Neolithization of North Africa Involved The Migration of 2 People From Both The Levant and Europe

bioRxiv preprint first posted online Sep. 21, 2017; doi: http://dx.doi.org/10.1101/191569.
The copyright holder for this preprint (which was

not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
1 Neolithization of North Africa involved the migration of

2 people from both the Levant and Europe
3 Rosa Fregel1*, Fernando L. Méndez1, Youssef Bokbot2, Dimas Martín-Socas3, María D.

4 Camalich-Massieu3, María C. Ávila-Arcos1,4, Peter A. Underhill1, Beth Shapiro5,
5 Genevieve Wojcik1, Morten Rasmussen1, Andre E. R. Soares5§, Joshua Kapp5, Alexandra
6 Sockell1, Francisco J. Rodríguez-Santos6, Abdeslam Mikdad2, Jonathan Santana7, Aioze
7 Trujillo-Mederos3 & Carlos D. Bustamante1¶
1
8 Department of Genetics, School of Medicine, Stanford University, Stanford, US. 2Institut
9 National des Sciences de l'Archéologie et du Patrimoine, Rabat, Morocco. 3Department
10 of Prehistory, Faculty of History, Universidad de La Laguna, San Cristóbal de La
11 Laguna, Spain. 4International Laboratory for Human Genome Research, National
12 University of Mexico, Querétaro, Mexico. 5Department of Ecology and Evolutionary
13 Biology, University of California, Santa Cruz, US. 6Instituto Internacional de
14 Investigaciones Prehistóricas de Cantabria, Cantabria, Spain. 7Department of
15 Archaeology, Faculty of Arts and Humanities. Durham University, Durham, UK.
¶
16 Present address: Department of Biomedical Data Science, School of Medicine, Stanford University,
17 Stanford, US.
18 §
Present address: Laboratório Nacional de Computação Científica, Petrópolis, Brazil
19 One of the greatest transitions in the human story was the change from hunter-
20 gatherer to farmer. How farming traditions expanded from their birthplace in the
21 Fertile Crescent has always been a matter of contention. Two models were
22 proposed, one involving the movement of people and the other based on the
23 transmission of ideas. Over the last decade, paleogenomics has been instrumental in
24 settling long-disputed archaeological questions1, including those surrounding the
25 Neolithic revolution2. Compared to the extensive genetic work done on Europe and
26 the Near East, the Neolithic transition in North Africa, including the Maghreb,
27 remains largely uncharacterized. Archaeological evidence suggests this process may
28 have happened through an in situ development from Epipaleolithic communities3,4,
29 or by demic diffusion from the Eastern Mediterranean shores5 or Iberia6. In fact,
bioRxiv preprint first posted online Sep. 21, 2017; doi: http://dx.doi.org/10.1101/191569. The copyright holder for this preprint (which was
30 Neolithic pottery in North Africa strongly resembles that of European cultures like
31 Cardial and Andalusian Early Neolithic, the southern-most early farmer culture
32 from Iberia. Here, we present the first analysis of individuals’ genome sequences
33 from early and late Neolithic sites in Morocco, as well as Andalusian Early Neolithic
34 individuals. We show that Early Neolithic Moroccans are distinct from any other
35 reported ancient individuals and possess an endemic element retained in present-
36 day Maghrebi populations, indicating long-term genetic continuity in the region.
37 Among ancient populations, early Neolithic Moroccans share affinities with
38 Levantine Natufian hunter-gatherers (~9,000 BCE) and Pre-Pottery Neolithic
39 farmers (~6,500 BCE). Late Neolithic (~3,000 BCE) Moroccan remains, in
40 comparison, share an Iberian component of a prominent European-wide demic
41 expansion, supporting theories of trans-Gibraltar gene flow. Finally, the Andalusian
42 Early Neolithic samples share the same genetic composition as the Cardial
43 Mediterranean Neolithic culture that reached Iberia ~5,500 BCE. The cultural and
44 genetic similarities of the Iberian Neolithic cultures with that of North African
45 Neolithic sites further reinforce the model of an Iberian intrusion into the Maghreb.
46 Present genetic data from modern samples7-9 suggests that North Africans’ ancestry has
47 contributions from four main sources: 1) an autochthonous Maghrebi component related
48 to a back migration to Africa ~12,000 years ago from the Levant; 2) a Middle Eastern
49 component probably associated with the Arab conquest; 3) a sub-Saharan component
50 derived from trans-Saharan migrations; and 4) a European component that has been
51 linked to recent historic movements. Paleogenomic studies have begun to provide
52 insights into North African Prehistory10,11; however, no research to date has tested
53 whether the Neolithic transition in the Maghreb was driven by an in situ development or
54 the migration of people. Here, we perform genome-wide analysis of remains from the
55 Early Neolithic site of Ifri n'Amr or Moussa (IAM; ~5,000 BCE, n=7) and the Late
56 Neolithic site of Kelif el Boroud (KEB; ~3,000 BCE; n=8) (Supplementary Note 1). To
57 test possible migrations through the Strait of Gibraltar, we also analyse samples from
58 Early Neolithic sites in southern Iberia: El Toro (TOR; ~5,000 BCE; n=12) and Los
59 Botijos (BOT; n=1) (Figure 1). This Andalusian Early Neolithic culture is thought to
60 have arrived prior to Cardial technology, and bears similarities with early Maghrebi
61 farming traditions12 (Supplementary Note 1). Including these southern samples in our
62 analysis enables a direct test of this hypothesis.
63 [Figure 1]
64 We sequenced 39 Illumina pair-end libraries from 28 individuals, and selected best

65 conserved libraries for subsequent analyses. Endogenous DNA content was generally low
66 (2.06% on average) (Supplementary Note 2). Depth of coverage was consistently
67 improved when enriching using baits targeting specific sites (~100X), compared to
68 whole-genome capture (~15X) (Supplementary Note 2). Following enrichment, we
69 generated fifteen low-coverage genomes (5 from IAM, 4 from KEB and 5 from
70 TOR/BOT), with coverage ranging from 0.04X to 0.73X depth. All samples considered
71 in this study met the standard aDNA authentication criteria, including observation of
72 DNA fragmentation (∼46 bp average read length) and damage patterns due to cytosine
73 deamination toward the 5′ ends of molecules (Supplementary Note 3).
74 Mitochondrial DNA and Y-chromosome haplogroups obtained for IAM (Moroccan

75 Early Neolithic) and KEB (Moroccan Late Neolithic) indicate either a population
76 replacement or an important genetic influx into Morocco between 5,000–3,000 BCE.
77 IAM samples belong to the mtDNA haplogroups U6a and M1—both of which are
78 associated with back migration to Africa13,14—while KEB samples belong to haplogroups
79 K1, T2 and X2, prominently found in Anatolian and European Neolithic samples2,15
80 (Supplementary Note 4). Regarding the paternal lineages, IAM individuals carry Y
81 chromosomes distantly related to the typically North African E-M81 haplogroup, while
82 the Y chromosome from KEB belongs to the T-M184 haplogroup; though scarce and
83 broadly distributed today, this haplogroup has also been observed in European Neolithic
84 individuals16 (Supplementary Note 5). Both mtDNA and Y-chromosome lineages (K1, J2
85 and T2 haplogroups, and G-M201 haplogroup, respectively) for samples from TOR/BOT
86 (Iberian Early Neolithic) are similar to those observed in Europe during Neolithic times15.
87 West Eurasian populations can be modelled as admixture of four different ancestral

88 components2: Eastern and Western European hunter-gatherers, Iranian and Levant
89 Neolithic. We explored the placement of Moroccan and Southern Iberian Neolithic
90 samples in this context, and compared their genetic affinities to ancient and present-day
91 West Eurasian and Levant populations. Interestingly, Principal Components Analysis
92 (PCA) reveals that IAM individuals are different from any aDNA sample studied to date
93 (Figure 2; Supplementary Note 6). When projected, IAM samples are close to modern
94 North Africans, in the Levantine corner of the PCA space (Figure 2). Southern Iberian
95 Neolithic individuals from TOR and BOT cluster with Sardinians and with other
96 Anatolian and European Neolithic samples. Moreover, KEB samples are placed halfway
97 between the IAM and Anatolian/European farmer clusters, in close proximity to Levant
98 aDNA samples. We further explored the genetic structure of these samples using the
99 program ADMIXTURE16 (See Supplementary Note 7 for details), with values of K
100 ranging between 2 and 8. At lower K values, IAM samples possess ~100% of a
101 component partially shared by aDNA samples from the Middle East and Levant. At K=6,
102 this IAM-like component is observed mainly in modern North Africa, following a west-
103 to-east cline. TOR and other Early Neolithic samples from Iberia cluster together with
104 farmers from Anatolia, the Aegean area and Europe. At K=8 the Early Neolithic
105 individuals from Iberia differentiate from the Anatolian, Aegean and European Early
106 Neolithic samples, and share their main component (purple) with Middle
107 Neolithic/Chalcolitic samples (Figure 2). Finally, at low K values, KEB can be explained
108 as having both IAM-like and European Neolithic components, suggesting an admixture
109 process between IAM-like people and early farmers. Nevertheless, at K=8, the European
110 component in KEB is predominantly “purple,” with some “green” component. This
111 “green” component is also present, at a low frequency, in Natufians and other ancient
112 Levantine populations. The substantially larger contribution of the “purple” component,
113 when compared with the “green”, suggests a significant genetic contribution of ancient
114 Iberians in Morocco (Figure 2).
115 [Figure 2 here]
116 To compare our samples directly to the genomes of ancient and modern populations, we
117 calculated pair-wise FST distances, which, unlike PCA and global ancestry analyses, are
118 insensitive to the inclusion of large numbers of individuals from modern populations. FST
119 values indicate that the IAM samples are as differentiated from all other populations as
120 Yoruba are from non-Africans (Supplementary Note 9), with the sole exception of KEB
121 and, to a lesser extent, modern North African populations. Given the relatively low
122 heterozygosity (~6.6 x 10-4) and high identity-by-descent (~37%) proportions observed in
123 IAM (Supplementary Note 8), this differentiation could be related to isolation and genetic
124 drift. Although IAM is clearly more similar to KEB than any other population, the
125 converse is not true. KEB has lower FST distances with any Anatolian, European
126 (excluding European hunter gatherers), Levantine and Iranian population, rather than
127 with IAM. In the modern DNA reference panel, KEB is similar to North African,
128 European and Middle Eastern populations. Among the ancient populations, TOR is more
129 similar to Middle Neolithic/Chalcolithic Europeans, and, among modern populations, to
130 populations from Spain, North Italy and Sardinia.
131 To further investigate the genetic affinities of IAM, KEB and TOR samples, we
132 conducted outgroup f3-statistic analysis17. Results indicate that, when KEB is excluded,
133 IAM shares more drift with ancient Levantine populations, such as Natufians and Levant
134 Neolithic (Figure 3; Supplementary Note 10), than with any other ancient population.
135 This result is analogous to preliminary archaeological data pointing to links between
136 funerary practices in IAM and Pre-Pottery Neolithic B sites in Cyprus (Supplementary
137 Note 1).
138 Both FST and outgroup-f3 statistic analyses indicate that KEB shares ancestry with
139 IAM, but also more genetic drift with Neolithic and Chalcolithic populations from
140 Anatolia and Europe, with the highest shared genetic drift appearing in Iberian Early
141 Neolithic samples (Figure 3; Supplementary Note 10). This pattern and the result from
142 ADMIXTURE could be explained if the KEB population was a mixture between IAM-
143 related and European Neolithic groups. To formally test this hypothesis, we used an
144 admixture-f3 test17, using KEB as the test population, IAM as a reference population and
145 one of the Anatolian and European Neolithic and Chalcolithic populations as the second
146 reference population. All comparisons produced negative values of the f3-statistic, which
147 suggests the KEB population can be modelled as a mixture of IAM and
148 Anatolian/European Neolithic. These results also parallel archaeological findings in the
149 region: Late Neolithic sites in North Africa contain pottery resembling that of the
150 Andalusian Early Neolithic and Cardial cultures, and ivory tools distinctly associated
151 with those of Iberian Neolithic sites (Supplementary Note 1).
152 TOR has more shared ancestry with Iberian Early Neolithic samples and other
153 Neolithic and Chalcolithic populations from Europe. Archaeological work in southern
154 Iberia, especially in the Nerja site, has pointed out that the Andalusian Early Neolithic
155 culture, previous to the Cardial expansion, may have had connections to farmer traditions
156 in the Maghreb18. However, we observe that TOR samples have a similar genetic
157 composition to that of Cardial individuals from Iberia, evidencing a common origin.
158 [Figure 3 here]
159 Finally, phenotypic predictions based on genetic variants of known effects agree with our
160 estimates of global ancestry. IAM people do not possess any of the European SNPs
161 associated with light pigmentation, and most likely had dark skin and eyes. IAM samples
162 present ancestral alleles for pigmentation-associated variants present in SLC24A5
163 (rs1426654), SLC45A2 (rs16891982) and OCA2 (rs16891982 and 12913832) genes. On
164 the other hand, KEB individuals exhibit some European- derived alleles that predispose
165 individuals to lighter skin and eye colour, including those on genes SLC24A5
166 (rs1426654) and OCA2 (rs16891982) (Supplementary Note 11).
167 Genetic analyses have revealed that the population history of modern North
168 Africans is quite complex7. Based on our aDNA analysis, we identify an Early Neolithic
169 Moroccan component that is restricted to North Africa in present-day populations7, which
170 is the sole ancestry in IAM samples. We hypothesize that this component represents the
171 autochthonous Maghrebi ancestry associated with Berber populations. This Maghrebi
172 component was related to that of Epipaleolithic and Pre-Pottery Neolithic people from
173 the Levant. By 3,000 BCE, a European Neolithic expansion brought Mediterranean-like
174 ancestry to the Maghreb, most likely from Iberia. Our analyses demonstrate that at least
175 some of the European ancestry observed today in North Africa is related to prehistoric
176 migrations, and local Berber populations were already admixed with Europeans before
177 the Roman conquest. Furthermore, additional European/Iberian ancestry could have
178 reached the Maghreb after KEB people; this scenario is supported by the presence of
179 Iberian-like Bell-Beaker pottery in more recent stratigraphic layers of IAM and KEB
180 caves. Future palaeogenomic efforts in North Africa will help further disentangle the
181 complex history of migrations that forged the ancestry of many admixed populations we
182 observe today.
183 Methods
184 Measures to avoid and monitor contamination from modern DNA were applied, at all
185 times, during sample manipulation. Ancient DNA was extracted from teeth or bone, built
186 into double-stranded indexed libraries and sequenced on an Illumina NextSeq 500
187 (Supplementary Note 2). Due to the environmental conditions of the burial sites, we
188 expected to recover low proportions of endogenous DNA from these ancient remains. To
189 overcome limitations due to DNA degradation, we applied two different capture methods
190 to enrich for human reads (Supplementary Note 2): one targeting the whole genome19 and
191 one targeting the variants of the Multiethnic Genotyping Array (MEGA) array (Illumina
192 Inc.).
193 Reads were trimmed and adapters removed using AdapterRemoval20, and then
194 mapped to the human reference genome (hg19) using BWA21. Low quality (MAPQ<30)
195 and duplicate reads were removed using SAMtools22. MapDamage23 was used to
196 visualize misincorporation and fragmentation patterns, and to rescale the quality of bases
197 likely affected by post-mortem damage. Confidence intervals of sex determination were
198 calculated following Skoglund et al.24. MtDNA haplogroups were determined using
199 HaploGrep25. Y-chromosome haplogroup inference was carried out as in Schroeder et
200 al.26. As the reference panel, we used both the Human Origins panel2 and the HGDP
201 dataset genotyped with MEGA-ex (Illumina Inc.). For principal component analysis, we
202 projected the aDNA samples on the PCA space built with the modern dataset, using
203 smartpca27 and LASER28. Admixture estimations were done using ADMIXTURE
204 software16. FST distances were calculated using smartpca27. Identity-by-descent
205 proportions were estimated using PLINK29, and heterozygosity estimations using a newly
206 developed method for low-coverage genomes (Supplementary Note 8). f-statistics
207 estimates were calculated using admixtools software17. All plots were prepared using R
208 software30. Detailed information about methods is included in the Supplementary Notes.
209
210 Acknowledgements R.F. and C.D.B were funded by a grant from the National Science Foundation
211 (1201234). R.F. was funded by Fundación Canaria Dr. Manuel Morales fellowship. A.E.R.S. was funded
212 by Ciencia sem Fronteiras fellowship - CAPES, Brazil. BS and JK were funded by a grant from the Gordon
213 and Betty Moore Foundation (GBMF-3804).
214 Author Contributions R.F. and C.D.B conceived the idea for the study, Y.B., D.M.S, M.D.C.M, F.J.R.S,
215 A.M., J.S. and A.T.M assembled skeletal material, R.F., A.E.R.S., J.K. and A.S. performed wet laboratory
216 work, F.M. developed methods for data analysis, M.R. developed methods for DNA capture, R.F., F.M.,
217 M.A.A, P.A.U, G.W., analysed data, C.D.B and B.S. supervised the study, R.F., F.M. and C.D.B. wrote the
218 manuscript and supplements with input from all co-authors.
219 Author Information Sequence data are available through the European Nucleotide Archive
220 (PRJEB22699). Consensus mtDNA sequences are available at the National Center of Biotechnology
221 Information (Accession Numbers XXXXXXX-XXXXXXX). The authors declare no competing financial
222 interests. Correspondence and requests for materials should be addressed to R.F. (e-mail:
223 rfregel@stanford.edu).
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310
311
12
311 Figure 1. Geographical location (A) and calibrated radiocarbon date (B) of the samples included in
312 this study, as well as other ancient DNA samples from the literature. *BOT sample was not
313 radiocarbon dated, but was assigned to the Early Andalusian period on the basis of the associated
314 material culture.
Aegean_N Europe_EN Iran_recent SHG ● This_study: Switzerland_HG

Anatolia_ChL ● Europe_LNBA Ireland_N Steppe_EMBA BOT Natufian
Anatolia_N Europe_MNChL Kostenki14 Steppe_Eneolithic ● IAM CHG
Armenia_ChL ● Iberia_BA ● Levant_BA Steppe_IA ● KEB Iran_HotuIIIb
● Armenia_EBA Iran_ChL Levant_N Steppe_MLBA TOR Iran_N
● Armenia_MLBA Iran_HotuIIIb Mal'ta Switzerland_HG Levant_N
CHG ● Iran_LN ● Mota Ust_Ishim Anatolia_N
EHG Iran_N Natufian WHG WHG
EHG
Iran_LN ●
SHG
Aegean_N
● TOR
● IAM ●
● ●
●
●●● Europe_EN
● BOT*
●●
●
● ● Steppe_Eneolithic
● ●
●● ●
●● Iran_ChL
●●●
●●
Armenia_ChL
● Mota ●
●●
●
● Anatolia_ChL
●
KEB ●
● ●
Ireland_N
●● ●●
● ●
Armenia_EBA ●
●
Europe_MNChL
Steppe_EMBA
Levant_BA ●
Steppe_MLBA
● Europe_LNBA ●
Iberia_BA ●
Iran_recent
Armenia_MLBA ●
Steppe_IA
0
00
00
00
0
A B
00
●●
30
60
90
12
● calibrated date (BCE)
315
316
13
317 Figure 2. Ancestry inference in ancient samples from North Africa and the Iberian Peninsula. (a) PCA
318 analysis, (b) ADMIXTURE analysis (K=2 - K=8), and (c) detailed ADMIXTURE analysis for European
319 Neolithic samples (K=8).

0.0 0.2 0.4 0.6 0.8 1.0
HUMAN ORIGINS LSQPROJECT 455,884 SNPs

I0046
I0048
C
I0057
A
I0100
I0659
I0821
Germany
Europe_EN
I1550
I0795
I0797
I0054
I0022
I0025
I0026
Stuttgart
I0174
I1508
I1506
I0176
●
0.10
I1495
I1496 Hungary
I1498
I1499
I1500
I1505
CB13
I0409
● I0410
I0412
Iberia
I0413
● I0172
I0807
● I0559 Germany
Europe_MNChL
I0560
● I0551
I1497
Hungary
RISE486
RISE487 Italy
0.05
RISE489
I0405
I0406
I0407
I0408
I1271
● ●
I1272
I1276
I1277
I1280 Iberia
●● I1281
● I1282
I1284
● ● I1300
I1303
I1314
ATP16
Matojo
PC2 (0.46%)
ATP9
●●● ● ●
●● ●● ●
●●● ●●● ● ● ●
● ●
RISE568
●
●●●●● ●
●● ● ●●●
RISE569
Czech Rep.
●●
RISE566
●● ● ● RISE586
0.00
●●●● ● RISE577
● ●●● ●● ● ●
● RISE61
Denmark
●●
RISE71
●●
●
RISE47
RISE276
●● ●
●● ● ●
RISE00 Estonia
● ● ●●
I0118
I0059
I0171
I0550
●●
RISE559
RISE560
●●
●●
I1546
I1549
●● RISE562
RISE563
RISE564
I0805
Europe_LNBA
I0806
I0112
●
−0.05
I0113
● I0060
I0108
●
● I0111
RISE446
I0049
I0103
I0104
I0106 Germany
I1532
Ancient samples I1534
I1536
I1538
I1539
I1540
Aegean_N Europe_MNChL Steppe_EMBA I1542
I1544
RISE434
RISE435
Anatolia_ChL ● Iberia_BA Steppe_Eneolithic ● RISE436
I0115
Anatolia_EN Iran_ChL Steppe_IA I0116
I0117
I0803
I0804
Anatolia_N Iran_HotuIIIb Steppe_MLBA I0047
I0164
−0.10
Anatolia_N_H ● Iran_LN Switzerland_HG RISE471

I0099
Anatolia_N_K Iran_N WHG RISE349

I1502
I1504
Armenia_ChL Iran_N_GL ● This_study: RISE371
RISE373
RISE374
RISE479 Hungary
● Armenia_EBA Iran_recent BOT RISE480
RISE483
● Armenia_MLBA Ireland_N ● IAM Modern samples RISE484

RISE247
RISE254
CHG ● Levant_BA ● KEB Canary_Islands Sardinia RISE431

Poland
RISE150
RISE154
EHG Levant_N TOR Eastern_Europe Southern_Europe RISE109
RISE179
Europe_EN Natufian Middle_East Western_Europe RISE97
RISE98
RISE175 Sweden
−0.15
● Europe_LNBA SHG North_Africa RISE210

RISE94
KEB
KEB
−0.05 0.00 0.05 TOR

TOR
B
8.0 4.0 0.0 8.0 4.0 0.0 8.0 4.0 0.0 8.0 4.0 0.0 8.0 4.0 0.0 8.0 4.0 0.0 8.0 4.0 0.0 8.0 4.0 0.0 8.0 4.0 0.0 8.0 4.0 0.0 8.0 4.0 0.0 8.0 4.0 0.0 8.0 4.0 0.0 8.0 4.0 0.0
PC1 (1.03%)
K=2 K=3 K=4 K=5 K=6 K=7 K=8 K=2 K=3 K=4 K=5 K=6 K=7 K=8
WHG
SHG
Switzerland_HG
Anatolia_N Eastern
Europe
Aegean_N
Europe_EN
Southern
Europe
Europe_MNChL
Western
Europe
Europe_LNBA
Sardinia
EHG Canary Islands
Steppe_Eneolithic
Steppe_EMBA
Steppe_MLBA
Anatolia_ChL
Armenia_ChL Middle East
Armenia_EBA
Armenia_MLBA
CHG
Iran_HotuIIIb
Iran_N
Iran_LN
Iran_ChL
Natufian
Levant_N
Levant_BA
IAM
North Africa
KEB
320
TOR
14
321 Figure 3. Outgroup f3-statistic for IAM (A), KEB (B) and TOR (C), and admixture f3-statistic for KEB
322 (D).
A IAM
B KEB
C TOR
KEB ● Iberia_EN ● Iberia_EN ●
Natufian ● Anatolia_ChL ● Aegean_N ●
Levant_N ● Europe_MNChL ● Iberia_MNChL ●
Anatolia_ChL ● Europe_EN ● Europe_MNChL ●
Levant_BA ● Iberia_MNChL ● Europe_EN ●
Aegean_N ● Anatolia_N ● Anatolia_N ●
Europe_MNChL ● Aegean_N ● Iberia_BA ●
Iberia_EN ● Levant_N ● WHG ●
Anatolia_N ● Iberia_BA ● Anatolia_ChL ●
Iberia_MNChL ● Iran_recent ● Europe_LNBA ●
Europe_EN ● Armenia_EBA ● Steppe_MLBA ●
WHG ● Europe_LNBA ● Levant_N ●
Steppe_MLBA ● Steppe_MLBA ● SHG ●
Europe_LNBA ● WHG ● KEB ●
Switzerland_HG ● Armenia_ChL ● Switzerland_HG ●
Iran_recent ● Levant_BA ● Armenia_ChL ●
Armenia_ChL ● Natufian ● Armenia_MLBA ●
Armenia_EBA ●
population
SHG ●
Iran_recent ●
population
population
AG1 Steppe_EMBA ●
SHG ● ●
Armenia_EBA ●
Armenia_MLBA ● Switzerland_HG ●
Natufian ●
AG1 ● Iran_ChL ●
Levant_BA ●
Iberia_BA ● Armenia_MLBA ●
Iran_ChL ●
Steppe_EMBA ● Steppe_EMBA ●
EHG ●
Kostenki14 ● CHG ●
Steppe_Eneolithic ●
Iran_ChL ● Steppe_Eneolithic ●
Steppe_IA ●
EHG ● EHG ●
Iran_LN ●
CHG ● Iran_LN ●
CHG ●
Steppe_Eneolithic ● IAM ●
Kostenki14 ●
Iran_LN ● Steppe_IA ●
MA1 ●
Iran_N ● MA1 ●
Iran_N ●
Steppe_IA ● Iran_N ●
AG1 ●
Iran_HotuIIIb ● Kostenki14 ●
Anzick ●
MA1 ● Iran_HotuIIIb ●
Kennewick ●
Kennewick ● Anzick ●
Iran_HotuIIIb ●
Anzick ● Kennewick ●
Ust_Ishim ●
Ust_Ishim ● Ust_Ishim ● IAM ●
Mota ● Mota ● Mota ●
MezE ● MezE ● MezE ●
Altai ● Altai ● Altai ●
Denisova ● Denisova ● Denisova ●
0.05 0.10 0.15 0.20 0.1 0.2 0.1 0.2 0.3

f3(aDNA,population;Ju_hoan_North) f3(aDNA,population;Ju_hoan_North) f3(aDNA,population;Ju_hoan_North)
D KEB Tajik 10.73

Tajik ● BedouinB 10.66
BedouinB ● Turkmen 9.04
Turkmen ● Italian_South 7.82
Italian_South ● Basque 7.78
Basque ● Iranian 6.60
Iranian ● Iranian_Bandari 5.62
Iranian_Bandari ● Assyrian 5.47
Assyrian ● Spanish_North 4.24
Spanish_North ● Druze 4.42
Druze ●
Saudi 2.97
Saudi ●
Turkish 3.47
Turkish ●
Sardinian 3.00
Sardinian ●
Greek 2.82
Greek ●
Cypriot 1.92
Cypriot ●
Italian_North 2.08
Italian_North ●
Lebanese 1.36
population
Lebanese ●
Maltese 0.93
Maltese ●
Lebanese_Christian 0.80
Lebanese_Christian ●
Spanish 0.58
Spanish ●
Syrian 0.27
Syrian ●
Sicilian 0.22
Sicilian ●
Palestinian 0.12
Palestinian ●
Jordanian −0.51
Jordanian ●
Lebanese_Muslim −0.71
Lebanese_Muslim ●
Algerian −1.10
Algerian ●
Yemeni ●
Yemeni −1.41
BedouinA ● BedouinA −1.99
Egyptian ● Egyptian −4.73

Mozabite ● Mozabite −6.16
Canary_Islander ● Canary_Islander −3.34
Libyan ● Libyan −5.70
Tunisian ● Tunisian −9.12
Saharawi ● Saharawi −8.73
Moroccan ● Moroccan −11.78
KEB ● KEB −2.22
−0.03 −0.02 −0.01 0.00 0.01 0.02 −15 −10 −5 0 5 10

f3(IAM,population;Iberia_EN) Z−score
323

Neolithization of North Africa Involved The Migration of 2 People From Both The Levant and Europe

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Neolithization of North Africa Involved The Migration of 2 People From Both The Levant and Europe

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bioRxiv preprint first posted online Sep. 21, 2017; doi: http://dx.doi.org/10.1101/191569.

The copyright holder for this preprint (which was

1 Neolithization of North Africa involved the migration of

3 Rosa Fregel1*, Fernando L. Méndez1, Youssef Bokbot2, Dimas Martín-Socas3, María D.

64 We sequenced 39 Illumina pair-end libraries from 28 individuals, and selected best

74 Mitochondrial DNA and Y-chromosome haplogroups obtained for IAM (Moroccan

87 West Eurasian populations can be modelled as admixture of four different ancestral

115 [Figure 2 here]

158 [Figure 3 here]

255 11 Schuenemann, V. J. et al. Ancient Egyptian mummy genomes suggest an increase

314 material culture.

Aegean_N Europe_EN Iran_recent SHG ● This_study: Switzerland_HG

319 Neolithic samples (K=8).

HUMAN ORIGINS LSQPROJECT 455,884 SNPs

Anatolia_N_H ● Iran_LN Switzerland_HG RISE471

Anatolia_N_K Iran_N WHG RISE349

● Armenia_MLBA Ireland_N ● IAM Modern samples RISE484

CHG ● Levant_BA ● KEB Canary_Islands Sardinia RISE431

● Europe_LNBA SHG North_Africa RISE210

−0.05 0.00 0.05 TOR

Natufian ● Anatolia_ChL ● Aegean_N ●

Levant_N ● Europe_MNChL ● Iberia_MNChL ●

Anatolia_ChL ● Europe_EN ● Europe_MNChL ●

Levant_BA ● Iberia_MNChL ● Europe_EN ●

Aegean_N ● Anatolia_N ● Anatolia_N ●

Europe_MNChL ● Aegean_N ● Iberia_BA ●

Iberia_EN ● Levant_N ● WHG ●

Anatolia_N ● Iberia_BA ● Anatolia_ChL ●

Iberia_MNChL ● Iran_recent ● Europe_LNBA ●

Europe_EN ● Armenia_EBA ● Steppe_MLBA ●

WHG ● Europe_LNBA ● Levant_N ●

Steppe_MLBA ● Steppe_MLBA ● SHG ●

Europe_LNBA ● WHG ● KEB ●

Switzerland_HG ● Armenia_ChL ● Switzerland_HG ●

Iran_recent ● Levant_BA ● Armenia_ChL ●

Armenia_ChL ● Natufian ● Armenia_MLBA ●

Altai ● Altai ● Altai ●

Denisova ● Denisova ● Denisova ●

0.05 0.10 0.15 0.20 0.1 0.2 0.1 0.2 0.3

D KEB Tajik 10.73

BedouinA ● BedouinA −1.99

Egyptian ● Egyptian −4.73

−0.03 −0.02 −0.01 0.00 0.01 0.02 −15 −10 −5 0 5 10

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