North Africa9s geographic location, centred betweenthe vast Saharan desert, the fertile Near East and Mediterranean Europe, has resulted in a complex human history in the area7,8. The fossil record suggests long-term hominid and human presence9, although continuity over the past 100,000)years cannot be deduced due to the fragmented nature of therecord.IntheLatePleistocene,15,000)yearsago,theremainsof foragers excavated in Morocco show a distinct genetic make-up intermediate between contemporary Levantine foragers and sub-Saharan African populations 10. Current-day North Africans are largely related toEurasian populations, which was probably caused by 8back-to- Africa9 migration7s.

Both archaeological records and archaeogenomic data show that Neolithic farmers (genetically distinct from European foragers) dispersed from the northern Levant and Anatolia to theMediterranean islands, Italian peninsula and Iberia 11318. Mediterranean coastal routes have long been recognized in the archaeological record as an important part of the Neolithic expansion in Europe. In the western Mediterranean, Impressed Ware technology4and further the Cardial Horizon4spread along the European mainland coast and islands to re ach the Iberian peninsula, where both phenomena are present at 7,55 0)calibrated years before the present)(calb)p) (refs.19,20).

Whereas some studies support a simultaneous appeara nce of the Neolithic in northwestern Africa (Eastern Rif, IfrOiudadane site) and Iberia around 7,550)cal)bp (ref.21), the earliest evidence for pottery, domestic cereals and husbandry is found in northern Morocco approximately two centuries later at Kaf Taht el-Ghar (KTG) around 7,350)cal)bp(refs.2,3,22,23). Although Early Neolithic material culture and the first domestic mammals and pulses suggest aconnection to Iberia133, the extent and legacy of these connections remainunclear.

However, the first genomic analysis of Early Neolihtic farmers from northwestern Africa (from the site Ifri n9Amr o9Msosua (IAM) in central Morocco) shows no traces of admixture with European Neolithic farmers. Instead, it shows long-term population continuity since the Upper Palaeolithic in the region 6. This result aligns with the hypothesis that the Neolithic transition in northwestern Africa was initiated by local Epipalaeolithic communities adopting technolo gical innovations4,5, such as those found at IAM: impressed Cardial-like ceramics, similar to those present throughout the western Mediterranean Neo lithic Europe, and domestic cereals (for example, a grain ofHordeum vulgaredatedaround7,050)calb)p)2.ThispatternimpliesaNeolithization process that contrasts markedly with that of Europe, where it has been established that agriculture was introduced by the west- and northward demic diffusion of Anatolian early farme1r1s,12. The local development, or acculturation, of the North African Neolithic isfurther supported by signs of increasingly sedentary Epipalaeolithic groups developing strategies for resource management, such as the exploitation of Contamination estimates were generally low for boththe nuclear wild plants and pottery 1,4,24326. Rapid climatic changes favoured mobile genome and mitochondria except for individual skh003, which showed herding27 and, whereas it has been hypothesized that cattle were inde- 10316% nuclear contamination (Table 1). To assess the relationship pendently domesticated in the Sahara 28, radiocarbon data suggest a of the ancient northwestern African individuals to other ancient and gradual introduction of pastoralism in the Sahara in a southwestwards present-day West Eurasian and African populations, we co-analysed direction 7,00036,000)cal)bp, possibly from the Near East29,30. our data with relevant ancient (Supplementary Data  2) and current-day

Whereas palaeogenomic studies on the European Medit erranean groups from Africa, the Middle East and Europe34. Neolithic transition are abundant15,31333, North Africa has been the focus of only a single study that generated human geneticdata from one Early and one Late Neolithic site6, leaving substantial gaps in the chronology Eight thousand years of population continuity of events. It is evident that the site of IAM showsa Neolithic lifestyle From the Upper Palaeolithic people of Taforalt (TAF) via the Epipalaeo and an absence of European Neolithic ancestry, but whether this was an lithic at OUB to the Early Neolithic at IAM, we observe the persistence independent development or the inspiration came from other groups in of the unique genetic make-up that existed in northwestern African northwestern Africa or across the Mediterranean Searemains unclear. inhabitants 15,000)years ago (Fig. 1c,d and Supplementary Fig. 5), Hence, the timeline and processes involved in the N eolithization of the and possibly even further back in time. The Epipalaeolithic individual region, the nature and dynamics of different econo mies in North Africa oub002, dating to 7,66037,506)cal)bp, is genetically very similar to and the role they may have played in the broader European Neolithic individuals from TAF ( 15,086314,046 )calb)p)35 and Early Neolithic indiremain understudied and controversial. viduals from IAM ( 7,31636,679 )calb)p; Fig. 1)6,36. The genome of Oub002

In this study we investigate a time series of humanremains from four demonstrates a marked population continuity in nort hwest Africa archaeological sites spanning the Epipalaeolithic to Middle Neolithic with no substantial gene flow across the Mediterranean Sea for at least in current-day Morocco: the Epipalaeolithic site of Ifri Ouberrid (OUB), 7,000)years across the Epipalaeolithic (Fig. 1c,d), linking the Maghrebi the Early Neolithic sites of IAM and KTG and the Middle Neolithic cem- genetic ancestry found in the Upper Palaeolithic to the Early Neolithic etery of Skhirat-Rouazi (SKH), co-analysed with previously published individuals at IAM. genetic data from that region6,10. By sequencing the genomes of nine The Maghrebi lineage shows outstandingly low genetic diversity6,10 individuals excavated from these four archaeologicalsites, we can (Fig. 2b and Supplementary Fig. 9) and long and frequent runs of demonstrate that the Neolithic transition in northwestern Africa was homozygosity (RoH) (Fig. 2a), probably as a consequence of long-lasting ignited by migration of Neolithic farmers from Medtierranean Europe. isolation. By investigation of the 45.8-fold genomeof oub002 we show

We generated genomic sequence data from nine ancient individu- that ancient northwestern Africans went through a severe populaals from modern-day Morocco (Table1 ), ranging in genome coverage tion bottleneck. Until some 70,000360,000)years agothe effective from 45.75- to 0.017-fold, including five individulas with more than population size ( Ne) changes of oub002 follow a pattern similar to that onefold coverage and three with more than ninefold. Chronologically of Eurasian populations with a relatively small effective population the data span more than 1,000)years, covering the Late Epipaleolithic size reached 50,000)years ago (Fig.2 c), which is consistent with the (n)=)1), Early Neolithic n()=)5) and Middle Neolithic n()=)3). Two Early Neo- Maghrebi lineage being related to the populations that migrated out lithic sites were studied4KTG ( n)=)4) and IAM4where we co-analysed of Africa. Interestingly, modern-day Eurasians and North Africans, as the newly generated genomic data of one individual and those previ- well as Neolithic Eurasians effective population size remained at around ously reported 6 (Fig. 1a,b). DNA libraries were generated from DNA 5,000 until about 30,000)years ago but the effectiev population size of extracts obtained from bones and teeth and subsequently shotgun the Maghrebi lineage continues to decrease and reached its lowest point sequenced on an Illumina platform. All libraries presented the degra- (Ne)j)1,400) between 50,000 and 27,000)years ago during the peak of dation patterns expected from ancient DNA, including short fragment the Last Glaciation. Remarkably similar patterns are observed for the sizes and cytosine deamination at read ends (Supple mentary Fig. 1). Mesolithic western hunter-gatherers (WHG) of Europe(represented

SKH

KEB d

Sub-Saharan

Africa by Loschbour in Fig. 2c), for which low diversity measures have been attributed to high levels of background relatedness and autozygosity due to small population size 37.

At the site of IAM, a multitude of artefacts representing the Neolithic package have been identified. However, it has been shown that the people living at IAM show autochthonous Maghrebi an cestry6 and were the descendants of earlier (Upper Palaeolithic and Epipaleolithic) northwestern African groups (Fig. 1c,d). These two observations sup port the view that the first stage of the Neolithic transition in Morocco was driven by local populations adopting technologi cal innovations based on contacts across the Mediterranean2.

The Early Neolithic site of KTG, located on the North African Mediterranean coast near the Gibraltar strait (Fig. 1a), predates and partly overlaps in time with IAM 2 (Table 1). At KTG a full Neolithic assemblage is found, including a diversity of cultivated cereals, domestic mammals and cardial ceramics38,39. In contrast to the people at IAM, those at KTG are genetically similar to European Early Ne olithic populations (Figs. 1c,d and 3a). Interestingly, all four KTG individuals show admixture (15.4327.4%) with local North African groups (Fig.  1d), consistent with significantly positive values for the f4 test of admixture (KTG, Each projected ancient individual is represented by a coloured symb ol. W. Eur., West European; hist., historical. d, Estimated ancestry proportions for relevant African, Middle Eastern and European (Eur.) modern- day and ancient individuals (assuming five ancestry components; additional results are presen ted in Supplementary Fig. 4). Pre-Neolithic and Neolithic northwest ern African populations/individuals are highlighted by the same symbols used in a and c.

Mediterranean EN; TAF, Mbuti) (Supplementary Data 7). Furthermore we identify a small proportion of WHG ancestry in KTG (Fig.  1d), consistent with the observation of Early Neolithic Europeans carrying WHG ancestry14,15,31,33,40. A population history model for the KTG people with 72)±)4.4% Anatolian Neolithic ancestry, 10)±).26% WHG ancestry and 18)±)3.3% Maghrebi ancestry is consistent with the data (qpAdm, P)=)0.193). Taken together, these results suggest aEuropean Neo lithic origin of KTG farmers whose ancestors dispersed from Anatolia throughout Europe, admixing with European hunter-ga therers on their path to southwestern Europe 33,40 before crossing the Mediterranean to North Africa. The presence of European hunter-ga therer ancestry excludes the possibility that Early Neolithic migrants exclusively followed North African Mediterranean shores from Anatolia or the Levant.

Iberian Early Neolithic (both as a whole and region ally) was found to be the best source population for the European a ncestry in KTG, followed by Sicily Stentinello Early Neolithic (Supplementary Data 9).

This is consistent with low levels of genetic differentiation in Cardial Ware-associated groups along the European shores of the Mediterranean Sea41, confirmed by direct radiocarbon dates showing tha t Impressed Ware farmers expanded rapidly across the western Mediterranean3,19,42.

It has been debated whether European farmers crosse d from Iberia to Morocco2,3 or whether earlier crossings of the Mediterranean ) b k ( s tn400,000 e m g e s e t go300,000 y z o m o h f tho200,000 g n e lf o um100,000 S 0

0 500,000 e z i s n o it lau 50,000 p o p e v it ffce 5,000 E b would have happened, through the Sicilian3Tunisian Strait followed by a Maghrebi route of expansion 4,43. Direct comparisons of Early Neolithic farmers from Sicily and Iberia as ancestors of KTG farmers provide stronger evidence for an Iberian Neolithic origin (Supplementary Data 9 and Supplementary Information 8), but we cannot exclude some con tribution from Sicilian farmers. Genetic data are consistent with the most parsimonious explanation for archaeological ev idence on the Neolithic transition in northwestern Africa: the crossing from southern Iberia by Iberian Neolithic farmers 2,23. The close geographical proximity between southern Iberia and the Tangitana Peninsula adds strength to this observation whereas the lack of reliable archaeological evidence of early domestic elements in relevant sites along the eastern Maghreb and Tunis, including sites with pottery and obsidian from Pantelleria Island, undermines the Sicily3Tunis crossing hypoth esis3. Interestingly, gene flow from North Africa was found only in Mediterranean European individuals much later, from around 4,500)years ago31,44.

Different individuals from KTG date to slightly different time periods.

We find a twofold larger proportion of Maghrebi anc estry in earlier KTG individuals (roughly 25%, ktg001 and ktg005, ap proximately 7,42937,267)cal)bp) than in later ones (about 13%, ktg004 and ktg006, around 7,24736,945)cal)bp) (Fig. 1d). This coincides with an increase in European Neolithic ancestry, shown by the signif icantly negative result for f4(KTG earlier, KTG later, Iberia Early Neolithic, Mb uti; z-score)=)25.01). Approximately one quarter of Maghrebi ancestry in early KTG suggests that they represent at least the second generation of interbreeding between the groups. We estimated t he time of admixture using two approaches based on ancestry covaria nce patterns and linkage disequilibrium decay, using Iberia or Sicily Early Neolithic and TAF as admixture sources. Both methods date the contact within the last six to 13)generations (Supplementary Information 8), suggesting that mixing between groups occurred for a few hundr ed years, which is consistent with analysis of pottery style that poin ts to the first contact at 7,50037,400)cal)bp (ref. 23).

Kaf Taht el-Ghar farmers had slightly lower genetic diversity levels and greater RoH than most Early Neolithic European populations (Fig. 2a,b and Supplementary Fig. 9). The Maghrebi ancestry c arried by KTG people shows markedly lower diversity and mo re extensive RoH, and is probably the cause of the reduction in overall diversity. iltano ilitch 0.025 anA eoN

0

Archaeological evidence suggests that Early Neolithic farming was If a European Neolithic (for example, from Iberia) additional source restricted to enclaves in westernmost Maghreb, poss ibly due to climatic population is added, the model is rejected. constraints to the south4,22. This could have limited the potential of Because this Neolithic Levantine ancestry has not been observed on these groups to recover from an initial founder effect. the European side of the Mediterranean during the N eolithic, it proba

Overall, the genetic patterns of local interaction between different bly represents an independent expansion of people f rom the Levant into groups in northwestern Africa are comparable to tho se found in Europe: North Africa. Migrations from the Levant to eastern Africa have been farmers assimilated local foragers9 ancestry in a unidirectional admix- identified for Neolithic pastoralist individuals around 4,000)years ago, ture process. Cases of hunter-gatherer communities adopting certain who are presumed descendants of unsampled northeast ern African elements of the Neolithic have been described in Eu rope 11,14,45. However, populations associated with the spread of Saharan p astoralism46. Both the northwestern Africa Neolithization process involved the notable in SKH and eastern African Neolithic pastoralists, Levantine ancestry is survival of genetically unadmixed local populations (represented by admixed with local ancestries (Fig. 1d, Supplementary Information 8 IAM), despite coexisting for at least 300)years with foreign farming and Supplementary Data 12). The arrival of this Lev antine ancestry communities (KTG), and still adopted several elemen ts of the Neolithic coincides with the appearance of a new ceramic tradition in northern ways of living from them. Whereas the archaeological findings in IAM Morocco, often characterized by cord-impressed motifs (8roulette9 or and KTG point to the exchange of ideas between groups and support wavy line), like the grave goods at Skhirat belonging to Ashakar Ware an acculturation process of foraging communities 1,4, our genetic data pottery 47,48. In parallel, cattle pastoralism was expanding in the current show that the exchange of genes was unidirectional. Sahara territory30,47 and Afro-Asiatic language groups spread through out the whole of North Africa22.

Our analyses show that the Levantine-associated component also Influx of Levantine ancestry remains in the Maghreb during the Late Neolithic in individuals from Another, distinct, ancestry was introduced to northwestern Africa dur- Kehf el Baroud (KEB) and in the Guanches of the Canary Islands (around ing the Middle Neolithic. All individuals from SKH show large propor - 1,000)cal)bp; Fig. 1c,d)6,49. Individuals from these sites are shifted tions of a genetic component maximized in individua ls from Neolithic towards ancient Levantine populations on the princi pal component and Chalcolithic Levant, Ptolemaic Egypt and modern -day Near Eastern analysis (PCA) space (Fig. 1c). This highlights the complex demographic populations (Fig.  1d). The ancestry in SKH can be modelled as a two-way processes that took place in northwestern Africa, i n contrast to the admixture between Levant Neolithic populations (rou ghly 76.4)±)4.0%) gradual increase in hunter-gatherer ancestry described in Middle and and local northwestern Africans (represented by TAF ; 23.6)±)4.0%). Late Neolithic Europe 32,33,40.

The complex population structure in modern-day nort hwestern Africa has been linked to various historical events, such as the Arab expansion7,8. However, our detailed chronology and high-resolution genomic data provide a new understanding of these prehistor ic processes in the Maghreb and unveil a rich and diversified genetic substrate with Neolithic origin. First, human populations in north western Africa show genetic continuity and isolation since the Upper Palaeolithic, from at least 15,000 to around 7,500)years ago, when this period of isolation was interrupted by the migration of European Early Neolithic groups introducing farming practices. Hence, despite a relatively small geographic distance between southern Iberia and northw estern Africa (the distance today is only 13)km across the Gibraltar straight), and the fact that both regions were populated by foragers for many millennia prior to the Neolithic, gene flow across the Medite rranean Sea was not established until the Early Neolithic. The newcomers brought new ways of life, farming practices, domestication and potte ry traditions that were subsequently adopted by local populations. Our results show that the Neolithization process in northwestern Afr ica was ignited by migrant Neolithic Europeans, but that local grou ps (at least the individuals analysed at IAM) adopted some of these practices without mixing with the newcomers. Two genetically distinct groups coexisted in close proximity in the region. Interestingly, cu ltural and technological knowledge appear to have been transferred mainl y from European Neolithic farmers to local groups (for example, at IAM) whereas genetic ancestry flowed only from local groups to the incoming farmers, such as the population of KTG. Furthermore, in the Middle Neolithic a new ancestry with an eastern origin is detected in northwestern Africa. This ancestry indicates new migrating groups, potentially associated with Sahara pastoralists, which admixed with local groups (Fig.  3c).

The various waves of migration and admixture into northwestern Africa during the Neolithic possibly resulted in a heterogeneous eco nomic and cultural landscape in that region4a mosaic of groups that included incoming farmers from Iberia, foragers adopting farming practices and eastern pastoralists admixing with lo cal people. Most of these groups showed reduced effective population size and lower diversity than the contemporary populations in Euro pe (Fig. 2), suggesting that population sizes remained modest throughout the Neolithic. These patterns were probably caused by periods of i solation, which may have contributed to the distinct genetic ancestry seen in the Maghreb today. A recent study from the Iron Age suggests that northwestern Africa remained home to a diverse set of groups thr oughout prehistory50, making this part of the world one of the most unique places to have been studied with the archaeogenomic toolkit.

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Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Detailed descriptions for each section can be found in Supplementary Information.

The sequence data generated for this study are available from the European Nucleotide Archive under accession no. PRJEB59008.

Funding Open access funding provided by Uppsala University.

Competing interests The authors declare no competing interests.

Additional information Supplementary information The online version contains supplementary material available at https://doi.org/10.1038/s41586-023-06166-6.

Correspondence and requests for materials should be addressed to Cristina Valdiosera or Mattias Jakobsson.

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Data collection Data analysis

Sequence demultiplexing: MergeReadsFastQ_cc.py, Adapter Removal v2.1.7.

Simons Genome Diversity Project datasets (https://www.simonsfoundation.org/simons-genome-diversity-project/) available on UPPMAX. Comparative ancient individuals' genomic data downloaded from the European Nucleotide Archive (ENA), under the accession numbers provided in the references listed in Supplementary Data File 2.

A full description of all software and respective packages used for data analysis can be found in the Supplementary Information document and are publicly available. For genomic reads mapping: Burrows-Wheller Aligner (BWA, v. 0.7.13); genomic libraries merging: samtools v. 1.5. mtDNA contamination estimates: contamMix (1.0-10); X-chromosome contamination estimates: ANGSD v. 0.902; autosomal contamination estimates: verifyBamID v.1.1.2. Mt haplogroup assignement: Haplogrep v. 2.1.16 and PhyloTree mtDNA tree Build 17 (18 Feb 2016); Y chromosome haplogroup assignement: ISOGG (10, April 21, 2016) SNPs called using samtools v. 1.5. Pseudohaploid genomic dataset management (including LD pruning and datasets merging): PLINK v. 1.9. Kinship analysis: READ. PCA: smartpca v.10210 (EIGENSOFT package); model-based clustering analysis: ADMIXTURE v. 1.3.0 and PONG v. 1.5. f -statistics: python script POPSTATS (https://github.com/pontussk/ popstats); Admixture modelling: qpAdm (ADMIXTOOLS v. 5.0) via qpAdm_wrapper (https://github.com/pontussk/qpAdm_wrapper); Admixture graphs: ADMIXTOOLS2 findGraphs function. Admixture dating: ALDER v. 1.03 and DATES v. 753. Diploid genotype calling GATK v. 3.5.0. Diploid genomic dataset management (including SNP selection) Vcftools v. 0.1.16 and Plink v. 1.9. Runs of Homozygosity: Plink v. 1.9. Pairwise Sequentially Markovian Coalescent (PSMC) implemented on MSMC v. 0.1.0. Phenotypic variation analysis: ANGSD v. 0.933. Results visualization and plot generation: R v. 3.4.067, ggplot2. Radiocarbon dates calibration: Oxcal v4.4 and IntCal20.

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Sample size Data exclusions

Genomic and radiocarbon data from nine ancient individuals from Morocco were analysed in this study. The sample size was dependent on the availability of human remains dating to the Stone Age from northwestern Africa, with preserved and retrievable ancient DNA sequences. These specimens are very rare, given the poor molecular preservation of human remains from this period in that region. Given the millions of genetic variants analysed for each individual, information about the genetic history can be retrieved.

Reads shorter than 35 base pairs (bp), with more than 10% mismatch from the Reference genome and mapping quality score below 30 were discarded while preparing bamfiles for merged genomic libraries data. For samples not subjected to Uracil-Specific Excision Reagent (USER) treatment, 10 bp at the reads ends were excluded. For samples with partial treatment (comparative dataset) 2 bp were trimmed off of the reads ends. For analyses, minimum mapping and read qualities were set to 30. Pseudohaploid dataset was generated by randomly drawing one read at each SNP site, and that allele assumed to be homozygous. LD pruning for ADMIXTURE resulted in a reduction of the number of analysed SNPs (originally 1,379,466) to 812,092. When pairs of first-degree relatives (of comparative populations) were found, the individual with lower genomic coverage of the pair was excluded from analysis. Diploid dataset was generated with samples with a minimum of 9x genomic coverage. For MSMC's implementation of PSMC', minimum mapping quality of 30 and minimum genotype quality of 50 were used. For phenotypic analysis, genotype likelihoods were computed based on minimum mapping and read quality of 30 and read depth of 5. Several DNA extracts and multiple genomic libraries were generated for each sample (as reported in Table S1), and several rounds of sequencing were performed for each library (as reported in Supplementary Data File 15) as replication. Data was merged for downstream analysis after confirming similar results, as expected of different replicates of the same individual's genomic data, such as contamination estimates, mitochondrial haplogroup. Thousands to millions of genetic markers were then analysed as an internal replication of the results. Detailed description of the methods used, including samples included in the dataset, software employed and respective parameters is available in the Supplementary Information.

Randomization is not applicable to this study. Samples were grouped according to the archaeological site of origin and radiocarbon date. Groups are validated by verifying genetic affinities among its several individuals.

Blinding is not applicable to this study. The archaeological context, including site location and estimated date, of each individual analysed is known prior to sampling and analysis, as these are relevant for conceiving the study. Reporting for specific materials, systems and methods We require information from authors about some types of materials, experimental systems and methods used in many studies. Here, indicate whether each material, system or method listed is relevant to your study. If you are not sure if a list item applies to your research, read the appropriate section before selecting a response. Materials & experimental systems n/a Involved in the study

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Dual use research of concern Palaeontology and Archaeology Specimen provenance Specimen deposition Dating methods

Archaeological samples were excavated in Morocco at the archaeological sites of Ifri Ouberrid, Kaf Taht el Ghar, Ifri n’Amr ou Moussa and Skhirat-Rouazi Necropolis. Appropriate permits were obtained to conduct sampling and export archaeological material from the Institut National des Sciences de l´Archèologie et du Patrimoine (INSAP) in Rabat, Morocco.

The Institut National des Sciences de l´Archèologie et du Patrimoine (INSAP) in Rabat, Morocco is the sole curator of the specimens.

All individuals were directly radiocarbon dated using accelerator mass spectrometry (AMS) at the Tandem Laboratory at Ångström, Uppsala, except for ktg001, which was dated at the Beta Analytic Carbon dating laboratory and iam004, which date was obtained from the literature. Radiocarbon calibration was performed using OxCal v.4.4 and the IntCal20 dataset.

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Permits for sampling and analyses of the archaeological material were obtained from the appropriate institutions.

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The sex of the individuals for which archaeological remains were analysed was determined based on the ratio of coverage of the X chromosome and Y chromosome relative to the autosomes.