Annals of Forest Science

, 75:75 | Cite as

Genetic structure and phylogeography of Juniperus phoenicea complex throughout Mediterranean and Macaronesian regions: different stories in one

  • Pedro Sánchez-Gómez
  • Juan F. Jiménez
  • Jose Luis Cánovas
  • Juan Bautista Vera
  • Isabell Hensen
  • Miloud Aouissat
Research Paper


Key message

The genetic structure of Juniperus phoenicea in the Mediterranean Basin is inferred using amplified fragment length polymorphism markers (AFLP) markers. As other Mediterranean conifers, J. phoenicea populations show moderate levels of genetic diversity and interpopulational differentiation. The pattern of distribution of genetic diversity seems highly influenced by the climatic fluctuations which occurred in the Pleistocene.


It has been stated that the genetic structure of Mediterranean conifers is mediated by the historical climatic changes and the geological rearrangements which occurred in the Mediterranean Basin. J. phoenicea provides an excellent example to test how its genetic structure is influenced by these events.


In this work, we study the amount and distribution of genetic diversity of J. phoenicea complex, in order to evaluate its taxonomic status and to reveal underlying phylogeographic patterns.


The molecular diversity was analyzed for 805 individuals from 46 populations throughout its distribution range using AFLP markers. Principal coordinate analysis, analysis of molecular variance (AMOVA), and Bayesian-based analysis were applied to examine the population structure.


AFLP markers revealed moderate levels of intrapopulation genetic diversity, pairwise genetic differentiation, and a clear pattern of isolation by distance. Bayesian analysis of population structure showed five clusters related to the taxonomic status of J. phoenicea and J. turbinata, and a geographic pattern of genetic structure in J. turbinata.


All the analysis separate J. phoenicea from J. turbinata. For J. turbinata, up to four groups can be distinguished from a phylogeographic point of view. The genetic structure of J. turbinata seems highly influenced by climatic and geologic fluctuations occurring since the Oligocene.


AFLP markers Biogeography Cupressaceae Genetic diversity Inter-populational differentiation Taxonomy 



Authors wish to thank to Jaime Güemes, Gianluigi Bachetta, Jorge Balibrea, Laura Aznar, Jesús Muñoz, Mohammad Al-Gharaibeh, and David López for field assistance in collecting samples.


This work has been supported by a Ministry of Economy and Competitiveness CGL2011-30099 project grant to Pedro Sánchez Gómez.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

13595_2018_741_MOESM1_ESM.xls (58 kb)
Table S1 Pairwise genetic differentiation among populations. Upper section, Fst values obtained with AMOVA. Lower section, Fst values obtained with AFLPsurv. (XLS 57 kb)
13595_2018_741_Fig5_ESM.png (1.3 mb)
Fig. S1

Map of sampled populations. Codes of populations are listed in Table 1 (PNG 1.28 mb)

13595_2018_741_MOESM2_ESM.tif (690 kb)
High resolution image (TIF 690 kb)
13595_2018_741_Fig6_ESM.png (1.4 mb)
Fig. S2

Neighbour-joining phenogram based on Nei's unbiased genetic distance for the 46 populations. Bootstrap values (>70%) over loci (based on 1000 replicates) are indicated for each node (PNG 1.39 mb)

13595_2018_741_MOESM3_ESM.tif (536 kb)
High resolution image (TIF 536 kb)


  1. Adams RP (2014) Junipers of the world: the genus Juniperus, 4th edn. Trafford Publishing Co., BloomingtonGoogle Scholar
  2. Adams RP, Schwarzbach AE (2013) Phylogeny of Juniperus using nrDNA and four cpDNA regions. Phytologia 95:179–187Google Scholar
  3. Adams RP, Padney N, Rezzi S, Casanova J (2002) Geographic variation in the random amplified polymorphic DNAs (RAPDs) of Juniperus phoenicea, J. p. var. canariensis, J. p. subsp. eumediterranea and J. p. var turbinata. Biochem Syst Ecol 30:223–229CrossRefGoogle Scholar
  4. Adams RP, Nguyen S, Achak N (2006) Geographic variation in Juniperus phoenicea (Cupressaceae) from the Canary Islands, Morocco and Spain based on RAPDs analysis. Phytologia 88:270–278Google Scholar
  5. Adams RP, Rumeu BR, Nogales M, Fontinha SS (2010) Geographic variation and systematics of Juniperus phoenicea L. from Madeira and the Canary Islands: analyses of SNPs from nrDNA and petN-psbM DNA. Phytologia 92:59–67Google Scholar
  6. Adams RP, Boratyński A, Arista M, Schwarzbach AE, Leschner H, Liber Z, Minissale P, Mataraci T, Manolis A (2013) Analysis of Juniperus phoenicea from throughout its range in the Mediterranean using DNA sequence data from nrDNA and petN-psbM: the case for the recognition of J. turbinata Guss. Phytologia 95:202–209Google Scholar
  7. Arista M, Ortiz PL, Talavera S (1997) Reproductive isolation of two sympatric subspecies of Juniperus phoenicea (Cupressaceae) in southern Spain. Plant Syst Evol 208:225–237CrossRefGoogle Scholar
  8. Blondel J, Aronson J (1999) Biology and wildlife of the Mediterranean region. Oxford University Press, New YorkGoogle Scholar
  9. Boratyński A, Lewandowski A, Boratyńska K, Montserrat JM, Romo A (2009) High level of genetic differentiation of Juniperus phoenicea (Cupressaceae) in the Mediterranean region: geographic implications. Plant Syst Evol 277:163–172CrossRefGoogle Scholar
  10. Browicz K, Zieliński J (1982) Chorology of trees and shrubs in South-West Asia and adjacent regions. Polish Scientific Publishers, Warszawa-PoznanGoogle Scholar
  11. Burban C, Petit RJ (2003) Phylogeography of maritime pine inferred with organelle markers having contrasted inheritance. Mol Ecol 12:1487–1495CrossRefPubMedGoogle Scholar
  12. Charco J (2001) Guía de los árboles y arbustos del norte de África. Agencia Española de Cooperación Internacional, MadridGoogle Scholar
  13. Christensen KI (1997) Juniperus L. In: Strid A, Tan K (eds) Flora hellenica, vol 1. Koeltz Scientific Books, Königstein, pp 10–14Google Scholar
  14. Conord C, Gurevitch J, Fady B (2012) Large-scale longitudinal gradients of genetic diversity: a meta-analysis across six phyla in the Mediterranean basin. Ecol Evol 2:2595–2609. CrossRefGoogle Scholar
  15. Corander J, Marttinen P (2006) Bayesian identification of admixture events using multilocus molecular markers. Mol Ecol 15:2833–2843CrossRefPubMedGoogle Scholar
  16. do Amaral Franco J (1986) Juniperus L. In: Castroviejo S, Laínz M, López González G, Montserrat P, Muñoz Garmendia F, Paiva J, Villar L (eds) Flora iberica, vol 1. Real Jardín Botánico, CSIC, Madrid, pp 181–188Google Scholar
  17. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf material. Phytochem Bull 19:11–15Google Scholar
  18. Dzialuk A, Mazur M, Boratyńska K, Monstserrat JM, Romo A, Boratyński A (2011) Population genetic structure of Juniperus phoenicea (Cupressaceae) in the western Mediterranean Basin: gradient of diversity on a broad geographical scale. Ann For Sci 68:1341–1350CrossRefGoogle Scholar
  19. Earl DA, von Holdt BM (2012) Structure Harvester: a website and program for visualizing Structure output and implementing the Evanno method. Conserv Genet Resour 4:359–361. (available at Scholar
  20. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620. CrossRefPubMedPubMedCentralGoogle Scholar
  21. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perfom population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567CrossRefPubMedGoogle Scholar
  22. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondiral DNA restriction data. Genetics 131:479–491PubMedPubMedCentralGoogle Scholar
  23. Fady B, Conord C (2010) Macroecological patterns of species and genetic diversity in vascular plants of the Mediterranean Basin. Divers Distrib 16:53–64CrossRefGoogle Scholar
  24. Fady-Welterlen B (2005) Is there really more biodiversity in Mediterranean forest ecosystems? Taxon 54:905–910CrossRefGoogle Scholar
  25. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587PubMedPubMedCentralGoogle Scholar
  26. Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7:574–578. CrossRefPubMedPubMedCentralGoogle Scholar
  27. Farjon A (2005) A monograph of Cupressaceae and Sciadopitys. Royal Botanic Gardens, KewGoogle Scholar
  28. Felsenstein J (1989) PHYLIP—phylogeny inference package (version 3.2). Cladistics 5:164–166Google Scholar
  29. Greuter W, Burdet HM, Long G (1984) Med.-Checklist 1. Conservatoire et Jardin Botaniques de la Ville de Genève et Med.-Checklist Trust of OPTIMA, GenèveGoogle Scholar
  30. Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:1–9Google Scholar
  31. Hamrick JL, Godt MJW, Sherman-Broyles SL (1992) Factors influencing levels of genetic diversity in woody plant species. New For 6:95–124CrossRefGoogle Scholar
  32. Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806. CrossRefPubMedGoogle Scholar
  33. Jalas J, Suominen J (eds) (1973) Atlas florae europaeae 2. The Committee for Mapping the Flora of Europe and Societas Biologica Fennica Vanamo, HelsinkiGoogle Scholar
  34. Jiménez JF, Werner O, Sánchez-Gómez P, Fernández S, Guerra J (2003) Genetic variation and migration pathways of Juniperus thurifera L. (Cupressaceae) in the western Mediterranean region. Israel J Plant Sci 51:11–22CrossRefGoogle Scholar
  35. Jiménez JF, Sánchez-Gómez P, Cánovas JL, Hensen I, Aouissat M (2017) Influence of natural habitat fragmentation on the genetic structure of Canarian populations of Juniperus turbinata. Silva Fenn.
  36. Jordano P (1993) Geographic ecology and variation of plant-seed disperser interaction: southern Spanish junipers and frugivorous thrushes. Vegetatio 107/108:85–104Google Scholar
  37. Koopman W (2005) Phylogenetic signal in AFLP data sets. Syst Biol 54:197–217. CrossRefPubMedGoogle Scholar
  38. Korol L, Kara N, Isik K, Schiller G (1997) Differentiation among and within natural and planted Cupressus sempervirens L. eastern Mediterranean populations. Silvae Genet 46:151–155Google Scholar
  39. Krauss SL (2000) Accurate gene diversity estimated from amplified fragment length polymorphism (AFLP) markers. Mol Ecol 9:1241–1245CrossRefPubMedGoogle Scholar
  40. Krutovskii KV, Erofeeva SY, Aagaard JE, Strauss SH (1999) Simulation of effects of dominance on estimates of population genetic diversity and differentiation. J Hered 90:499–502. CrossRefGoogle Scholar
  41. Lagercrantz U, Ryman N (1990) Genetic structure of Norway spruce (Picea abies): concordance of morphological and allozymatic variation. Evolution 44:38–53PubMedGoogle Scholar
  42. Lebreton P, Pérez de Paz PL (2001) Définition du Genévrier de Phénicie (Juniperus aggr. phoenicea), reconsidéré à ses limites biogéographiques: Méditerranée orientale (Crète et Chypre) et Atlantique (Iles Canaries). Bull Mens Soc Linn Lyon 70:73–92. CrossRefGoogle Scholar
  43. Linares JC (2011) Biogeography and evolution of Abies (Pinaceae) in the Mediterranean Basin: the roles of long-term climatic change and glacial refugia. J Biogeogr 38:619–630. CrossRefGoogle Scholar
  44. Lumaret R, Mir C, Michaud H, Raynal V (2002) Phylogeographical variation of chloroplast DNA in holm oak (Quercus ilex). Mol Ecol 11:2327–2336CrossRefPubMedGoogle Scholar
  45. Lynch M, Milligan BG (1994) Analysis of population genetic structure with RAPD markers. Mol Ecol 3:91–99CrossRefPubMedGoogle Scholar
  46. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220PubMedGoogle Scholar
  47. Mao K, Hao G, Liu J, Adams RP, Milne RI (2010) Diversification and biogeography of Juniperus (Cupressaceae): variable diversification rates and multiple intercontinental dispersals. New Phytol 188:254–272. CrossRefPubMedGoogle Scholar
  48. Mazur M, Klajbor K, Kielich M, Sowinska M, Romo A, Montserrat JM, Boratyński A (2010) Intra-specific differentiation of Juniperus phoenicea in the western Mediterranean region revealed in morphological multivariate analysis. Dendrobiology 63:21–31Google Scholar
  49. Mazur M, Minissale P, Sciandrello S, Boratyński A (2016) Morphological and ecological comparison of populations of Juniperus turbinata Guss. and J. phoenicea L. from the Mediterranean region. Plant Biosyst 150:313–322. CrossRefGoogle Scholar
  50. Médail F, Diadema K (2009) Glacial refugia influence plant diversity patterns in the Mediterranean Basin. J Biogeogr 36:1335–1345CrossRefGoogle Scholar
  51. Médail F, Quézel P (1997) Hot-spots analysis for conservation of plant biodiversity in the Mediterranean basin. Ann Mo Bot Gard 84:112–127CrossRefGoogle Scholar
  52. Meloni M, Perini D, Filigheddu R, Binelli G (2006) Genetic variation in five Mediterranean populations of Juniperus phoenicea as revealed by inter-simple sequence repeat (ISSR) markers. Ann Bot 97:299–304CrossRefPubMedPubMedCentralGoogle Scholar
  53. Meudt HM, Clarke AC (2007) Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant Sci 12:106–117. CrossRefPubMedGoogle Scholar
  54. Mueller UG, Wolfenbarger L (1999) AFLP genotyping and fingerprinting. Trends Ecol Evol 14:389–394CrossRefPubMedGoogle Scholar
  55. Müller-Starck G, Baradat P, Bergmann F (1992) Genetic variation within European tree species. New For 6:23–47CrossRefGoogle Scholar
  56. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590PubMedPubMedCentralGoogle Scholar
  57. Nieto Feliner G (2014) Patterns and processes in plant phylogeography in the Mediterranean Basin. A review. Perspect Plant Ecol 16:265–278. CrossRefGoogle Scholar
  58. Nybom H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol Ecol 13:1143–1155. CrossRefPubMedGoogle Scholar
  59. Nybom H, Bartish I (2000) Effects of life history traits and sampling strategies on genetic diversity estimates obtained with RAPD markers in plants. Perspect Plant Ecol 3:93–114. CrossRefGoogle Scholar
  60. Padilla DP, González-Castro A, Nogales M (2012) Significance and extent of secondary seed dispersal by predatory birds on oceanic islands: the case of the Canary archipelago. J Ecol 100:416–427. CrossRefGoogle Scholar
  61. Panagiotopoulos K, Böhm A, Leng MJ, Wagner B, Schäbitz F (2014) Climate variability over the last 92 ka in SW Balkans from analysis of sediments from Lake Prespa. Clim Past 10:643–660. CrossRefGoogle Scholar
  62. Peakall R, Smouse PE (2006) Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295. CrossRefGoogle Scholar
  63. Petit RJ, Csaikl UM, Bordács S, Burg K, Coart E, Cottrell J, van Dam B, Deans JD, Dumolin-Lapegue S, Fineschi S, Finkeldey R, Gillies A, Glaz I, Goicoechea PG, Jensen JS, Konig AO, Lowe AJ, Madsen SF, Matyas G, Munro RC, Olalde M, Pemonge MH, Popescu F, Slade D, Tabbener H, Taurchini D, de Vries SGM, Ziegenhagen B, Kremer A (2002) Chloroplast DNA variation in European white oaks: phylogeography and patterns of diversity based on data from over 2600 populations. For Ecol Manag 156:5–26CrossRefGoogle Scholar
  64. Pritchard JK, Wen W (2004) Documentation for STRUCTURE software: version 2. University of Chicago, ChicagoGoogle Scholar
  65. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedPubMedCentralGoogle Scholar
  66. Quézel P, Pesson P (1980) Biogeographie et ecologie des coniferes sur le poutrour mediterraneen. In: Pesson P (ed) Actualites d’ecologie forestiere. Gauthier-Villars, Paris, pp 205–255Google Scholar
  67. Quézel P, Barbero M, Benabid A, Rivas-Martines S (1992) Contributions à l’étude des groupements forestiers et pre-forestiers du Maroc oriental. Studia Bot 10:57–90Google Scholar
  68. Reyes-Betancort JA, Santos-Guerra A, Rosana-Guma I, Humphries CJ, Carine MA (2008) Diversity, rarity and the evolution and conservation of the Canary Islands endemic flora. Anales Jard Bot Madrid 65:25–45Google Scholar
  69. Rivas-Martínez S, Wildpret M, del Arco M, Rodríguez O, Pérez-de-Paz PL, García-Gallo A, Acebes JR, Díaz-González TE, Fernández-González F (1993) Las comunidades vegetales de la Isla de Tenerife (Islas Canarias). Itinera Geobotanica 7:169–374Google Scholar
  70. Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138. CrossRefGoogle Scholar
  71. Sánchez-Gómez P, Soriano MC, Sotomayor JA, García-Vallejo MC, Sáez F, Correal E (1993) Estudio del Aceite esencial de diversas Cupresáceas autóctonas del SE. de España. Actas del I Congreso Forestal Español 4:359–364Google Scholar
  72. Sánchez-Gómez P, Jiménez JF, Vera JB, Sánchez-Saorín FJ, Martínez JF, Buhagiar J (2013) Genetic structure of Tetraclinis articulata, an endangered conifer of the western Mediterranean basin. Silva Fenn.
  73. Sánchez-Goñi MF, Cacho I, Turon JL, Guiot J, Sierro FJ, Peypouquet JP, Grimalt J, Shackleton N (2002) Synchroneity between marine and terrestrial responses to millennial scale climatic variability during the last glacial period in the Mediterranean region. Clim Dyn 19:95–105CrossRefGoogle Scholar
  74. Santos-Guerra A (2001) Flora vascular nativa. In: Fernández-Palacios JM, Martín Esquivel JL (eds) Naturaleza de las Islas Canarias. Ecología y Conservación, Santa Cruz de Tenerife, pp 185–192Google Scholar
  75. Sękiewicz K, Dering M, Sękiewicz M, Boratyńska K, Iszkulo G, Litkowiec M, Ok T, Dagher-Kharrat MB, Boratyński A (2015) Effect of geographic range discontinuity on species differentiation—East-Mediterranean Abies cilicica: a case study. Tree Genet Genomes 11:810. CrossRefGoogle Scholar
  76. Sobierajska K, Boratyńska K, Jasińska A, Dering M, Ok T, Douaihy B, Dagher-Kharrat MB, Romo A, Boratyński A (2016) Effect of the Aegean Sea barrier between Europe and Asia on differentiation in Juniperus drupacea (Cupressaceae). Bot J Linn Soc 180:365–385. CrossRefGoogle Scholar
  77. Stuessy TF, Jakubowsky G, Salguero-Gómez R, Pfosser M, Schluter PM, Fer T, Sun B-Y, Kato H (2006) Anagenetic evolution in island plants. J Biogeogr 33:1259–1265CrossRefGoogle Scholar
  78. Sytsma KJ, Givnish TJ, Smith JF, Hain WJ (1993) Collection and storage of land plant samples for macromolecular comparisons. Methods Enzymol 224:23–37CrossRefPubMedGoogle Scholar
  79. Terrab A, Schönswetter P, Talavera S, Vela E, Stuessey TF (2008) Range-wide phylogeography of Juniperus thurifera L., a presumptive keystone species of western Mediterranean vegetation during cold stages of the Pleistocene. Mol Phylogenet Evol 48:94–102CrossRefPubMedGoogle Scholar
  80. Thompson JD (2005) Plant evolution in the Mediterranean. Oxford University Press, OxfordCrossRefGoogle Scholar
  81. Van Andel TH (2002) The climate and landscape of middle part of Weichselian glaciation in Europe: the stage 3 project. Quat Res 57:2–8CrossRefGoogle Scholar
  82. Vekemans X (2002) AFLP-SURV version 1.0. Distributed by the author. Laboratoire de Génétique et Ecologie Végétale, Université Libre de Bruxelles, BruxellesGoogle Scholar
  83. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acid Res 11:4407–4414CrossRefGoogle Scholar
  84. Zamora C, Grandal A (1997) Reconstrucción de la vegetación potencial del Campo de Cartagena a la luz de la documentación de su archivo municipal. An Biol 22:67–76Google Scholar

Copyright information

© INRA and Springer-Verlag France SAS, part of Springer Nature 2018

Authors and Affiliations

  • Pedro Sánchez-Gómez
    • 1
  • Juan F. Jiménez
    • 1
    • 2
  • Jose Luis Cánovas
    • 1
  • Juan Bautista Vera
    • 1
  • Isabell Hensen
    • 3
  • Miloud Aouissat
    • 4
  1. 1.Departamento de Biología Vegetal (Botánica)Universidad de MurciaMurciaSpain
  2. 2.Departamento de Botánica, Facultad de CienciasUniversidad de GranadaGranadaSpain
  3. 3.Institut für BiologieMartin-Luther UniversitatHalleGermany
  4. 4.Centre Universitaire Salhi Ahmed NaamaNaâmaAlgeria

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