In this study, we seek to understand and to correlate the genetic patterns observed in the population of the island of Ibiza in the Western Mediterranean basin with past events. Genome-wide genotypes of 189 samples representing 13 of 17 regions in Spain have been analyzed, in addition to 105 samples from the Levant, 157 samples from North Africa, and one ancient sample from the Phoenician Cas Molí site in Ibiza. Before the Catalans conquered the island in 1235 CE, Ibiza (Eivissa) had already been influenced by several cultures, starting with the Phoenicians, then the Carthaginians, followed by the Umayyads. The impact of these various cultures on the genetic structure of the islanders is still unexplored. Our results show a clear distinction between Ibiza and the rest of Spain. To investigate whether this was due to the Phoenician colonization or to more recent events, we compared the genomes of current Ibizans to that of an ancient Phoenician sample from Ibiza and to both modern Levantine and North African genomes. We did not identify any trace of Phoenician ancestry in the current Ibizans. Interestingly, the analysis of runs of homozygosity and changes in the effective population size through time support the idea that drift has shaped the genetic structure of current Ibizans. In addition to the small carrying capacity of the island, Ibiza experienced a series of dramatic demographic changes due to several instances of famine, war, malaria and plague that could have significantly contributed to its current genetic differentiation.

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  1. 1.

    Somers M, Olde Loohuis LM, Aukes MF, et al. A genetic population isolate in the Netherlands showing extensive haplotype sharing and long regions of homozygosity. Genes. 2017;8:1–14.

  2. 2.

    Braudel F. Une Leçon d’histoire. 1985. Paris (France): Flammarion.

  3. 3.

    Institut d’Estadística de les Illes Balears (IBESTAT). IBESTAT (2017). Cifras de población. https://ibestat.caib.es/ibestat/estadistiques/poblacio/padro/2acef6cf-175a-4826-b71e-8302b13c1262.

  4. 4.

    Ribas BC Eivissa-Prehistòria. Enciclopèdia d’Eivissa i Formentera. 2006. http://www.eeif.es/veus/Eivissa-historia-prehistoria/.

  5. 5.

    Picornell A, Ana M, Castro JA, Ramon MM, Arya R, Crawfor MH. Genetic variation in the population of ibiza (spain): genetic structure, geography, and language. Hum Biol. 1996;68:899–913.

  6. 6.

    Armstrong S. The White Island. London (UK): Transworld books. 2004.

  7. 7.

    Gurrea Barricarte R, Martín Parrilla Á. Eivissa història època califal. Enciclopèdia d’Eivissa i Formentera. 2015. http://www.eeif.es/veus/Eivissa-historia-epoca-andalusina/.

  8. 8.

    Picornell A, Gómez-Barbeito L, Tomàs C, Castro JA, Ramon MM. Mitochondrial DNA HVRI variation in Balearic populations. Am J Phys Anthropol. 2005;128:119–30.

  9. 9.

    Tomàs C, Jiménez G, Picornell A, Castro JA, Ramon MM. Differential maternal and paternal contributions to the genetic pool of Ibiza Island, Balearic Archipelago. Am J Phys Anthropol. 2006;129:268–78.

  10. 10.

    Solé-Morata N, Bertranpetit J, Comas D, Calafell F. Y-chromosome diversity in Catalan suRNAme samples: Insights into suRNAme origin and frequency. Eur J Hum Genet. 2015;23:1549–57.

  11. 11.

    Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y. Ancient admixture in human history. Genetics. 2012;192:1065–93.

  12. 12.

    Lazaridis I, Patterson N, Mittnik A, et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature. 2014;513:409–13.

  13. 13.

    Zalloua P, Collins CJ, Gosling A, et al. Ancient DNA of Phoenician remains indicates discontinuity in the settlement history of Ibiza. Sci Rep. 2018;8:17567.

  14. 14.

    Arauna LR, Mendoza-Revilla J, Mas-Sandoval A, et al. Recent historical migrations have shaped the gene pool of Arabs and Berbers in North Africa. Mol Biol Evol. 2017;34:318–29.

  15. 15.

    Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81:559–75.

  16. 16.

    Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS Genet. 2006;2:2074–93.

  17. 17.

    Weir BS, Clark Cockerham C. Estimating F-statistics for the analysis of population structure. Evol Vol38. 1984;38:1358–70.

  18. 18.

    Pembleton LW, Cogan NOI, Forster JW. StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations. Mol Ecol Resour. 2013;13:946–52.

  19. 19.

    RStudio Team. RStudio Team. RStudio: integrated development for R. 2015. http://www.rstudio.com/.

  20. 20.

    R Core Team. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing. 2018.

  21. 21.

    Dray S, Dufour A-B. The ade4 Package: Implementing the duality diagram for ecologists. J Stat Softw. 2007;22. https://doi.org/10.18637/jss.v022.i04.

  22. 22.

    Wickham H. Reshaping data with the /pkgreshape package. J Stat Softw. 2007;21:1–20.

  23. 23.

    Wickham H. ggplot2: elegant graphics for data analysis. Media. 2009;35:211.

  24. 24.

    Alexander DH, Novembre J. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19:1655–64.

  25. 25.

    Jakobsson M, Rosenberg NA. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics. 2007;23:1801–6.

  26. 26.

    Rosenberg NA. DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes. 2004;4:137–8.

  27. 27.

    Pickrell JK, Pritchard JK. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 2012;8. https://doi.org/10.1371/journal.pgen.1002967.

  28. 28.

    McQuillan R, Leutenegger AL, Abdel-Rahman R, et al. Runs of homozygosity in european populations. Am J Hum Genet. 2008;83:359–72.

  29. 29.

    Browning BL, Browning SR. Detecting identity by descent and estimating genotype error rates in sequence data. Am J Hum Genet. 2013;93:840–51.

  30. 30.

    Browning SR, Browning BL. Accurate non-parametric estimation of recent effective population size from segments of identity by descent. Am J Hum Genet. 2015;97:404–18.

  31. 31.

    McVean G. A genealogical interpretation of principal components analysis. PLoS Genet. 2009;5. https://doi.org/10.1371/journal.pgen.1000686.

  32. 32.

    Kirin M, McQuillan R, Franklin CS, Campbell H, McKeigue PM, Wilson JF. Genomic runs of homozygosity record population history and consanguinity. PLoS ONE. 2010;5:e13996.

  33. 33.

    Ceballos FC, Joshi PK, Clark DW, Ramsay M, Wilson JF. Runs of homozygosity: Windows into population history and trait architecture. Nat Rev Genet. 2018;19:220–34.

  34. 34.

    Rodríguez-Ezpeleta N, Álvarez-Busto J, Imaz L, et al. High-density SNP genotyping detects homogeneity of Spanish and French Basques, and confirms their genomic distinctiveness from other European populations. Hum Genet. 2010;128:113–7.

  35. 35.

    Comas D, Mateu E, Calafell F, et al. HLA class I and class II DNA typing and the origin of Basques. Tissue Antigens. 1998;51:30–40.

  36. 36.

    Calafell F, Bertranpetit J. Principal component analysis of gene frequencies and the origin of Basques. Am J Phys Anthr. 1994;93:201–15.

  37. 37.

    Fiorito G, Di Gaetano C, Guarrera S, et al. The Italian genome reflects the history of Europe and the Mediterranean basin. Eur J Hum Genet. 2016;24:1056–62.

  38. 38.

    Ayub Q, Mezzavilla M, Pagani L, et al. The kalash genetic isolate: Ancient divergence, drift, and selection. Am J Hum Genet. 2015;96:775–83.

  39. 39.

    Di Gaetano C, Fiorito G, Ortu MF, et al. Sardinians genetic background explained by runs of homozygosity and genomic regions under positive selection. PLoS One. 2014;9:1–8.

  40. 40.

    Listman JB, Malison RT, Sughondhabirom A, et al. Demographic changes and marker properties affect detection of human population differentiation. BMC Genet. 2007;8:21.

  41. 41.

    Adams SM, Bosch E, Balaresque PL, et al. The genetic legacy of religious diversity and intolerance: paternal lineages of christians, jews, and muslims in the iberian peninsula. Am J Hum Genet. 2008;83:725–36.

  42. 42.

    Claudio Alarco von Perfall. Sobre los matrimonios consanguíneos en Ibiza. Eivissa, num8. 1976;16:328–31.

  43. 43.

    Gibson J, Morton NE, Collins A. Extended tracts of homozygosity in outbred human populations. Hum Mol Genet. 2006;15:789–95.

  44. 44.

    Christofidou P, Nelson CP, Nikpay M, et al. Runs of homozygosity: association with coronary artery disease and gene expression in monocytes and macrophages. Am J Hum Genet. 2015;97:228–37.

  45. 45.

    Pemberton TJ, Absher D, Feldman MW, Myers RM, Rosenberg NA, Li JZ. Genomic patterns of homozygosity in worldwide human populations. Am J Hum Genet. 2012;91:275–92.

  46. 46.

    Ceballos FC. La genética de los matrimonios consanguíneos. Dendra Médica Rev Humanid. 2011;10:160–76.

  47. 47.

    Jalkh N, Sahbatou M, Chouery E, Megarbane A, Leutenegger AL, Serre JL. Genome-wide inbreeding estimation within Lebanese communities using SNP arrays. Eur J Hum Genet. 2015;23:1364–9.

  48. 48.

    Rozenberg D. Endogàmia i problemes d’identificació a Eivissa: l’exemple de Sant Miquel. Eivissa, num. 1981;12:515–8.

  49. 49.

    Kohn GC. Encyclopedia of plague and pestilence: from ancient times to the present. New York (USA): Checkmark Books. 1995.

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We thank Maria Ferrer (IBE, CSIC-UPF) for her invaluable help in finding the Ibiza sample donors, and Inés Quintela (CEGEN - USC) for her assistance in genotyping the samples. Of course, this work would not have been possible without the kind collaboration of all the sample donors. Funding was provided by the Agencia Estatal de Investigación and Fondo Europeo de Desarollo Regional (FEDER) (grant CGL2016-75389-P), Agència de Gestió d’Ajuts Universitaris i de la Recerca (Generalitat de Catalunya) grant 2014 SGR 866, and “Unidad de Excelencia María de Maeztu”, funded by the MINECO (ref: MDM-2014-0370). SAB was supported by the Agencia Estatal de Investigación FPI grant BES-2014-069224.

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  1. Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain

    • Simone Andrea Biagini
    • , Neus Solé-Morata
    • , David Comas
    •  & Francesc Calafell
  2. Department of Anatomy, University of Otago, Dunedin, New Zealand

    • Elizabeth Matisoo-Smith
  3. School of Medicine, The Lebanese American University, Chouran, Beirut, Lebanon

    • Pierre Zalloua


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Correspondence to Francesc Calafell.

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