,14IP280 CLM R1b3* 14 12 13 16 25 11 13 13 12 11 12 15 12 11 11 12 11 11,14IP293 CLM R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 12 10 12 11 11,14IP300 CLM R1b3* 13 12 14 16 24 13 13 14 11 11 12 14 12 11 10 12 11 11,14IP302 CLM R1b3* 14 12 12 16 23 11 13 13 11 11 12 15 12 12 10 12 11 11,15IP304 CLM R1b3* 14 12 14 17 24 11 13 13 11 11 12 14 9 13 10 12 11 11,14IP305 CLM R1b3* 14 12 13 15 24 11 13 13 11 11 12 15 12 13 10 12 11 11,14IP307 CLM R1b3* 14 12 14 18 24 11 13 13 11 11 12 15 12 13 11 11 11 11,14IP308 CLM R1b3* 14 12 14 16 23 10 13 13 11 11 12 15 12 13 11 12 11 11,11

Adams et al., Supplementary Table 1: Haplotype data 5

IP318 CLM R1b3* 14 12 14 16 24 10 12 13 11 11 12 14 13 13 10 12 11 11,12IP323 CLM R1b3* 14 12 13 15 24 11 13 13 11 11 12 15 11 13 11 12 11 11,14IP324 CLM R1b3* 14 12 14 16 23 10 13 13 11 11 12 15 12 13 11 12 11 11,11IP325 CLM R1b3* 14 12 14 17 24 11 12 13 11 11 12 14 12 13 10 12 11 11,14IP338 CLM R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 10,14IP348 CLM R1b3* 14 12 13 16 24 10 13 12 11 11 12 15 12 12 11 12 11 11,14IP351 CLM R1b3* 14 12 12 16 24 10 14 13 11 11 12 14 12 12 10 13 11 11,14IP361 CLM R1b3* 15 12 14 16 24 10 13 13 11 11 12 15 12 13 11 12 11 11,14IP362 CLM R1b3* 15 12 13 16 24 11 13 12 11 11 12 15 12 13 10 11 11 11,14IP367 CLM R1b3* 14 12 13 17 25 11 13 13 12 11 12 15 12 12 11 12 11 12,14IP368 CLM R1b3* 14 12 13 17 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP370 CLM R1b3* 14 12 13 18 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP372 CLM R1b3* 15 12 13 16 23 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP375 CLM R1b3* 14 12 14 17 24 11 13 13 11 11 12 14 12 11 10 12 11 11,15IP376 CLM R1b3* 14 12 12 16 23 11 13 13 11 11 12 15 12 12 10 13 11 11,14IP466 CLM R1b3* 15 12 13 16 24 11 13 13 11 11 12 15 12 13 10 12 11 11,14IP487 CLM R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 13 11 13 11 11,14IP488 CLM R1b3* 15 12 13 16 23 11 13 13 11 11 12 15 12 12 10 12 11 11,15IP490 CLM R1b3* 14 12 14 16 24 11 13 13 11 11 12 14 12 12 10 12 11 12,14IP496 CLM R1b3* 15 12 13 16 24 11 15 13 11 11 12 15 13 11 12 12 11 13,14IP661 CLM R1b3* 14 12 13 16,17 24 11 13 13 11 11 12 15 12 10,13 11 13 11 12,14IP667 CLM R1b3* 15 12 12 16 24 11 13 13 11 11 12 14 12 12 10 12 11 11,15IP698 CLM R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 13 10 11 11 11,13IP703 CLM R1b3* 15 12 13 16 23 11 13 13 11 11 12 15 12 13 11 12 11 11,14IP721 CLM R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 12 13 11 11,14IP766 CLM R1b3* 14 12 13 16 25 11 13 14 11 11 12 14 12 12 10 11 11 12,15IP790 CLM R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 13 10 12 11 11,14IP800 CLM R1b3* 14 12 13 16 23 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP826 CLM R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP854 CLM R1b3* 14 12 14 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP863 CLM R1b3* 14 12 14 16 24 10 13 13 11 11 12 14 12 12 10 13 11 11,14IP873 CLM R1b3* 14 12 14 16 24 12 13 13 11 11 12 14 12 12 10 12 11 11,14IP312 CLM R1b3d 14 12 13 16 24 10 13 13 11 11 12 14 12 13 10 12 11 11,14IP717 CLM R1b3d 14 12 13 17 24 11 13 12 12 11 12 14 12 12 11 13 11 11,14IP320 CLM R1b3f 14 12 14 16 23 11 13 13 11 11 12 15 12 13 11 12 11 11,14IP628 CLM R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 12 12 13 11 11,14IP635 CLM R1b3f 14 12 13 17 25 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP648 CLM R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 11 10 12 11 11,14

East AndalusiaIP758 EAN E3b1 13 12 12 16 24 10 11 13 11 11 12 14 10 11 9 12 12 17,19IP463 EAN E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 11 13 12 13,14IP734 EAN E3b2 13 12 14 16 24 10 11 13 11 11 12 14 10 10 11 13 12 13,14IP231 EAN E3b3 13 12 13 17 24 10 11 14 11 11 12 14 11 12 10 13 12 16,19IP277 EAN G 15 13 13 17 22 10 11 13 11 11 12 16 10 11 10 11 12 15,15IP326 EAN G 15 12 12 17 23 10 11 13 11 11 12 16 10 11 10 11 11 14,14IP842 EAN G 15 12 12 17 22 10 11 14 11 11 12 16 10 13 11 11 12 12,15IP484 EAN I 16 13 13 15 23 10 11 13 11 11 12 15 10 11 10 11 12 12,12IP502 EAN I 17 13 14 15 25 9 11 13 11 11 12 15 10 12 10 12 12 12,12IP503 EAN I 14 12 13 17 23 10 12 14 11 11 12 14 10 11 11 12 12 15,16IP727 EAN I 17 13 13 15 23 10 11 13 11 11 12 15 10 11 10 11 12 12,12IP753 EAN I 16 13 12 16 23 10 11 14 11 11 12 15 8 11 11 12 12 15,15IP756 EAN I 17 13 14 15 25 9 12 13 11 11 12 15 10 11 10 12 12 12,12IP684 EAN J(xJ2) 14 15 13 18 22 10 11 12 11 11 12 14 10 12 11 11 11 14,18IP724 EAN J(XJ2) 14 14 14 16 23 10 11 13 10 11 11 14 10 11 11 12 12 12,12IP736 EAN J(xJ2) 14 16 13 16 24 10 11 12 11 11 12 14 10 11 11 11 11 12,18IP273 EAN J2 14 15 13 17 23 11 11 12 11 11 12 15 9 12 11 12 11 14,18IP278 EAN J2 14 15 13 16 23 9 11 13 11 11 12 16 7 11 10 13 11 14,14IP481 EAN J2 15 15 13 16 23 10 11 12 11 11 12 15 9 11 10 13 11 13,18IP498 EAN J2 15 15 13 16 23 9 11 12 11 11 12 14 9 12 11 12 10 13,16IP779 EAN J2 14 15 12 16 24 11 11 12 11 11 12 16 9 12 11 13 11 13,16IP794 EAN J2 14 15 13 16 23 9 11 13 11 11 12 16 7 11 10 13 11 14,14IP827 EAN J2 14 14 13 17 25 10 11 12 11 11 12 15 9 12 11 14 11 15,16IP831 EAN J2 15 14 13 16 23 9 11 12 11 11 12 14 9 12 10 13 10 13,18IP848 EAN J2 15 14 14 15 22 10 11 12 11 11 12 15 9 11 10 12 11 13,18IP506 EAN R1a1 15 12 13 17 25 11 11 13 11 11 12 14 11 11 11 11 11 11,15IP235 EAN R1b3* 14 13 13 16 23 11 13 13 11 11 12 15 13 12 10 12 11 11,14IP238 EAN R1b3* 14 12 13 15 24 11 13 13 12 11 12 15 12 8 10 12 11 9,14IP252 EAN R1b3* 14 12 12 16 24 12 13 13 11 11 12 15 12 13 11 12 10 11,15IP254 EAN R1b3* 14 12 14 17 24 11 13 13 11 11 12 14 12 12 11 13 11 11,15IP255 EAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 12 11 12 11 11,13IP257 EAN R1b3* 14 12 14 16 24 11 14 13 11 11 12 14 12 12 11 12 11 11,14

Adams et al., Supplementary Table 1: Haplotype data 6

IP258 EAN R1b3* 15 12 13 16 24 11 13 13 11 11 12 14 12 11 11 12 11 12,15IP286 EAN R1b3* 14 12 12 16 23 11 13 13 11 11 12 15 12 13 11 12 11 11,14IP311 EAN R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,15IP322 EAN R1b3* 14 12 12 15 23 11 14 12 11 11 12 15 12 14 11 11 11 11,14IP332 EAN R1b3* 14 12 14 16 24 10 13 13 11 11 12 15 12 11 11 12 11 11,14IP344 EAN R1b3* 14 12 13 16 24 11 13 12 11 11 12 15 12 12 11 12 11 11,14IP349 EAN R1b3* 14 12 14 17 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP358 EAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 11 12 11 12,14IP365 EAN R1b3* 14 12 13 16 25 11 13 12 11 11 13 15 12 11 8 11 11 11,14IP383 EAN R1b3* 14 12 13 16 24 11 13 12 11 11 12 15 12 12 11 12 11 11,14IP460 EAN R1b3* 14 12 14 16 24 11 13 13 11 11 12 14 9 11 10 12 11 11,14IP479 EAN R1b3* 14 12 14 16 23 10 13 13 11 11 12 14 12 13 11 12 11 11,14IP480 EAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 12 10 12 11 11,14IP482 EAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 10 12 11 11,15IP485 EAN R1b3* 14 12 14 16 25 11 13 13 11 11 12 15 12 12 11 11 11 11,14IP491 EAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP497 EAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 13 11 11,14IP499 EAN R1b3* 15 12 13 16 24 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP500 EAN R1b3* 14 12 13 16 24 10 13 14 11 11 12 14 12 12 11 12 11 11,14IP504 EAN R1b3* 14 12 13 16 25 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP505 EAN R1b3* 14 12 13 16 23 10 13 13 11 11 12 15 12 12 10 12 11 13,14IP507 EAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 11 12 12 11,15IP508 EAN R1b3* 14 12 13 17 24 11 13 13 11 11 12 15 12 13 11 13 11 15,15IP510 EAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,15IP511 EAN R1b3* 14 12 14 17 23 10 13 13 11 11 12 15 12 12 10 12 11 11,11IP651 EAN R1b3* 14 12 13 16 23 10 13 13 11 11 12 15 12 11 11 12 11 11,14IP653 EAN R1b3* 14 12 13 17 23 10 13 13 11 11 12 14 12 13 11 12 11 11,14IP671 EAN R1b3* 14 12 13 16 24 10 13 13 11 11 12 14 12 11 10 11 11 11,14IP679 EAN R1b3* 14 12 13 17 24 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP691 EAN R1b3* 12 12 14 16 24 11 13 13 11 11 12 14 12 12 10 12 11 11,14IP710 EAN R1b3* 14 12 14 16 25 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP720 EAN R1b3* 14 12 13 15 24 11 14 13 11 11 12 15 12 12 11 11 11 11,14IP722 EAN R1b3* 14 12 14 19 25 11 13 13 11 11 12 15 12 11 10 12 11 11,14IP729 EAN R1b3* 14 12 12 16 24 11 14 13 11 11 12 14 12 12 10 12 11 11,14IP731 EAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP745 EAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 12 11 12 11 11,14IP746 EAN R1b3* 14 12 12 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP751 EAN R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 13 10 11 11 11,14IP764 EAN R1b3* 14 12 14 15 24 11 14 13 11 11 12 16 12 11 11 12 12 11,14IP770 EAN R1b3* 14 12 15 16 23 11 13 13 11 11 12 15 12 12 11 11 11 11,15IP778 EAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 11 11 11 11,14IP781 EAN R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 10 11 12 11 11,14IP785 EAN R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 12 12 11 12 11 11,13IP796 EAN R1b3* 14 12 14 16 24 11 13 13 12 11 12 14 12 12 10 13 11 11,14IP798 EAN R1b3* 14 12 14 17 24 11 13 13 11 11 12 15 12 11 11 12 11 11,16IP801 EAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP819 EAN R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP820 EAN R1b3* 14 12 13 16 24 12 13 13 11 11 12 15 10 12 11 12 11 11,14IP823 EAN R1b3* 14 12 13 16 23 11 13 13 11 11 12 14 12 11 11 12 12 11,14IP832 EAN R1b3* 14 12 13 16 24 10 13 12 11 11 12 15 12 13 10 12 11 11,14IP838 EAN R1b3* 14 12 13 16 23 11 13 13 11 11 12 14 12 11 11 12 11 11,14IP844 EAN R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 11 11 13 11 11,13IP847 EAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 13 11 10,15IP297 EAN R1b3d 14 12 13 16 23 10 13 13 11 11 12 14 12 12 10 12 11 11,13IP723 EAN R1b3d 14 12 13 16 24 10 13 13 11 11 12 14 12 12 10 11 11 11,14IP743 EAN R1b3d 14 12 13 16 24 10 13 13 12 11 12 14 12 12 10 11 11 11,14IP476 EAN R1b3f 14 12 14 16 24 11 12 13 11 11 12 15 12 13 11 12 11 11,14IP665 EAN R1b3f 14 12 13 17 24 10 13 13 11 11 12 15 12 13 11 12 11 11,15IP712 EAN R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,15IP761 EAN R1b3f 14 12 14 16 23 11 13 13 11 11 12 14 12 13 11 12 11 11,14IP772 EAN R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 13 11 12 11 11,14IP858 EAN R1b3f 14 12 13 18 24 11 13 13 11 11 12 16 12 12 11 12 11 11,14IP875 EAN R1b3f 14 12 14 16 24 10 12 13 11 11 12 15 12 13 11 12 11 11,14

ExtremaduraIP256 EXT E3b1 13 13 13 17 24 10 11 13 11 11 12 14 10 12 9 12 12 16,18IP262 EXT E3b1 14 12 13 17 25 10 11 13 11 11 12 14 10 12 11 12 12 17,18IP719 EXT E3b1 13 12 13 17 24 10 11 13 11 11 12 14 10 13 10 12 12 17,17IP868 EXT E3b1 13 12 12 17 24 10 11 13 11 11 12 14 9 10 10 13 13 16,17IP244 EXT E3b2 13 12 13 16 25 9 11 13 11 11 12 14 10 10 11 13 12 14,14IP245 EXT E3b2 13 13 13 16 24 9 11 13 11 11 12 14 10 10 11 13 12 13,14IP352 EXT E3b2 13 13 13 16 24 9 11 13 11 11 12 14 10 10 11 13 12 13,14

Adams et al., Supplementary Table 1: Haplotype data 7

IP750 EXT E3b2 13 12 15 17 24 9 11 13 11 11 12 14 10 10 11 14 12 13,14IP330 EXT E3b3 13 12 13 16 24 9 11 13 12 11 12 14 10 10 11 14 12 13,14IP339 EXT F* 14 13 14 16 23 10 11 12 11 11 12 14 10 11 11 13 12 13,14IP478 EXT G 15 13 12 18 22 10 11 14 11 11 12 16 10 13 11 11 12 12,14IP769 EXT G 15 12 12 17 23 10 12 14 11 11 12 16 9 11 11 11 12 14,14IP265 EXT I 16 13 13 15 26 9 11 13 11 11 12 15 10 11 10 12 12 12,12IP268 EXT I 14 15 12 17 22 10 11 14 11 11 12 16 10 11 10 12 12 13,14IP299 EXT I 14 14 12 16 23 10 11 13 11 11 12 16 10 12 10 12 12 14,14IP857 EXT I 15 13 12 17 23 10 12 15 11 11 12 15 10 11 11 12 12 14,15IP874 EXT I 14 14 12 16 23 10 11 13 11 11 12 16 10 11 10 12 13 14,14IP281 EXT J2 15 16 13 17 23 10 11 12 11 11 12 14 9 11 10 12 10 13,18IP329 EXT J2 16 16 13 17 23 11 11 12 11 11 12 15 9 14 10 13 11 12,18IP773 EXT J2 15 15 12 15 23 10 11 13 11 11 12 16 9 12 12 10 11 18,18IP784 EXT J2 15 16 13 17 23 10 11 12 11 11 12 14 9 11 10 12 10 13,18IP795 EXT J2 14 15 13 16 23 9 11 13 11 11 12 16 7 11 10 13 11 14,14IP817 EXT J2 14 15 13 17 23 10 11 12 11 11 12 14 9 11 10 13 12 13,16IP371 EXT K(xP) 13 12 13 16 23 10 13 13 11 11 12 15 9 13 10 11 12 14,16IP755 EXT K(xP) 15 12 13 17 25 10 14 13 11 11 12 14 9 11 10 11 12 14,16IP815 EXT K(xP) 14 12 13 16 23 10 15 13 11 11 12 14 8 11 11 12 12 15,17IP233 EXT R1b3* 15 12 13 16 23 11 13 13 11 11 12 15 10 12 11 12 11 11,14IP237 EXT R1b3* 15 12 13 16 24 11 13 14 11 11 12 15 12 12 11 12 11 11,15IP242 EXT R1b3* 13 12 13 17 22 10 13 13 11 11 12 15 12 12 11 12 11 12,14IP261 EXT R1b3* 14 12 13 15 23 10 13 13 11 11 12 15 12 11 12 12 11 11,14IP346 EXT R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 13 11 11 12 11 11,15IP357 EXT R1b3* 14 12 14 17 24 11 13 13 11 11 12 15 12 12 10 12 12 12,14IP366 EXT R1b3* 15 12 13 18 24 13 13 13 11 11 12 15 12 12 11 12 11 11,15IP477 EXT R1b3* 14 12 13 16 24 10 13 13 11 11 12 16 12 12 10 12 11 11,13IP483 EXT R1b3* 15 12 13 16 23 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP494 EXT R1b3* 15 12 14 16 24 10 13 13 11 11 12 14 12 13 10 12 11 11,13IP501 EXT R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 13 12 11 11 11 11,14IP739 EXT R1b3* 14 12 14 16 24 11 14 13 11 11 12 15 12 12 11 12 11 11,14IP744 EXT R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 14 11 12 11 11,14IP760 EXT R1b3* 14 12 14 16 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP771 EXT R1b3* 12 12 13 17 24 10 13 13 11 11 12 15 12 12 11 12 11 11,15IP807 EXT R1b3* 12 12 13 17 24 10 14 13 11 11 12 15 12 12 11 12 11 11,15IP811 EXT R1b3* 14 14 14 16 24 10 13 13 11 11 12 15 12 11 11 12 11 11,14IP816 EXT R1b3* 14 12 13 16 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP818 EXT R1b3* 14 12 14 17 24 11 13 13 11 11 12 14 12 12 10 12 11 11,14IP822 EXT R1b3* 14 12 14 16 24 11 13 13 11 11 12 14 12 12 10 12 12 10,13IP829 EXT R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 13 11 12 11 11,14IP836 EXT R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 13 11 12 11 12,14IP846 EXT R1b3* 15 12 13 16 24 10 13 13 12 11 12 14 12 12 11 12 11 11,13IP856 EXT R1b3* 14 12 13 16 24 11 13 12 11 11 12 15 12 12 10 12 11 11,14IP861 EXT R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP803 EXT R1b3f 14 12 14 16 24 9 13 13 11 11 12 15 12 13 10 12 11 11,14

GaliciaIP409 GAL E3b* 13 12 13 16 24 10 11 12 11 11 12 14 11 12 10 13 12 16,18IP234 GAL E3b1 13 12 13 17 23 10 11 13 11 11 12 14 10 12 11 11 13 15,16IP397 GAL E3b1 13 12 13 17 23 10 11 13 11 11 12 14 10 12 11 11 13 16,16IP416 GAL E3b1 13 12 13 17 24 10 11 13 11 11 12 14 10 12 9 12 12 16,18IP683 GAL E3b1 13 12 14 17 23 10 11 13 11 11 12 14 10 12 11 11 12 15,16IP765 GAL E3b1 13 12 13 17 23 10 11 13 11 11 12 14 10 11 9 12 12 18,18IP777 GAL E3b1 14 12 13 18 24 10 11 13 11 11 12 14 10 12 11 12 11 17,19IP387 GAL E3b2 13 12 13 16 24 9 11 14 11 11 12 14 10 10 11 12 12 13,14IP399 GAL E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 12 13 12 12,15IP413 GAL E3b2 13 12 14 17 25 9 11 13 11 11 12 14 10 10 11 13 12 13,15IP419 GAL E3b2 13 13 14 16 24 9 11 13 11 11 12 14 10 11 11 13 12 14,14IP725 GAL E3b2 13 12 14 16 23 9 11 13 11 11 12 14 10 10 11 13 12 13,14IP740 GAL E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 11 12 13 12 13,14IP799 GAL E3b2 13 12 14 16 23 10 12 13 11 11 12 14 10 10 11 12 12 13,14IP855 GAL E3b2 13 12 14 16 23 9 11 13 11 11 12 14 10 10 10 13 12 13,14IP294 GAL G 15 13 12 16 22 10 11 14 11 11 12 16 11 11 9 11 12 14,14IP400 GAL G 15 12 12 16 21 10 11 14 11 11 12 16 10 12 10 11 12 13,15IP406 GAL G 17 13 13 17 22 10 11 14 11 11 12 16 11 11 11 11 12 14,14IP699 GAL G 15 12 12 18 23 10 11 15 11 11 12 16 10 11 11 12 12 13,14IP718 GAL G 16 12 12 17 21 10 11 15 11 11 14 16 10 11 10 11 12 13,16IP276 GAL I 14 14 12 16 23 10 11 13 11 11 12 16 10 13 10 12 12 13,15IP282 GAL I 14 14 12 16 22 10 11 13 11 11 12 16 10 12 10 12 12 13,15IP386 GAL I 16 13 13 16 23 11 12 14 11 11 12 15 10 11 11 12 11 12,16IP404 GAL I 15 13 14 18 23 11 12 14 11 11 12 15 10 11 11 12 12 15,15IP411 GAL I 14 14 12 16 23 10 11 13 11 11 12 16 10 11 10 12 12 13,15

Adams et al., Supplementary Table 1: Haplotype data 8

IP422 GAL I 16 13 13 16 23 11 12 14 11 11 12 15 10 11 11 12 11 12,16IP673 GAL I 15 13 13 17 24 10 12 15 11 11 12 15 10 11 11 12 12 14,15IP747 GAL I 14 14 12 17 23 10 11 13 11 11 12 16 10 11 10 12 12 13,15IP809 GAL I 14 13 13 19 25 11 11 13 11 11 12 15 10 11 10 11 12 12,15IP266 GAL J(xJ2) 14 16 13 17 23 10 11 12 11 11 12 14 10 11 11 11 11 13,16IP295 GAL J2 14 15 13 17 22 10 11 12 11 11 12 15 9 10 10 12 11 14,14IP389 GAL J2 14 16 12 16 23 10 11 12 11 11 12 14 9 11 11 13 11 13,16IP423 GAL J2 15 15 12 16 24 10 11 13 11 11 12 16 9 11 11 10 11 13,17IP802 GAL J2 15 16 13 16 23 9 11 13 11 11 12 14 9 12 10 13 10 13,16IP833 GAL J2 15 16 13 16 22 10 11 12 11 11 12 15 9 11 10 13 11 14,15IP872 GAL J2 15 15 12 16 26 10 11 12 11 11 12 16 9 11 11 10 11 15,18IP414 GAL K(xP) 15 12 12 15 24 10 14 13 11 11 12 14 9 11 10 11 13 13,15IP85 GAL R1b3* 14 12 13 16 25 11 13 13 11 11 12 15 12 12 11 12 11 12,14IP227 GAL R1b3* 14 12 13 16 23 10 13 13 11 11 12 15 12 12 11 11 11 11,13IP229 GAL R1b3* 14 12 13 16 24 11 13 12 11 11 12 15 12 12 11 11 11 11,13IP259 GAL R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP270 GAL R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 10 13 11 11,15IP287 GAL R1b3* 14 12 13 16 24 11 14 13 11 11 12 14 12 12 11 12 11 11,16IP289 GAL R1b3* 14 12 12 16 23 11 13 13 11 11 12 15 12 11 10 12 11 11,14IP317 GAL R1b3* 14 12 13 16 25 11 14 13 11 11 12 15 12 12 10 12 11 11,14IP354 GAL R1b3* 14 12 13 14 24 11 13 14 11 11 13 15 11 12 11 12 11 11,14IP384 GAL R1b3* 14 12 13 17 23 10 13 13 11 11 12 14 12 13 11 12 11 11,14IP385 GAL R1b3* 15 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,15IP388 GAL R1b3* 14 12 13 16 24 11 14 14 11 11 12 15 12 12 10 11 11 11,11IP391 GAL R1b3* 13 12 13 16 25 11 13 13 11 11 12 15 12 13 11 12 11 12,14IP392 GAL R1b3* 14 12 13 15 23 12 13 13 11 11 12 15 12 11 10 11 11 10,14IP393 GAL R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 13 10 12 11 11,14IP394 GAL R1b3* 14 12 13 17 24 11 13 13 11 11 12 15 12 12 10 12 11 11,15IP395 GAL R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 10 12 11 12,14IP396 GAL R1b3* 14 12 13 16 24 11 13 12 11 11 12 15 12 12 10 11 11 11,14IP398 GAL R1b3* 14 12 13 14 24 11 13 13 11 11 12 15 13 13 10 12 11 11,14IP401 GAL R1b3* 14 12 13 16 24 11 13 15 11 11 12 14 12 12 10 11 11 12,15IP402 GAL R1b3* 14 12 14 15 24 11 13 13 11 11 12 15 12 13 12 13 11 11,13IP403 GAL R1b3* 15 12 13 16 24 10 13 14 11 11 12 15 12 11 11 12 10 11,14IP407 GAL R1b3* 14 12 12 15 24 10 13 13 11 11 12 15 11 11 10 12 11 11,16IP408 GAL R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 13 13 10 12 11 11,16IP410 GAL R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 13 13 10 12 11 11,14IP415 GAL R1b3* 15 12 13 16 24 11 13 13 11 11 13 14 13 12 10 12 11 12,14IP417 GAL R1b3* 14 12 12 16 24 10 13 13 11 11 12 15 12 12 11 11 11 11,14IP420 GAL R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP421 GAL R1b3* 15 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,15IP668 GAL R1b3* 14 12 13 16 23 12 13 13 11 11 12 15 12 13 11 12 11 12,12IP669 GAL R1b3* 14 12 13 16 24 11 13 12 11 11 12 15 12 12 10 12 11 11,12,14IP694 GAL R1b3* 14 12 14 17 24 10 13 14 11 11 12 15 12 14 11 12 11 11,13IP695 GAL R1b3* 14 12 13 16 24 10 13 13 10 11 12 15 11 12 11 12 11 11,14IP702 GAL R1b3* 14 12 15 16 24 11 13 13 11 11 12 15 13 14 10 12 11 11,13IP704 GAL R1b3* 14 12 14 16 23 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP705 GAL R1b3* 14 12 13 17 24 11 14 13 11 11 12 15 12 13 10 12 12 11,17IP714 GAL R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 11 11 12 12 11,15IP715 GAL R1b3* 14 12 14 17 23 11 13 13 11 11 12 14 12 13 10 12 11 11,14IP733 GAL R1b3* 14 12 13 16 23 10 13 13 11 11 12 15 12 12 11 12 11 11,15IP748 GAL R1b3* 14 12 13 16 24 11 14 13 11 11 12 14 12 12 11 12 11 11,16IP763 GAL R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP806 GAL R1b3* 14 12 12 16 24 11 13 12 11 11 12 15 12 12 11 12 11 12,14IP845 GAL R1b3* 14 12 13 15 22 10 13 13 11 11 12 15 11 11 11 12 11 11,16IP865 GAL R1b3* 14 12 13 16 25 11 14 13 11 11 12 15 12 12 10 12 11 11,14IP867 GAL R1b3* 14 12 13 15 25 10 13 14 11 11 12 15 12 13 10 12 11 11,14IP871 GAL R1b3* 15 12 13 16 24 11 13 13 11 11 12 14 12 12 11 10 11 11,13IP390 GAL R1b3d 14 12 13 17 24 11 13 13 11 11 12 14 12 12 11 12 11 11,15IP824 GAL R1b3d 14 12 13 16 25 11 13 13 11 11 12 14 12 11 11 12 11 11,14IP405 GAL R1b3f 14 12 12 16 24 11 13 13 11 11 12 15 12 13 11 12 11 11,14IP412 GAL R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 11 11 12 12 11,14IP708 GAL R1b3f 14 12 13 16 23 11 13 13 11 11 12 15 12 12 12 12 11 11,14

GasconyIP921 GAS J2 15 15 12 16 24 10 11 12 11 11 12 16 9 12 11 10 11 14,16IP587 GAS R1b3* 14 12 12 16 23 11 13 13 11 11 12 15 12 11 11 13 11 12,15IP593 GAS R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP594 GAS R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP595 GAS R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP596 GAS R1b3* 14 12 12 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,15IP601 GAS R1b3* 14 12 13 16 24 10 13 13 11 11 12 14 12 12 10 12 11 10,14

Adams et al., Supplementary Table 1: Haplotype data 9

IP605 GAS R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 11 10 12 12 11,14IP913 GAS R1b3* 14 12 14 16 24 11 13 13 11 11 12 14 12 12 10 12 11 11,14IP914 GAS R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 11 11 12 11 11,14IP915 GAS R1b3* 14 12 13 16 24 11 13 14 11 11 12 14 12 12 11 12 11 11,13IP919 GAS R1b3* 14 12 14 16 24 10 13 13 11 11 12 14 12 12 11 12 11 12,14IP920 GAS R1b3* 15 12 13 17 24 11 13 13 11 11 12 14 11 11 10 12 11 11,13IP922 GAS R1b3* 14 12 14 16 22 10 13 13 11 11 12 15 12 12 11 13 11 11,11IP923 GAS R1b3* 14 12 12 16 24 11 13 13 11 11 12 15 12 12 10 12 11 12,14IP924 GAS R1b3* 15 12 13 16 24 11 12 13 11 11 12 15 12 12 11 13 10 11,14IP912 GAS R1b3d 14 12 13 16 24 10 13 13 11 11 12 14 12 12 11 12 11 11,14IP916 GAS R1b3d 14 12 13 16 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP917 GAS R1b3d 14 12 13 16 24 11 13 13 11 11 12 14 12 12 10 12 11 12,14IP918 GAS R1b3d 14 12 14 16 24 11 13 14 11 11 12 14 12 11 10 12 11 11,14IP84 GAS R1b3f 14 12 13 15 24 10 13 13 11 11 12 15 12 12 11 12 11 11,15IP597 GAS R1b3f 14 12 13 15 24 11 13 13 11 11 12 15 12 13 11 12 11 11,14IP598 GAS R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP602 GAS R1b3f 14 12 13 15 23 11 13 13 11 11 12 15 12 14 10 12 11 11,14

Northeast CastilleIP341 NEC E3b* 14 12 13 17 23 9 11 13 11 11 12 14 10 12 10 13 12 12,15IP342 NEC E3b1 13 14 13 18 24 11 11 13 11 11 12 14 10 13 10 11 12 15,15IP364 NEC E3b2 13 12 14 17 24 9 11 13 11 11 12 14 10 11 11 13 12 13,14IP788 NEC G 15 12 13 17 22 10 11 12 11 11 12 16 10 10 10 13 12 12,13IP428 NEC I 17 13 13 15 24 9 11 13 11 11 12 15 10 12 10 12 12 12,12IP447 NEC J2 14 15 13 16 24 10 11 12 11 11 12 14 9 12 10 12 12 13,15IP427 NEC K(xP) 15 12 13 16 23 10 15 13 11 11 12 14 9 10 10 11 13 16,17IP86 NEC R1b3* 14 12 13 16 24 11 13 14 11 11 12 15 12 13 11 12 11 11,15IP319 NEC R1b3* 14 12 13 16 23 10 13 13 11 11 12 15 12 12 11 12 11 12,14IP321 NEC R1b3* 15 12 13 16 25 11 13 13 11 11 12 15 12 11 11 12 11 10,14IP378 NEC R1b3* 14 12 13 17 24 11 13 13 11 11 12 14 12 11 10 12 11 11,15IP424 NEC R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP425 NEC R1b3* 14 12 13 18 24 11 13 13 11 11 12 15 12 13 11 12 11 11,12IP426 NEC R1b3* 14 11 13 16 24 11 13 13 11 11 12 15 12 13 11 11 11 12,14IP429 NEC R1b3* 14 12 13 16 25 12 13 13 11 11 12 15 12 12 10 12 11 11,15IP430 NEC R1b3* 15 12 13 16 24 11 13 13 11 11 12 15 12 11 10 12 12 11,14IP431 NEC R1b3* 14 12 12 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP432 NEC R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 12 10 12 11 11,14IP433 NEC R1b3* 14 12 14 16 24 10 13 14 11 11 12 14 12 13 10 12 12 11,14IP435 NEC R1b3* 13 12 13 16 25 12 13 13 11 11 12 15 12 13 11 12 11 11,14IP436 NEC R1b3* 15 12 12 16 25 11 13 13 11 11 12 15 12 11 11 12 11 12,14IP437 NEC R1b3* 14 12 13 16 25 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP446 NEC R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 11 12 11 12,14IP681 NEC R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 13 10 12 11 11,14IP732 NEC R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 13 10 12 11 11,14IP735 NEC R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 10 12 11 11,13IP775 NEC R1b3* 14 12 13 15 23 10 13 13 11 11 12 15 12 12 10 12 10 11,14IP787 NEC R1b3* 14 13 13 16 24 11 13 13 11 11 12 15 12 12 11 12 12 10,15IP862 NEC R1b3* 14 12 14 16 24 12 13 13 11 11 12 15 12 12 11 12 11 11,14IP434 NEC R1b3d 14 12 14 15 23 11 13 13 11 11 12 14 12 11 10 12 11 11,14IP285 NEC R1b3f* 15 12 13 16 24 10 13 13 11 11 12 15 12 12 11 13 11 11,14

North PortugalIP118 NPO E1 17 12 12 17 22 9 12 13 11 12 12 15 11 13 10 13 12 14,16IP124 NPO E1 17 12 12 17 22 9 12 13 11 12 12 16 10 13 10 13 12 15,16IP113 NPO E3b* 14 12 13 17 25 10 11 14 11 11 12 14 10 11 11 12 13 16,17IP91 NPO E3b1 13 12 13 17 24 10 11 13 11 11 12 14 10 12 10 12 12 16,18IP103 NPO E3b1 13 12 13 16 24 10 11 13 11 11 12 15 10 12 9 12 12 16,18IP138 NPO E3b1 13 12 11 18 25 10 12 13 10 11 12 14 10 11 11 11 12 16,19IP95 NPO E3b2 13 12 13 17 23 9 11 13 11 11 12 14 10 10 11 13 12 13,14IP114 NPO E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 11 11 12 12 13,14IP143 NPO E3b3 13 12 13 19 24 10 11 13 11 11 12 14 10 14 10 11 10 15,16IP87 NPO G 15 12 12 17 22 10 11 15 11 11 14 16 10 11 10 11 12 13,17IP89 NPO G 15 12 13 16 24 10 13 13 11 11 12 14 12 12 11 12 11 11,14IP94 NPO G 15 12 12 17 22 10 11 13 11 11 12 16 10 12 11 11 12 12,15IP104 NPO G 16 12 12 16 21 11 11 14 11 11 12 16 10 12 10 11 12 15,15IP107 NPO G 15 12 12 17 22 10 11 14 11 11 12 16 10 12 11 11 12 12,16IP127 NPO G 15 12 12 17 22 10 11 13 11 11 12 16 11 14 11 10 12 15,15IP133 NPO G 15 12 11 17 23 11 11 14 11 11 12 16 10 12 10 11 12 13,14IP111 NPO I 16 13 14 16 24 11 12 14 11 11 12 15 8 12 11 12 12 15,15IP93 NPO J(xJ2) 14 13 13 16 24 10 11 13 11 11 11 14 10 13 11 12 12 13,19IP109 NPO J2 15 16 13 17 23 10 11 12 11 11 12 15 9 11 10 8 11 13,15IP117 NPO J2 15 15 13 16 24 10 11 12 11 11 12 16 9 13 11 10 11 15,17

Adams et al., Supplementary Table 1: Haplotype data 10

IP136 NPO J2 15 15 12 16 24 10 11 13 11 11 12 16 9 11 11 10 11 13,17IP139 NPO J2 15 16 13 16 23 9 11 13 11 11 12 14 9 11 10 13 10 13,16IP146 NPO K(xP) 14 12 13 16 23 10 14 13 11 11 12 14 9 11 10 11 11 15,16IP128 NPO R1a1 15 12 13 20 26 11 11 13 11 11 12 14 11 10 11 11 11 11,14IP142 NPO R1a1 15 12 13 17 24 10 13 13 11 11 12 15 12 14 11 12 11 11,14IP88 NPO R1b3* 14 12 13 16 22 10 13 12 11 11 12 15 12 12 11 12 11 11,14IP92 NPO R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 13 11 11 12 11 11,15IP96 NPO R1b3* 14 12 14 16 25 11 13 13 11 11 12 15 12 12 11 13 11 11,14IP97 NPO R1b3* 14 12 13 17 24 11 13 13 11 11 12 15 12 12 10 12 11 12,14IP98 NPO R1b3* 14 12 14 16 24 11 13 12 11 11 12 15 12 12 10 11 11 11,14IP102 NPO R1b3* 14 12 14 16 24 11 13 14 11 11 12 15 12 13 10 12 11 11,14IP105 NPO R1b3* 14 12 13 15 24 11 13 13 11 11 12 15 12 13 11 12 11 11,14IP106 NPO R1b3* 14 12 13 16 23 10 13 13 11 11 12 15 12 12 10 12 11 11,14IP108 NPO R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,15IP110 NPO R1b3* 15 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,16IP112 NPO R1b3* 13 12 14 16 23 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP115 NPO R1b3* 14 12 13 17 24 11 13 11 11 11 12 14 12 12 11 12 11 11,15IP116 NPO R1b3* 14 12 13 15 23 12 13 13 11 11 12 14 12 11 10 13 11 11,14IP120 NPO R1b3* 14 12 13 16 25 11 13 13 11 11 12 14 12 12 11 12 11 12,14IP121 NPO R1b3* 14 12 13 16 24 12 13 13 11 11 12 15 12 12 11 12 11 11,14IP123 NPO R1b3* 16 12 13 16 23 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP125 NPO R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 10 12 11 11,14IP126 NPO R1b3* 15 12 13 16 24 10 13 13 11 11 12 15 12 11 11 12 11 11,14IP129 NPO R1b3* 14 12 13 16 25 11 12 13 11 11 12 15 13 12 12 12 11 12,16IP130 NPO R1b3* 14 12 13 16 24 11 13 13 11 11 12 16 12 12 10 12 11 11,13IP131 NPO R1b3* 14 12 13 16 24 10 13 13 11 11 12 14 12 11 11 12 11 11,14IP132 NPO R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 13 12 11 11 11 11,14IP135 NPO R1b3* 15 12 13 16 24 10 14 13 11 11 12 15 12 11 11 12 11 11,14IP137 NPO R1b3* 14 12 13 16 25 11 13 12 11 11 12 15 12 14 10 12 11 11,14IP140 NPO R1b3* 15 12 13 17 24 11 13 13 11 11 12 15 12 12 11 13 11 11,14IP145 NPO R1b3* 14 12 14 17 24 11 13 13 11 11 12 15 12 13 11 13 11 11,14IP147 NPO R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 10 13 11 11,14IP148 NPO R1b3* 15 12 13 18 24 11 14 13 11 11 12 14 12 12 11 12 11 11,13IP100 NPO R1b3d 14 12 13 16 24 11 13 13 11 11 12 14 12 12 10 12 11 11,14IP99 NPO R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 11 11 12 13 10 11,14IP119 NPO R1b3f 14 12 13 16 23 11 13 12 11 11 12 15 12 12 11 13 11 11,14IP122 NPO R1b3f 14 12 13 17 23 11 13 13 11 11 12 15 12 12 11 13 11 11,14IP134 NPO R1b3f 14 12 13 17 23 11 13 13 11 11 12 15 12 12 11 13 11 11,14IP141 NPO R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 11 12 11 13 11 11,14IP144 NPO R1b3f 14 12 13 16 24 11 13 14 11 11 12 15 12 11 12 13 11 11,13

Northwest CastilleIP439 NWC E3b* 15 12 13 16 22 9 11 14 11 11 12 14 10 11 11 12 12 14,15IP963 NWC E3b* 14 12 14 16 23 9 11 13 11 11 12 14 10 11,12 10 13 12 12,17IP443 NWC E3b1 13 12 13 17 24 10 11 13 11 11 12 14 10 12 9 12 11 15,18IP450 NWC E3b1 13 12 13 17 24 10 11 13 11 11 12 14 10 12 9 12 12 16,18IP675 NWC E3b1 14 12 13 17 25 10 11 13 11 11 12 14 10 14 11 12 12 18,19IP678 NWC E3b1 13 12 13 17 24 10 11 13 11 11 12 14 10 12 9 12 12 16,18IP749 NWC E3b1 13 12 13 17 24 10 11 13 11 11 12 14 10 12 10 12 12 17,17IP960 NWC E3b1 13 12 13 17 24 10 11 13 11 11 12 14 10 12 10 12 12 16,17IP448 NWC E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 11 13 12 13,14IP451 NWC E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 11 12 12 13,15IP782 NWC E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 10 13 12 14,14IP828 NWC E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 11 13 13 13,14IP952 NWC E3b2 13 12 13 16 24 9 11 13 11 11 12 14 10 10 11 13 12 13,14IP956 NWC E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 12 13 12 13,14IP958 NWC E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 11 13 12 13,14IP971 NWC E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 11 12 12 13,14IP977 NWC E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 11 13 12 12,14IP980 NWC E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 11 13 11 13,15IP373 NWC E3b3 13 12 12 18 24 10 11 13 11 11 12 14 10 12 11 13 11 15,19IP228 NWC G 15 12 11 17 22 10 11 14 11 11 12 16 10 11 10 12 12 13,14IP377 NWC G 15 13 12 16 22 10 11 14 11 11 12 16 10 11 10 11 12 14,15IP454 NWC G 15 13 12 17 22 10 11 14 11 11 12 16 10 11 10 11 12 14,14IP455 NWC G 15 12 13 16 23 11 11 14 11 11 12 16 10 11 11 12 12 14,15IP752 NWC G 15 12 13 17 22 11 11 13 11 11 12 15 9 10 10 11 12 14,14IP876 NWC I 17 13 13 15 23 10 11 13 11 11 12 15 10 12 10 11 12 12,12IP966 NWC I 15 13 15 17 23 11 12 14 11 11 12 14 10 11 11 12 12 15,16IP987 NWC I 14 14 12 16 22 11 11 13 11 11 12 16 10 11 10 12 12 12,13IP967 NWC J(xJ2) 13 15 12 17 24 10 11 12 11 11 12 14 10 12 10 11 11 12,17IP243 NWC J2 14 15 12 18 24 10 11 12 10 11 12 16 11 11 10 13 11 13,16IP440 NWC J2 14 15 13 17 23 10 11 12 11 11 12 15 9 12 10 13 11 13,20

Adams et al., Supplementary Table 1: Haplotype data 11

IP441 NWC J2 17 15 12 16 24 10 11 12 11 11 12 16 9 12 10 10 11 16,17IP449 NWC J2 14 14 13 17 24 10 11 12 11 11 12 15 9 12 11 15 11 15,15IP741 NWC J2 14 14 14 18 25 10 11 12 11 11 12 15 9 11 10 12 11 13,15IP837 NWC J2 15 16 13 16 23 9 11 12 11 11 12 14 9 11 10 13 10 13,16IP860 NWC J2 14 16 12 17 23 10 11 12 11 11 12 15 9 11 12 12 11 13,17IP985 NWC J2 16 15 12 16 25 10 11 12 11 11 12 16 9 11 11 10 11 14,16IP248 NWC K(xP) 15 11 14 16 23 10 13 13 11 11 12 14 9 11 11 11 12 14,16IP309 NWC K(xP) 13 12 13 17 23 9 11 13 11 11 12 14 10 12 10 13 12 12,15IP959 NWC R1a1 16 12 13 19 25 11 11 13 11 11 12 14 11 10 11 11 11 11,15IP974 NWC R1a1 15 12 14 17 25 10 11 12 11 11 12 14 11 10 11 12 11 11,14IP232 NWC R1b3* 14 12 13 16 24 11 14 13 11 11 12 14 12 12 10 13 11 11,12,14IP247 NWC R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 13 11 12,14IP269 NWC R1b3* 16 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP284 NWC R1b3* 14 12 14 16 25 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP288 NWC R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 12 12 11 11 11,14IP290 NWC R1b3* 14 12 13 16 23 10 13 13 11 11 12 14 12 11 11 12 11 11,14IP306 NWC R1b3* 14 12 14 16 24 10 13 13 11 11 12 15 12 11 11 12 11 11,14IP337 NWC R1b3* 14 12 14 17 24 11 13 13 11 11 12 14 12 12 10 11 11 11,14IP343 NWC R1b3* 14 12 12 17 24 11 13 13 11 11 12 16 12 12 10 12 11 11,14IP353 NWC R1b3* 15 12 13 16 24 10 13 13 11 11 12 15 12 13 11 12 11 11,14IP355 NWC R1b3* 14 12 13 15 24 11 13 13 11 11 12 15 12 13 11 11 10 11,14IP356 NWC R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 13 10 12 11 11,13IP360 NWC R1b3* 14 12 13 16 23 11 13 12 11 11 12 15 12 12 11 11 11 11,11IP363 NWC R1b3* 14 13 13 16 23 10 13 14 11 11 12 15 12 12 11 12 11 11,14IP382 NWC R1b3* 14 11 13 16 24 11 14 13 11 11 12 15 12 11 11 12 11 11,14IP438 NWC R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 13 11 11 12 11 11,17IP442 NWC R1b3* 14 12 12 16 23 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP444 NWC R1b3* 14 12 13 17 24 11 13 13 11 11 12 14 12 12 11 12 11 12,14IP445 NWC R1b3* 14 12 13 16 23 11 13 13 11 11 12 14 11 12 11 12 11 11,15IP452 NWC R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP453 NWC R1b3* 14 13 12 15 25 10 13 13 11 11 12 15 12 11 10 11 11 12,14IP687 NWC R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP709 NWC R1b3* 14 12 14 16 24 10 13 13 11 11 12 14 12 11 10 14 11 11,13IP711 NWC R1b3* 14 12 13 17 22 11 13 13 11 11 12 15 13 12 10 12 11 11,14IP767 NWC R1b3* 14 13 13 15 25 10 13 13 11 11 12 16 12 12 10 11 11 12,14IP786 NWC R1b3* 14 12 14 16 25 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP792 NWC R1b3* 14 12 13 15 22 10 13 13 11 11 12 15 11 11 11 12 11 11,16IP804 NWC R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 11 11 12 11 13,14IP805 NWC R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 11 12 11 12,14IP821 NWC R1b3* 14.5 12 13 17 24 11 13 13 11 11 12 15 12 11 11 12 11 12,15IP830 NWC R1b3* 15 12 13 16 24 11 13 14 11 11 12 15 12 12 10 12 11 11,15IP843 NWC R1b3* 14 12 14 15 24 11 13 12 11 11 12 15 12 12 11 11 11 11,14IP851 NWC R1b3* 13 12 13 17 24 10 13 13 11 11 12 14 12 12 11 12 11 11,14IP866 NWC R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 13 12 10 12 11 11,14IP869 NWC R1b3* 14 12 12 16 24 10 13 13 11 11 12 15 12 11 10 12 11 11,14IP948 NWC R1b3* 14 12 14 16 23 11 13 14 11 11 12 14 12 12 11 12 11 11,14IP949 NWC R1b3* 14 12 13 17 24 12 13 13 11 11 12 15 12 11 10 12 11 11,15IP950 NWC R1b3* 14 12 14 16 24 10 13 13 11 11 12 15 12 12 10 12 11 11,14IP951 NWC R1b3* 14 12 13 16 25 10 13 13 11 11 12 15 12 12 10 12 11 11,14IP953 NWC R1b3* 14 12 13 17 24 10 13 13 11 11 12 15 12 11 10 12 11 11,15IP954 NWC R1b3* 13 12 13 16 25 12 13 13 11 11 12 15 12 13 11 12 11 11,14IP955 NWC R1b3* 13 12 15 16 24 11 13 13 11 11 12 14 12 12 10 12 11 11,14IP961 NWC R1b3* 14 12 14 17 24 11 13 13 11 11 12 14 12 11 10 12 11 11,15IP962 NWC R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP964 NWC R1b3* 14 12 14 16 25 11 13 13 11 11 12 14 12 12 10 12 11 11,14IP965 NWC R1b3* 13 12 13 17 24 10 13 13 11 11 12 15 12 12 11 11 11 11,13IP968 NWC R1b3* 14 12 10 16 23 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP969 NWC R1b3* 14 12 12 16 24 11 13 13 11 11 12 15 12 13 11 12 11 11,14IP970 NWC R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 11 11 12 11 11,14IP972 NWC R1b3* 14 12 13 16 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP973 NWC R1b3* 14 12 14 16 24 10 13 13 11 11 12 14 12 12 11 12 11 11,14IP975 NWC R1b3* 15 12 13 16 24 10 11 13 11 11 12 14 12 12 11 12 11 14,14IP976 NWC R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 13 10 12 11 11,15IP978 NWC R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 14 11 12 11 11,14IP979 NWC R1b3* 14 12 15 16 24 11 13 13 11 11 12 14 12 12 10 12 11 12,14IP981 NWC R1b3* 14 14 13 17 25 11 13 13 11 11 12 15 12 13 11 12 11 12,14IP982 NWC R1b3* 16 12 12 16 23 10 13 13 11 11 12 15 12 11 10 12 11 11,14IP986 NWC R1b3* 14 12 14 17 24 11 12 13 11 11 12 14 12 11 10 12 11 11,13IP957 NWC R1b3d 14 12 13 16 24 11 13 13 11 11 12 14 12 12 10 12 11 11,14IP983 NWC R1b3f 14 12 12 16 23 11 13 13 11 11 12 15 12 12 11 12 12 11,14

South Portugal

Adams et al., Supplementary Table 1: Haplotype data 12

IP160 SPO E3a 17 12 13 17 21 11 11 13 11 11 12 14 11 11 11 13 12 17,17IP206 SPO E3b* 13 12 13 19 24 10 11 12 11 11 12 14 10 12 10 13 12 16,16IP210 SPO E3b* 14 12 14 19 25 10 12 14 11 11 12 14 11 13 10 12 12 17,18IP168 SPO E3b1 13 12 13 16 24 10 11 13 11 11 12 14 10 12 9 12 12 16,17IP180 SPO E3b1 13 12 13 17 23 10 11 13 11 11 12 14 10 11 11 12 12 15,15IP198 SPO E3b1 14 12 12 17 23 10 11 13 11 11 12 14 10 11 10 12 12 17,19IP149 SPO E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 11 13 12 13,14IP152 SPO E3b2 13 12 14 16 23 9 11 13 11 11 12 14 10 10 10 13 12 14,14IP162 SPO E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 11 13 12 14,14IP174 SPO E3b2 13 12 14 17 24 9 11 13 11 11 12 14 10 10 11 13 12 14,14IP178 SPO E3b2 13 12 13 16 24 9 11 13 11 11 12 14 10 10 12 12 11 11,14IP201 SPO E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 11 13 12 13,14IP184 SPO E3b3 13 12 13 17 24 11 11 13 11 11 12 14 10 13 10 11 11 16,16IP159 SPO G 15,16 12 14 16 22 10 11 14 11 11 12 16 10 10 11 13 12 13,16IP177 SPO G 15 12 13 17 21 10 13 14 11 11 14 16 10 13 11 11 12 13,16IP186 SPO G 15 12 12 16 22 10 11 14 11 11 12 16 10 13 12 11 12 12,16IP202 SPO G 15 12 12 16 22 9 11 14 11 11 12 16 10 13 12 11 12 12,16IP205 SPO G 15 12 12 18 23 10 11 14 12 11 12 16 10 12 11 11 12 14,15IP219 SPO G 15 12 12 17 22 10 11 14 11 11 12 16 11 12 11 10 12 15,15IP222 SPO G 15 12 14 16 22 10 11 14 11 11 12 17 10 10 11 12 12 13,16IP158 SPO I 16 15 13 18 25 10 12 14 11 11 12 15 10 13 10 11 12 12,15IP172 SPO I 16 13 13 15 22 11 11 13 11 11 12 15 10 12 11 11 12 12,12IP223 SPO I 16 13 13 15 23 10 11 13 11 11 12 14 10 12 10 11 13 12,12IP167 SPO J(xJ2) 14 16 13 18 23 10 11 12 11 11 12 14 10 11 11 12 11 13,19IP192 SPO J(xJ2) 14 16 13 17 23 10 11 12 11 11 12 14 10 14 11 11 11 13,15IP156 SPO J2 15 16 13 16 23 9 11 12 11 11 12 14 9 12 10 13 10 13,16IP157 SPO J2 14 15 13 17 24 10 11 12 10 11 12 16 7 12 11 13 11 13,15IP164 SPO J2 14 15 13 16 23 10 11 12 11 11 12 14 9 10 10 12 11 14,16IP173 SPO J2 14 15 13 17 22 10 11 12 11 11 12 15 9 11 10 14 11 13,15IP179 SPO J2 14 15 13 16 23 10 11 12 11 11 12 15 9 12 11 12 11 16,16IP181 SPO J2 15 15 12 16 25 10 11 12 11 11 12 16 9 11 11 10 11 14,17IP183 SPO J2 14 15 12 16 25 10 11 12 11 11 12 16 9 11 11 10 11 14,17IP187 SPO J2 15 15 12 17 23 10 11 12 11 11 12 15 9 12 10 10 11 14,17IP199 SPO J2 15 15 12 17 25 10 11 12 10 11 12 16 9 11 11 10 11 13,19IP203 SPO J2 14 15 14 17 23 10 11 12 11 11 12 14 9 11 9 13 11 13,16IP213 SPO J2 14 15 13 17 23 11 11 12 12 11 12 15 9 10 11 12 11 13,15IP225 SPO J2 14 15 13 17 21 10 11 12 11 11 12 15 9 11 10 14 11 13,15IP154 SPO K(XP) 13 12 14 16 22 10 13 13 11 11 12 15 9 11 10 11 12,13 13,13,14IP163 SPO K(xP) 13 12 13 16 23 10 13 14 11 11 12 15 9 11 11 11 13 15,16IP211 SPO K(xP) 13 12 14 15 24 10 13 13 11 11 12 14 9 12 10 12 12 13,15IP220 SPO K(xP) 13 12 14 15 24 10 13 13 11 11 12 14 9 12 10 12 12 13,15IP226 SPO R1a1 15 12 14 17 25 11 11 13 11 11 12 14 11 10 11 11 11 11,14IP150 SPO R1b3* 14 13 12 16 24 11 13 13 11 11 12 14 11 13 11 14 12 11,14IP151 SPO R1b3* 14 12 13 16 25 10 13 13 11 11 12 15 12 12 12 12 11 11,14IP153 SPO R1b3* 15 12 14 15 24 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP161 SPO R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 12 13 11 12 11 11,14IP165 SPO R1b3* 15 12 13 15 24 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP166 SPO R1b3* 15 12 13 17 24 11 13 14 11 11 12 15 12 12 10 12 12 11,14IP169 SPO R1b3* 14 12 13 16 25 11 13 13 11 11 12 15 12 11 11 11 11 11,13IP170 SPO R1b3* 14 12 12 16 24 11 12 13 11 11 12 15 12 12 10 12 11 11,14IP171 SPO R1b3* 15 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,15IP175 SPO R1b3* 14 12 14 16 24 10 13 13 11 11 12 14 12 11 10 12 11 11,14IP176 SPO R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 12 13 11 12 11 12,12IP182 SPO R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP185 SPO R1b3* 14 12 13 16 23 10 13 13 11 11 12 15 12 13 11 12 11 11,14IP188 SPO R1b3* 14 12 14 16 24 11 12 13 11 11 12 15 12 12 11 12 10 11,14IP189 SPO R1b3* 15 12 13 17 24 11 13 13 11 11 12 15 12 12 10 12 11 11,15IP190 SPO R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 12 10 13 11 11,15IP191 SPO R1b3* 14 12 15 16 24 11 12 13 11 11 12 15 12 12 11 12 10 11,14IP193 SPO R1b3* 14 12 13 17 24 11 13 13 11 11 12 15 12 13 10 12 11 11,14IP194 SPO R1b3* 14 12 13 16 24 10 13 12 11 11 12 16 12 12 10 13 11 11,13IP195 SPO R1b3* 14 12 13 16 25 11 13 13 11 11 12 15 12 12 10 13 11 11,14IP196 SPO R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 12 11 11 12 10 11,14IP197 SPO R1b3* 15 12 13 17 25 11 13 14 11 11 12 15 12 12 10 12 12 11,14IP200 SPO R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 12 13 11 12 12 11,14IP204 SPO R1b3* 14 13 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP207 SPO R1b3* 14 12 12 16 24 10 13 13 11 11 12 14 12 12 11 12 11 10,14IP209 SPO R1b3* 14 12 13 18 25 11 13 15 11 11 12 15 12 13 11 12 11 11,14IP212 SPO R1b3* 15 12 13 16 24 11 13 13 11 11 12 14 12 12 11 12 11 11,15IP214 SPO R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 12 10 12 11 11,14IP215 SPO R1b3* 14 12 14 17 24 11 13 13 11 11 12 14 12 14 10 12 11 12,14IP216 SPO R1b3* 14 12 14 16 24 11 14 13 11 11 12 15 12 12 12 12 11 11,14

Adams et al., Supplementary Table 1: Haplotype data 13

IP217 SPO R1b3* 14 12 13 16 24 11 14 14 11 11 12 15 12 12 11 13 11 11,15IP218 SPO R1b3* 14 12 13 17 24 10 13 13 11 11 12 15 12 11 12 13 11 13,13IP221 SPO R1b3* 14 12 13 16 25 11 12 12 11 11 12 15 12 12 10 12 11 11,14IP224 SPO R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 11 11 12 11 8,14IP155 SPO R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 11 12 11 13 11 11,15IP208 SPO R1b3f 15 12 13 16 24 11 13 13 11 11 12 15 12 12 12 12 11 11,14

ValenciaIP474 VAL E3a 16 12 13 18 21 11 11 14 11 11 12 15 11 12 10 13 12 17,17IP609 VAL E3b1 13 12 13 18 23 10 11 14 11 11 12 14 10 12 11 12 13 15,16IP627 VAL E3b1 13 12 13 17 24 10 11 13 11 11 12 14 10 11 9 12 13 15,18IP629 VAL E3b1 13 12 13 18 23 11 11 13 11 11 12 14 10 12 9 11 13 16,17IP649 VAL E3b1 13 12 13 17 24 10 11 13 11 11 12 14 10 11 9 12 12 16,16IP471 VAL E3b2 14 12 14 16 24 9 11 13 11 11 12 14 10 10 12 13 12 13,14IP611 VAL E3b2 13 10 14 16 24 9 11 13 11 11 12 14 10 10 11 13 12 13,14IP644 VAL E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 11 13 12 13,14IP619 VAL E3b3 13 12 14 18 23 10 11 13 11 11 12 14 10 12 10 12 11 15,18IP459 VAL G 15 13 12 16 22 10 11 15 11 12 12 16 10 11 11 11 12 14,15IP465 VAL I 15 13 13 16 23 11 12 14 11 11 12 15 10 12 10 12 12 15,15IP614 VAL I 14 14 12 17 23 10 11 13 11 11 12 16 10 11 10 12 12 13,15IP623 VAL I 17 13 14 15 23 10 11 13 11 11 12 15 10 11 10 11 12 12,12IP641 VAL I 14 14 12 15 22 10 11 13 11 11 12 17 10 11 11 12 12 13,14IP647 VAL I 14 14 12 16 22 10 11 13 11 11 12 16 10 11 9 12 12 13,14IP658 VAL I 17 13 14 16 23 10 11 13 11 11 12 15 10 12 10 12 12 12,12IP660 VAL I 14 14 12 16 23 10 11 13 11 11 12 16 10 11 10 12 12 13,14IP470 VAL J(xJ2) 14 17 14 17 23 11 11 13 11 11 13 14 10 10 11 12 12 11,18IP630 VAL J(xJ2) 14 16 12 18 23 10 11 12 11 11 12 14 10 11 11 11 11 12,17IP464 VAL J2 14 15 14 17 22 10 12 12 11 11 12 15 9 12 11 12 11 13,14IP606 VAL J2 13 15 13 16 22 11 11 12 11 11 12 15 9 11 11 13 11 13,16IP612 VAL J2 14 15 13 16 24 11 11 12 11 11 12 16 9 11 11 14 11 13,17IP624 VAL J2 14 15 14 17 23 10 11 12 11 11 12 14 9 11 9 13 11 13,16IP469 VAL K(xP) 14 12 13 15 23 10 13 13 11 11 12 14 9 11 10 11 13 13,16IP631 VAL R1a1 16 12 14 18 25 10 11 14 11 11 12 14 11 10 11 11 11 11,14IP632 VAL R1a1 15 12 13 18 25 11 11 13 11 11 12 14 11 10 12 11 11 11,14IP456 VAL R1b* 16 12 13 16 25 11 13 13 11 11 12 14 12 12 11 12 11 13,14IP637 VAL R1b* 17 12 13 15 22 11 13 13 11 11 12 14 11 12 11 12 11 13,14IP271 VAL R1b3* 15 12 12 16 25 11 14 13 11 11 12 15 12 12 10 13 11 11,14IP457 VAL R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP458 VAL R1b3* 14 12 14 17 25 11 13 13 11 11 12 14 12 11 10 13 11 11,14IP461 VAL R1b3* 14 12 14 16 24 11 13 14 11 11 12 15 12 12 10 12 11 11,15IP462 VAL R1b3* 14 12 13 16 23 12 13 13 11 11 12 14 12 13 10 12 11 11,15IP467 VAL R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP472 VAL R1b3* 15 12 13 16 24 10 13 13 11 11 12 15 12 13 11 12 11 11,14IP473 VAL R1b3* 14 12 14 17 24 10 13 13 11 11 12 14 12 12 10 11 11 11,14IP475 VAL R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP607 VAL R1b3* 14 12 13 16 23 10 13 13 11 11 12 15 12 12 10 12 11 12,14IP608 VAL R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP610 VAL R1b3* 14 12 13 16 23 12 13 13 12 11 12 14 12 12 10 12 11 11,14IP613 VAL R1b3* 14 12 12 16 24 10 13 13 11 11 12 15 12 12 11 12 11 10,16IP615 VAL R1b3* 14 12 13 16 24 10 13 13 11 11 12 14 12 13 11 12 11 11,14IP616 VAL R1b3* 14 12 13 16 24 11 13 12 11 11 12 14 12 12 10 12 11 13,14IP618 VAL R1b3* 14 12 13 15 24 11 13 14 11 11 13 15 12 12 11 12 11 11,14IP620 VAL R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP621 VAL R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 11 12 11 11,15IP622 VAL R1b3* 16 12 14 16 25 10 11 13 11 11 12 14 11 11 11 11 11 11,15IP625 VAL R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP626 VAL R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 10 11 11 11,14IP633 VAL R1b3* 14 12 13 17 23 11 13 13 11 11 12 14 12 11 11 10 11 11,13IP634 VAL R1b3* 14 12 14 15 24 10 13 13 11 11 12 15 12 11 11 12 11 12,14IP636 VAL R1b3* 14 12 13 15 24 11 12 13 11 11 12 15 12 12 11 12 11 11,14IP639 VAL R1b3* 15 12 13 16 24 10 13 13 12 11 12 15 12 12 11 12 11 11,14IP640 VAL R1b3* 16 12 13 17 23 10 13 13 11 11 12 15 12 13 11 12 11 11,13IP642 VAL R1b3* 14 12 13 16 26 11 13 13 11 11 12 15 12 13 10 12 11 11,15IP645 VAL R1b3* 14 12 14 16 24 11 13 13 11 11 12 14 9 12 10 12 11 11,14IP646 VAL R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 12 10 12 11 12,14IP650 VAL R1b3* 15 12 13 16 24 10 13 14 11 11 12 15 12 13 11 12 11 11,14IP652 VAL R1b3* 14 12 13 16 23 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP656 VAL R1b3* 14 12 13 16 24 11 14 13 11 11 12 15 12 13 10 14 11 11,13IP657 VAL R1b3* 14 12 13 17 25 11 13 12 11 11 12 14 12 14 11 13 11 11,14IP659 VAL R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,15IP662 VAL R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 12 11 12 11 11,14IP663 VAL R1b3* 14 12 13 17 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14

Adams et al., Supplementary Table 1: Haplotype data 14

IP693 VAL R1b3* 14 13 13 16 24 10 13 13 11 11 9 15 12 13 11 12 11 11,14IP697 VAL R1b3* 14 12 14 17 25 11 13 13 11 11 12 15 12 13 11 12 11 12,14IP700 VAL R1b3* 15 12 13 16 24 11 13 13 11 11 12 15 12 13 11 12 11 10,15IP707 VAL R1b3* 14 12 13 17 24 11 13 13 11 11 12 16 12 11 11 12 11 11,14IP468 VAL R1b3d 14 12 14 16 24 11 13 13 11 11 12 14 12 11 10 11 11 10,13IP617 VAL R1b3f 14 12 13 15 24 11 13 13 11 11 12 15 12 13 11 12 11 11,15IP655 VAL R1b3f 15 12 13 15 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP664 VAL R1b3f 14 12 13 16 24 11 12 14 11 11 12 15 12 11 11 12 11 10,14IP814 VAL R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14

West AndalusiaIP514 WAN E3b* 13 12 12 17 24 10 11 14 11 11 12 15 10 10 11 13 12 16,18IP272 WAN E3b1 13 12 13 17 24 10 11 12 11 11 12 14 10 12 9 12 13 16,18IP513 WAN E3b1 13 12 13 17 24 10 11 13 11 11 12 14 10 12 10 12 12 16,18IP759 WAN E3b1 13 12 13 18 24 11 11 13 11 11 12 14 11 11 11 12 12 18,18IP298 WAN E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 10 13 12 13,14IP515 WAN E3b2 13 12 14 16 23 9 11 13 11 11 12 14 10 10 11 13 12 13,14IP516 WAN E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 9 11 13 12 13,15IP791 WAN E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 10 13 12 13,14IP813 WAN E3b2 13 12 14 16 23 10 11 13 11 11 12 14 10 11 11 13 12 13,14IP852 WAN E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 11 10 13 12 13,14IP853 WAN E3b2 13 12 13 16 24 9 11 13 11 11 12 14 10 10 11 13 12 13,14IP674 WAN G 15 13 13 17 22 10 11 15 11 11 12 16 11 11 10 11 12 14,14IP696 WAN G 15 12 12 18 23 11 11 14 11 11 12 16 10 11 11 12 12 13,15IP839 WAN G 15 13 13 17 22 10 11 15 11 11 12 16 10 11 10 11 12 14,14IP374 WAN I 16 13 13 15 23 10 11 13 11 11 12 15 10 11 10 11 12 12,12IP517 WAN I 17 13 12 17 25 10 11 13 11 11 12 15 10 12 10 12 12 12,16IP754 WAN I 16 13 12 15 25 11 11 13 11 11 12 15 10 11 10 12 12 13,17IP783 WAN I 15 13 13 17 24 10 12 14 11 11 12 15 10 11 13 12 12 15,15IP797 WAN J(xJ2) 14 16 14 16 23 10 11 12 11 11 12 14 10 11 11 11 11 13,15IP279 WAN J2 14 15 12 17 22 10 11 12 11 11 12 15 9 11 9 14 11 13,15IP296 WAN J2 15 15 12 16 24 10 11 12 11 11 12 16 10 12 11 10 11 12,18IP666 WAN J2 15 16 13 16 23 9 11 12 11 11 12 15 9 12 10 13 10 13,16IP672 WAN J2 16 15 13 16 24 11 11 12 11 11 12 15 9 11 10 13 11 12,16IP690 WAN J2 15 16 13 16 23 11 11 12 11 11 12 15 9 12 11 12 11 13,13IP737 WAN J2 15 15 13 17 23 10 11 12 11 11 12 15 9 12 10 14 11 13,17IP738 WAN J2 15 16 13 16 24 9 11 12 11 11 12 14 9 12 10 12 10 13,16IP774 WAN J2 15 16 13 16 23 9 11 12 11 11 12 14 9 11 11 12 8 13,16IP316 WAN J2 15 14 13 16 23 10 11 12 11 11 12 15 9 14 11 13 11 13,15IP340 WAN J2 15 16 13 16 24 9 11 12 11 11 12 14 9 12 10 12 10 13,16IP246 WAN Q(XQ3) 13 12 14 17 25 10 14 12 11 11 12 13 9 13 11 13 12 15,17IP689 WAN R1* 15 12 14 16 24 10 13 13 11 11 12 14 11 11 11 12 11 11,13IP274 WAN R1a1 16 12 14 17 25 10 11 13 11 11 12 14 11 10 11 11 12 11,14IP350 WAN R1a1 16 12 13 19 24 11 11 13 11 11 12 14 11 10 12 11 11 11,11IP849 WAN R1a1 15 12 13 17 25 11 11 13 11 11 12 14 11 11 12 11 11 11,14IP230 WAN R1b3* 14 12 12 16 23 11 13 14 11 11 12 14 12 12 10 13 11 10,14IP236 WAN R1b3* 14 12 14 18 24 11 13 14 11 11 12 15 12 11 11 12 11 11,14IP240 WAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP241 WAN R1b3* 14 12 13 16 23 10 13 13 11 11 12 15 12 13 11 12 11 11,14IP249 WAN R1b3* 14 12 13 17 23 10 13 13 11 11 12 15 12 12 10 12 11 12,15IP260 WAN R1b3* 14 12 12 16 24 11 13 13 11 11 12 15 10 13 10 12 11 11,14IP291 WAN R1b3* 14 12 14 17 24 10 13 13 11 11 12 14 12 12 9 12 11 11,14IP301 WAN R1b3* 14 12 13 15 24 11 13 13 11 11 12 15 12 11 10 12 11 11,14IP310 WAN R1b3* 14 12 13 16 25 11 13 13 11 11 12 15 12 11 12 12 11 11,14IP313 WAN R1b3* 14 12 13 16 23 10 13 13 11 11 12 15 12 11 11 12 11 11,14IP315 WAN R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP327 WAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP328 WAN R1b3* 14 12 13 16 25 10 13 13 11 11 12 15 12 13 11 12 11 11,11IP331 WAN R1b3* 14 12 12 16 23 11 14 13 11 11 12 14 12 11 11 12 11 11,14IP380 WAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,12IP486 WAN R1b3* 14 12 14 16 24 11 13 12 11 11 12 15 12 13 11 11 11 11,14IP489 WAN R1b3* 14 12 12 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP493 WAN R1b3* 14 12 14 16 24 11 13 13 11 11 12 14 12 11 10 13 11 11,14IP495 WAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP512 WAN R1b3* 14 12 13 16 25 10 13 13 11 11 12 15 12 13 11 12 11 11,15IP654 WAN R1b3* 14 13 12 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP670 WAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 13 11 11,14IP686 WAN R1b3* 14 12 13 17 25 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP701 WAN R1b3* 15 12 13 16 23 11 13 13 11 11 12 15 12 12 10 12 11 11,14IP713 WAN R1b3* 14 12 13 16 24 10 13 13 11 11 12 14 12 12 11 12 12 11,16IP726 WAN R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 12 11 12 11 11,14IP757 WAN R1b3* 14 12 14 17 24 10 13 13 11 11 12 14 12 13 10 12 11 11,14

Adams et al., Supplementary Table 1: Haplotype data 15

IP762 WAN R1b3* 14 12 13 16 24 11 13 12 11 11 12 14 12 12 10 12 11 11,16IP768 WAN R1b3* 14 12 13 16 23 10 13 13 11 11 12 15 12 12 11 12 11 11,16IP776 WAN R1b3* 15 12 13 16 24 11 13 13 11 11 12 14 12 14 11 12 11 11,17IP780 WAN R1b3* 14 12 14 17 25 10 13 13 11 11 12 14 12 12 11 12 12 11,15IP825 WAN R1b3* 14 12 13 16 24 10 13 13 10 11 12 14 12 12 10 11 11 11,15IP840 WAN R1b3* 14 12 14 15 24 10 13 13 11 11 12 14 12 12 10 12 11 12,15IP841 WAN R1b3* 15 12 13 16 24 10 13 13 11 11 12 15 12 12 10 12 11 11,15IP850 WAN R1b3* 14 12 13 16 24 11 14 13 11 11 12 15 12 12 10 12 12 12,15IP275 WAN R1b3d 14 12 13 16 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP810 WAN R1b3d 14 12 13 18 24 10 13 14 11 11 12 14 12 12 11 12 11 11,14IP283 WAN R1b3f 14 12 12 16 24 11 13 13 11 11 12 15 12 12 10 12 11 11,15IP688 WAN R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 13 10 12 11 11,14

IbizaIP1056 IBZ E3b1 13 12 13 17 24 11 11 13 11 11 12 14 10 12 9 12 12 14,18IP1077 IBZ E3b1 13 12 13 17 24 11 11 13 11 11 12 14 10 12 10 12 12 14,18IP1030 IBZ E3b3 13 12 13 17 25 10 11 14 11 11 12 14 10 12 10 12 12 14,17IP1050 IBZ E3b3 13 12 13 17 25 10 11 14 11 11 12 14 10 13 10 12 12 14,17IP1025 IBZ G 15 12 12 16 22 10 11 14 11 11 12 16 10 13 10 12 12 14,14IP1032 IBZ G 15 12 12 16 22 10 11 14 11 11 12 16 10 13 10 12 12 14,14IP1037 IBZ G 15 13 12 17 22 10 11 14 11 11 12 16 10 12 10 11 12 14,14IP1045 IBZ G 15 12 12 16 22 10 11 14 11 11 12 16 10 13 10 12 12 14,14IP1054 IBZ G 15 13 12 17 22 10 11 14 11 11 12 16 10 12 10 11 12 14,14IP1059 IBZ G 15 12 12 16 22 10 11 14 11 11 12 16 10 13 10 12 12 14,14IP1060 IBZ G 15 13 12 17 22 10 11 14 11 11 12 16 10 12 10 11 12 13,14IP1075 IBZ I 16 13 13 19 24 11 11 13 11 11 12 15 10 13 10 11 12 14,15IP1028 IBZ J2 14 15 14 16 23 10 11 12 11 11 12 15 9 10 10 12 11 14,16IP1042 IBZ J2 14 15 14 17 23 10 11 12 11 11 12 16 9 10 10 12 11 14,16IP1024 IBZ K(xP) 14 12 14 16 23 11 13 13 11 11 12 14 9 11 10 11 12 17,17IP1047 IBZ K(xP) 14 12 14 16 23 12 13 13 11 11 12 14 9 11 10 11 12 17,17IP1049 IBZ K(xP) 14 12 14 16 23 11 13 13 11 11 12 14 9 11 10 11 12 17,17IP1053 IBZ K(xP) 14 12 14 16 23 11 13 13 11 11 12 14 9 11 10 11 12 17,17IP1058 IBZ K(xP) 14 12 14 16 23 12 13 13 11 11 12 14 9 11 10 12 12 17,17IP1064 IBZ K(xP) 14 12 14 16 23 12 13 13 11 11 12 14 9 11 10 11 12 17,17IP1065 IBZ K(xP) 14 12 14 16 23 11 13 13 11 11 12 14 9 11 10 11 12 17,17IP1071 IBZ K(xP) 14 12 14 16 23 12 13 13 11 11 12 14 9 11 10 11 12 17,17IP1073 IBZ K(xP) 14 12 14 16 23 11 13 13 11 11 12 14 9 11 10 11 12 17,17IP1027 IBZ R1b3* 15 12 13 16 23 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP1029 IBZ R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 13 12 11 12 11 12,14IP1031 IBZ R1b3* 14 12 13 16 24 10 13 13 11 11 12 14 12 13 11 12 11 11,14IP1034 IBZ R1b3* 14 12 13 17 24 11 13 10 11 11 12 15 12 12 11 12 11 11,14IP1036 IBZ R1b3* 14 12 13 16 24 10 13 13 11 11 12 14 12 13 11 12 11 11,14IP1038 IBZ R1b3* 15 12 13 16 23 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP1039 IBZ R1b3* 16 12 13 16 23 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP1040 IBZ R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 12 11,14IP1041 IBZ R1b3* 14 12 13 17 24 11 13 13 11 11 12 14 12 12 11 12 11 11,14IP1043 IBZ R1b3* 14 12 13 17 24 11 13 13 11 11 12 14 12 12 11 12 11 11,14IP1044 IBZ R1b3* 15 12 13 17 24 11 13 13 11 11 12 14 12 12 11 12 11 11,14IP1046 IBZ R1b3* 16 12 13 16 23 10 13 13 11 11 12 15 12 12 11 12 12 11,14IP1051 IBZ R1b3* 14 12 14 16 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP1052 IBZ R1b3* 15 12 13 16 24 11 15 13 11 11 12 15 12 13 11 12 11 11,14IP1057 IBZ R1b3* 14 12 13 16 24 11 13 10 11 11 12 14 12 12 11 13 11 11,14IP1061 IBZ R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 13 11 12 11 11,14IP1062 IBZ R1b3* 14 13 14 16 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP1063 IBZ R1b3* 14 13 14 16 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP1066 IBZ R1b3* 14 12 13 16 25 10 13 13 11 11 12 15 13 12 11 12 11 12,14IP1068 IBZ R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 12 11,14IP1069 IBZ R1b3* 14 12 13 16 24 11 13 10 11 11 12 15 12 12 12 12 11 11,14IP1070 IBZ R1b3* 14 12 13 16 24 10 13 13 11 11 12 14 12 13 11 12 11 11,14IP1072 IBZ R1b3* 14 12 14 16 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP1074 IBZ R1b3* 15 12 13 16 23 10 13 13 11 11 12 15 12 11 11 12 11 11,14IP1076 IBZ R1b3* 15 12 13 18 24 9 13 13 11 11 12 14 12 11 10 12 11 11,14IP1033 IBZ R1b3d 15 12 13 16 24 11 13 13 11 11 12 14 12 13 10 12 11 11,14IP1035 IBZ R1b3d 15 12 13 16 24 11 13 13 11 11 12 14 12 12 10 12 11 11,14IP1026 IBZ R1b3f 14 12 14 16 25 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP1048 IBZ R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 11 10 12 11 11,14IP1055 IBZ R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 11 10 12 11 11,14IP1067 IBZ R1b3f 14 12 14 16 25 11 13 13 11 11 12 15 12 12 11 12 11 11,14

MajorcaIP1139 MAJ E3a 15 12 13 18 21 10 11 14 11 11 12 14 11 11 11 13 12 16,18IP1081 MAJ E3b1 14 12 13 17 24 10 13 13 11 11 12 14 10 13 11 12 13 16,19

Adams et al., Supplementary Table 1: Haplotype data 16

IP1090 MAJ E3b1 13 12 13 17 24 10 11 13 11 11 12 14 10 11 9 12 12 16,17IP1091 MAJ E3b1 14 12 14 18 24 10 11 13 11 11 12 14 10 11 11 12 12 17,18IP1121 MAJ E3b2 13 12 14 16 24 9 11 13 11 11 12 14 10 10 11 13 12 13,14IP1084 MAJ G 15 12 12 17 23 10 12 12 11 11 12 16 10 11 10 13 13 15,15IP1085 MAJ G 16 12 12 16 21 11 11 13 11 11 12 16 10 11 10 11 12 13,15IP1088 MAJ G 15 12 12 16 21 10 11 15 11 11 12 15 10 11 10 11 13 13,16IP1097 MAJ G 15 13 12 17 22 10 11 14 11 11 12 16 10 11 10 11 12 14,14IP1089 MAJ I 14 14 12 16 23 10 11 13 11 11 12 16 10 11 10 12 12 13,15IP1093 MAJ I 17 13 15 15 25 9 11 13 11 11 12 15 10 12 11 12 12 12,12IP1095 MAJ I 14 14 12 16 22 10 11 13 11 11 12 15 10 12 10 12 12 13,14IP1129 MAJ I 14 14 12 16 23 10 11 13 11 11 12 16 10 11 10 12 12 13,15IP1137 MAJ I 15 13 12 16 25 10 11 13 11 11 12 15 10 11 10 14 12 13,17IP1099 MAJ J(xJ2) 14 17 13 18 23 10 11 12 11 11 12 14 10 12 11 12 11 13,17IP1080 MAJ J2 15 15 12 16 23 10 11 12 11 11 12 15 9 11 11 10 11 14,18IP1092 MAJ J2 16 15 13 16 23 10 12 12 11 11 12 14 9 12 10 13 10 13,17IP1120 MAJ J2 16 15 14 16 23 10 12 12 11 11 12 14 9 12 11 13 10 13,17IP1127 MAJ J2 14 15 12 16 23 10 11 12 11 11 12 16 9 11 11 10 11 14,17IP1134 MAJ J2 15 16 13 16 23 9 11 12 11 11 12 14 9 11 10 13 10 13,16IP1115 MAJ K(xP) 14 12 13 16 25 11 13 13 11 11 12 14 12 11 11 13 11 11,14IP1078 MAJ R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 11,14IP1079 MAJ R1b3* 14 12 13 16 25 11 13 13 11 11 12 15 12 12 10 12 11 11,15IP1082 MAJ R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 11 11 12 11 11,14IP1083 MAJ R1b3* 15 12 13 16 23 11 13 13 11 11 12 14 12 12 12 13 11 10,15IP1086 MAJ R1b3* 15 12 13 16 24 11 13 13 11 11 12 15 12 12 12 11 11 11,15IP1087 MAJ R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 11 11 12 11 11,14IP1094 MAJ R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 11 12 11 8,14IP1098 MAJ R1b3* 15 12 13 16 24 11 13 13 11 11 12 14 13 12 11 12 11 11,14IP1100 MAJ R1b3* 14 12 13 17 24 10 13 13 11 11 12 15 12 11 12 13 11 11,14IP1101 MAJ R1b3* 15 12 13 16 24 10 14 13 11 11 12 15 12 12 10 12 11 11,14IP1102 MAJ R1b3* 14 12 14 16 23 10 13 13 11 11 12 15 12 13 11 13 11 11,11IP1103 MAJ R1b3* 14 12 14 16 24 11 12 13 11 11 12 14 12 12 10 12 11 11,14IP1105 MAJ R1b3* 14 12 15 16 23 11 14 13 11 11 12 15 12 12 11 12 11 11,14IP1106 MAJ R1b3* 14 12 12 18 25 10 13 13 11 11 12 14 12 12 11 12 11 11,14IP1107 MAJ R1b3* 14 12 13 17 24 11 13 13 11 11 12 15 12 12 11 12 11 11,14IP1109 MAJ R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 11 11 12 11 11,15IP1110 MAJ R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP1111 MAJ R1b3* 15 12 14 18 24 11 13 13 11 11 12 15 12 12 11 11 11 11,14IP1113 MAJ R1b3* 16 12 13 16 23 10 13 13 11 11 12 14 12 12 11 14 11 10,14IP1116 MAJ R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 13 11 11 12 11 13,17IP1119 MAJ R1b3* 14 12 13 16 221 11 13 13 11 11 12 14 12 11 11 13 11 11,14IP1122 MAJ R1b3* 14 12 12 16 24 10 13 13 11 11 12 15 12 12 11 12 11 12,14IP1123 MAJ R1b3* 14 12 13 16 24 12 13 13 11 11 12 14 12 12 11 11 11 11,14IP1124 MAJ R1b3* 15 12 13 16 22 11 13 13 11 11 12 15 12 12 12 12 11 11,14IP1125 MAJ R1b3* 14 12 13 16 24 11 13 12 11 11 12 14 12 12 11 12 11 11,14IP1126 MAJ R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 13 11 11 12 11 13,17IP1128 MAJ R1b3* 16 12 13 16 23 10 13 13 11 11 12 15 12 12 11 12 12 11,14IP1130 MAJ R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 11 11 12 11 11,15IP1131 MAJ R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 11 11 12 11 11,14IP1133 MAJ R1b3* 13 12 14 16 23 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP1135 MAJ R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 13 11 11 12 11 13,17IP1136 MAJ R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 12 10 12 11 12,15IP1138 MAJ R1b3* 14 12 13 16 24 11 13 14 11 11 12 14 12 12 10 12 11 11,14IP1096 MAJ R1b3f 14 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 12 11,14IP1104 MAJ R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 13 11 12 11 11,14IP1108 MAJ R1b3f 14 12 13 16 25 11 13 13 11 11 12 14 12 12 11 12 11 11,14IP1112 MAJ R1b3f 13 12 12 16 24 11 13 13 11 11 12 15 12 11 11 12 11 11,14IP1114 MAJ R1b3f 14 12 13 16 24 10 12 14 11 11 12 15 12 11 11 12 11 11,14IP1117 MAJ R1b3f 14 12 13 16 24 10 12 14 11 11 12 15 12 11 11 12 11 11,14IP1118 MAJ R1b3f 14 12 13 16 24 10 12 14 11 11 12 15 12 11 11 12 11 11,14IP1132 MAJ R1b3f 14 12 13 16 24 10 12 14 11 11 12 15 12 11 11 12 11 11,14

MinorcaIP1157 MIN E3b1 14 12 13 16 24 10 11 13 11 11 12 14 10 12 10 12 12 17,19IP1160 MIN E3b1 13 12 14 17 22 10 11 13 11 11 12 14 10 12 11 11 13 15,15IP1168 MIN E3b1 14 12 13 16 24 10 11 13 11 11 12 14 10 12 10 12 12 17,19IP1175 MIN E3b1 14 12 13 16 23 11 11 13 11 11 12 14 10 12 10 12 12 17,19IP1140 MIN E3b2 13 12 14 16 24 9 11 13 12 11 12 14 10 10 10 13 12 14,14IP1152 MIN E3b3 13 12 13 18 24 10 11 13 11 11 12 13 10 12 10 12 11 15,16IP1162 MIN E3b3 13 12 13 18 24 10 11 13 11 11 12 13 10 12 10 12 11 14,16IP1144 MIN I 16 13 13 15 23 10 11 13 11 11 12 15 10 13 10 11 12 12,12IP1149 MIN J2 16 15 13 19 22 10 11 12 11 11 12 14 9 11 10 13 11 13,15IP1148 MIN R1a1 16 12 14 16 25 11 11 13 12 11 12 14 12 10 10 11 11 11,14

Adams et al., Supplementary Table 1: Haplotype data 17

IP1141 MIN R1b3* 15 12 14 16 24 11 13 13 11 11 12 14 12 12 10 13 11 11,14IP1145 MIN R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 12 11 12 11 11,14IP1147 MIN R1b3* 14 12 14 16 24 11 13 13 11 11 12 15 12 11 12 12 11 12,14IP1150 MIN R1b3* 14 12 13 16 23 11 13 12 11 11 12 15 12 12 11 11 11 11,14IP1151 MIN R1b3* 14 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 12,15IP1154 MIN R1b3* 14 12 13 17 24 11 13 13 11 11 12 15 12 13 10 12 11 11,14IP1155 MIN R1b3* 15 12 13 16 24 10 13 13 11 11 12 15 12 12 11 12 11 12,14IP1156 MIN R1b3* 15 12 13 16 23 11 13 13 11 11 12 14 12 11 11 12 11 11,14IP1158 MIN R1b3* 14 12 14 16 24 11 13 14 11 11 12 14 12 12 10 12 11 11,14IP1159 MIN R1b3* 14 12 14 17 24 10 13 13 11 11 12 14 12 12 10 12 11 11,14IP1161 MIN R1b3* 14 12 13 16 24 11 13 14 11 11 12 14 12 12 11 12 11 12,14IP1163 MIN R1b3* 14 12 12 16 24 11 13 13 11 11 12 15 12 12 11 12 11 12,13IP1164 MIN R1b3* 14 12 13 16 24 11 13 10 11 11 12 15 12 11 11 12 11 11,14IP1165 MIN R1b3* 14 12 13 17 24 11 13 13 11 11 12 15 12 13 11 12 11 11,14IP1166 MIN R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 12 11 12 11 11,14IP1167 MIN R1b3* 14 12 14 16 24 11 13 14 11 11 12 14 12 12 10 12 11 11,14IP1169 MIN R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 11 14 11 12 11 11,14IP1170 MIN R1b3* 14 12 13 16 24 11 13 13 11 11 12 14 12 12 11 12 11 11,14IP1171 MIN R1b3* 14 12 13 16 24 11 13 13 11 11 12 15 12 12 12 12 11 11,14IP1173 MIN R1b3* 14 12 13 17 24 10 13 13 11 11 12 15 13 13 11 12 11 11,13IP1174 MIN R1b3* 14 12 14 16 24 11 13 13 11 11 12 14 12 12 11 12 11 11,14IP1176 MIN R1b3* 14 12 13 16 23 11 13 13 11 11 12 15 12 12 11 13 11 11,14IP1142 MIN R1b3d 14 12 13 16 25 11 13 13 11 11 12 14 12 13 10 12 11 11,14IP1143 MIN R1b3f 14 12 13 16 24 10 12 14 11 11 12 15 12 11 11 12 11 11,14IP1146 MIN R1b3f 14 12 13 16 24 11 13 13 13 11 12 15 12 12 11 14 11 11,15IP1153 MIN R1b3f 14 12 13 16 24 11 13 13 12 11 12 15 12 12 11 12 11 11,15IP1172 MIN R1b3f 14 12 13 16 24 11 13 13 11 11 12 15 12 11 10 13 11 11,14

Sephardic Jewish sampleSj1 SJ E3a 13 14 13 16 23 10 11 13Sj2 SJ E3b* 13 12 13 19 25 10 11 14Sj3 SJ E3b* 13 12 14 18 23 10 11 12Sj4 SJ E3b1 13 12 12 17 24 10 11 13Sj5 SJ E3b1 13 12 12 17 23 10 11 13Sj6 SJ E3b1 13 12 13 17 24 10 11 13Sj7 SJ E3b1 13 12 12 18 23 10 11 13Sj8 SJ E3b1 13 12 13 18 25 10 11 12Sj9 SJ E3b1 13 12 13 17 24 10 11 13Sj10 SJ E3b2 13 12 14 16 24 9 11 13Sj11 SJ E3b3 14 12 13 17 24 9 11 14Sj12 SJ E3b3 13 13 12 17 24 10 11 13Sj13 SJ E3b3 13 13 12 17 24 10 11 13Sj14 SJ E3b3 13 12 14 17 24 9 11 13Sj15 SJ E3b3 14 12 13 17 24 9 11 14Sj16 SJ E3b3 13 12 13 17 24 10 11 13Sj17 SJ G 15 12 12 16 22 10 11 14Sj18 SJ G 15 12 12 17 22 11 11 14Sj19 SJ G 16 12 12 16 22 10 11 14Sj20 SJ G 15 12 12 16 23 11 12 13Sj21 SJ G 15 12 12 16 22 10 11 13Sj22 SJ G 15 13 13 17 22 10 11 13Sj23 SJ G 15 12 12 17 22 10 11 14Sj24 SJ G 15 12 11 18 23 10 10 14Sj25 SJ G 15 12 12 17 21 10 11 15Sj26 SJ G 16 12 12 19 22 10 10 14Sj27 SJ G 16 12 12 16 23 10 10 14Sj29 SJ G 16 12 12 16 22 10 11 14Sj30 SJ G 15 12 12 17 23 10 11 13Sj31 SJ G 16 12 12 16 22 10 11 14Sj32 SJ G 16 12 12 16 22 10 11 14Sj33 SJ G 15 12 12 17 22 10 11 13Sj34 SJ G 15 12 12 17 22 10 12 14Sj35 SJ G 15 12 12 17 23 10 11 14Sj36 SJ G 15 12 12 17 22 10 11 14Sj38 SJ G 16 12 12 16 22 10 11 13Sj39 SJ G 15 12 12 17 22 10 12 14Sj40 SJ G 16 12 13 16 24 10 10 14Sj41 SJ G 16 12 11 17 23 10 11 14Sj42 SJ G 15 12 12 17 22 10 11 13Sj43 SJ G 15 12 12 17 22 10 12 14Sj44 SJ I 17 13 14 15 23 10 11 13Sj45 SJ J(xJ2) 14 15 14 17 23 10 11 12

Adams et al., Supplementary Table 1: Haplotype data 18

Sj46 SJ J(xJ2) 14 15 14 17 23 10 11 12Sj47 SJ J(xJ2) 14 15 14 17 23 10 11 12Sj48 SJ J(xJ2) 14 15 14 17 23 10 11 12Sj49 SJ J(xJ2) 14 15 14 17 23 10 11 12Sj50 SJ J(xJ2) 14 15 14 17 23 10 11 12Sj51 SJ J(xJ2) 14 15 14 17 23 10 11 12Sj52 SJ J(xJ2) 14 15 14 17 23 10 11 12Sj53 SJ J(xJ2) 14 15 14 17 23 10 11 12Sj54 SJ J(xJ2) 14 15 14 17 23 10 11 12Sj55 SJ J(xJ2) 14 15 14 17 23 10 11 12Sj56 SJ J(xJ2) 14 16 13 17 23 10 11 12Sj57 SJ J(xJ2) 14 16 13 17 24 10 11 12Sj58 SJ J(xJ2) 14 16 13 17 23 10 11 12Sj59 SJ J(xJ2) 15 17 14 17 23 10 11 12Sj60 SJ J(xJ2) 14 15 14 17 23 10 11 12Sj61 SJ J(xJ2) 14 17 14 17 23 10 11 12Sj62 SJ J(xJ2) 14 16 13 18 23 10 11 12Sj63 SJ J(xJ2) 14 17 13 18 23 10 11 12Sj64 SJ J(xJ2) 14 16 13 18 23 10 11 9Sj65 SJ J(xJ2) 14 16 13 17 23 10 11 12Sj66 SJ J(xJ2) 14 16 13 17 24 10 11 12Sj67 SJ J(xJ2) 15 16 13 17 23 10 11 12Sj68 SJ J(xJ2) 14 16 13 17 23 10 11 12Sj69 SJ J(xJ2) 14 17 13 16 23 10 11 12Sj70 SJ J(xJ2) 14 16 14 16 23 10 11 12Sj71 SJ J(xJ2) 14 13 13 16 23 10 11 12Sj72 SJ J(xJ2) 14 16 13 17 23 10 11 12Sj73 SJ J(xJ2) 14 16 13 17 23 10 11 12Sj74 SJ J(xJ2) 14 16 13 17 23 10 11 12Sj75 SJ J(xJ2) 14 16 13 18 23 10 11 12Sj76 SJ J(xJ2) 14 13 13 16 23 10 11 12Sj77 SJ J(xJ2) 14 17 13 16 23 10 11 12Sj78 SJ J(xJ2) 14 16 13 17 23 10 10 12Sj79 SJ J(xJ2) 14 17 13 18 23 10 11 12Sj80 SJ J(xJ2) 14 16 13 16 25 10 13 12Sj81 SJ J(xJ2) 14 16 13 17 23 10 11 12Sj82 SJ J(xJ2) 14 17 13 18 23 10 11 12Sj83 SJ J2 14 16 14 16 24 9 11 12Sj84 SJ J2 15 16 14 16 24 9 11 12Sj85 SJ J2 15 16 14 17 24 9 11 12Sj86 SJ J2 15 16 13 16 24 9 11 12Sj87 SJ J2 15 16 14 16 24 9 11 12Sj88 SJ J2 14 16 14 17 23 10 11 12Sj89 SJ J2 15 16 14 16 23 10 11 12Sj90 SJ J2 14 15 14 17 24 10 11 12Sj91 SJ J2 15 16 14 16 23 10 11 12Sj92 SJ J2 15 16 14 16 24 9 11 12Sj93 SJ J2 15 16 14 17 24 9 11 12Sj94 SJ J2 15 16 14 16 24 9 11 12Sj95 SJ J2 17 15 13 16 23 10 11 12Sj96 SJ J2 14 15 12 15 24 10 11 12Sj97 SJ J2 15 15 12 16 24 11 11 12Sj98 SJ J2 16 13 14 17 22 10 10 12Sj99 SJ J2 14 14 13 17 24 10 12 12Sj100 SJ J2 17 15 13 17 25 9 11 12Sj101 SJ J2 15 17 13 17 23 10 11 12Sj102 SJ J2 15 15 12 19 23 10 11 12Sj103 SJ J2 14 14 13 17 24 10 11 13Sj104 SJ J2 14 14 13 18 23 10 11 12Sj105 SJ J2 14 14 13 17 24 10 12 12Sj106 SJ J2 17 15 13 17 23 10 11 12Sj107 SJ J2 14 14 13 17 22 10 11 12Sj108 SJ J2 15 16 13 16 23 9 11 12Sj109 SJ J2 16 15 13 16 23 9 11 12Sj110 SJ J2 14 15 14 18 22 10 11 12Sj111 SJ J2 14 16 13 16 23 10 11 12Sj112 SJ J2 13 15 12 15 24 10 11 12Sj113 SJ J2 15 15 12 16 24 11 11 12Sj114 SJ J2 15 15 12 17 24 10 11 12Sj115 SJ J2 15 16 13 16 23 9 11 12Sj116 SJ J2 16 15 13 16 22 10 12 12Sj117 SJ J2 15 16 14 16 23 10 11 12

Adams et al., Supplementary Table 1: Haplotype data 19

Sj118 SJ J2 14 14 13 16 23 10 11 12Sj119 SJ J2 15 14 13 16 23 10 11 12Sj120 SJ J2 13 15 13 15 24 10 11 12Sj121 SJ J2 14 15 14 16 23 10 11 12Sj122 SJ J2 16 15 13 15 23 9 11 13Sj123 SJ J2 16 15 13 16 22 10 12 12Sj124 SJ J2 14 15 13 17 22 10 11 12Sj125 SJ J2 13 15 14 19 23 10 11 12Sj126 SJ K(xP) 15 12 13 17 23 11 13 13Sj127 SJ K(xP) 14 12 13 17 23 10 13 13Sj128 SJ K(xP) 13 12 13 15 22 10 13 13Sj129 SJ K(xP) 15 12 13 16 23 11 13 13Sj130 SJ K(xP) 14 12 14 15 23 10 13 13Sj131 SJ K(xP) 14 12 13 18 23 10 13 13Sj132 SJ K(xP) 15 12 13 17 23 11 13 13Sj133 SJ K(xP) 13 12 13 16 22 10 13 13Sj134 SJ K(xP) 13 12 13 15 22 10 13 13Sj135 SJ K(xP) 14 12 14 16 23 10 14 12Sj136 SJ K(xP) 15 12 15 15 23 10 14 11Sj137 SJ Q(xQ3) 13 14 13 15 22 10 15 13Sj138 SJ Q(xQ3) 13 12 13 16 22 10 15 13Sj139 SJ Q(xQ3) 13 12 13 15 22 10 16 13Sj140 SJ Q(xQ3) 13 12 13 14 22 10 15 13Sj141 SJ R1a 15 12 13 16 24 11 11 13Sj142 SJ R1a 16 12 13 17 25 10 11 13Sj143 SJ R1a 16 12 12 18 25 11 11 13Sj144 SJ R1a 15 12 13 17 25 10 11 12Sj145 SJ R1a 16 12 13 17 25 10 11 14Sj146 SJ R1a 16 12 13 17 24 10 11 13Sj147 SJ R1a 16 12 13 17 25 10 11 13Sj148 SJ R1a 16 12 13 17 24 10 11 13Sj149 SJ R1b* 15 12 14 15 24 11 13 14Sj150 SJ R1b* 16 12 13 16 23 10 13 13Sj151 SJ R1b3 14 12 13 15 24 11 13 13Sj152 SJ R1b3 14 12 13 15 24 11 13 13Sj153 SJ R1b3 14 12 13 15 24 11 13 13Sj154 SJ R1b3 14 12 13 16 24 11 13 13Sj155 SJ R1b3 16 12 13 16 24 11 13 13Sj156 SJ R1b3 14 12 13 16 24 10 14 13Sj157 SJ R1b3 14 12 13 15 25 11 14 12Sj158 SJ R1b3 14 12 13 15 24 11 13 13Sj159 SJ R1b3 14 12 14 16 24 11 13 13Sj160 SJ R1b3 14 12 12 15 24 10 14 12Sj161 SJ R1b3 14 12 14 16 22 10 13 13Sj162 SJ R1b3 14 12 13 15 24 10 14 12Sj163 SJ R1b3 14 12 13 17 24 10 13 12Sj164 SJ R1b3 14 12 12 15 24 11 14 12Sj165 SJ R1b3 14 12 13 15 24 10 14 12Sj166 SJ R1b3 14 12 13 16 25 11 13 13Sj167 SJ R1b3 14 12 13 16 24 11 13 13Sj168 SJ R1b3 14 12 13 16 24 11 13 13Sj169 SJ R1b3 14 13 12 16 24 11 13 13Sj170 SJ R1b3 14 12 13 15 25 10 14 13Sj171 SJ R2 14 12 13 15 23 10 10 14Sj172 SJ R2 14 12 14 15 23 10 10 14Sj173 SJ R2 14 12 14 15 23 10 10 14Sj174 SJ R2 14 12 14 15 23 10 10 14NB no subtyping of R1b3 available for Sephardic Jewish sample

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