Genomic insights into population structure and conservation of wild olive (Olea europaea subsp. cuspidata) in Oman’s Dhofar and Hajar Mountains

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1. Green, P., Wickens, G., Tan, K., Mill, R. and Elias, T. The Olea europaea complex. The Davis and Hedge Festschrift. 1989, Edinburg University press, Scotland. 2. Zohary, D. Olive, Olea europaea (Oleaceae). Evolution of crop plants. Smartt, J. & Simmonds, NW Eds. 1995, Longman Scientific & Technical, Harlow, England. 3. Green, P.S. A revision of Olea L.(Oleaceae). Kew Bulletin, 2002: p. 91-140. https://doi.org/10.2307/4110824 4. Ghazanfar, S.A. Flora of the Sultanate of Oman. Volume 3. Loganiaceae-Asteraceae. 2015. 5. McGregor, S.E. Insect pollination of cultivated crop plants. 1976: Agricultural Research Service, US Department of Agriculture. 6. Canale, A. and Loni A. Insects visiting olive flowers (Olea europaea L.) in a Tuscan olive grove. Redia, 2010. 92: p. 95-98. 7. Cuneo, P. and Leishman M.R. African Olive (Olea europaea subsp. cuspidata) as an environmental weed in eastern Australia: a review. Cunninghamia, 2006. 9(4): p. 545-577. 8. Abiyu, A., Teketay, D., Glatzel, G. and Gratzer, G. Tree seed dispersal by African civets in the Afromontane Highlands: too long a latrine to be effective for tree population dynamics. African Journal of Ecology, 2015. 53(4). https://doi.org/10.1111/aje.12198 9. Baali-Cherif, D. and Besnard G. High genetic diversity and clonal growth in relict populations of Olea europaea subsp. laperrinei (Oleaceae) from Hoggar, Algeria. Annals of Botany, 2005. 96(5): p. 823-830. https://doi.org/10.1093/aob/mci232 10. Ghazanfar, S.A., Edible wild plants: a case study from Oman, in Global perspectives on underutilized crops. 2018, Springer. p. 207-216. https://doi.org/10.1007/978-3-319-77776-4_8 11. Patzelt, A., Oman plant: red data book. 2015: Oman Botanic Garden. 12. Allen, D., Westrip, J., Puttick, A., Harding, K., Hilton-Taylor, C. & Ali, H. UAE national red list of vascular plants. 2021, Technical Report. Ministry of Climate Change and Environment, United Arab Emirates. 13. Al-Charaabi, Y. and S. Al-Yahyai, Projection of future changes in rainfall and temperature patterns in Oman. J Earth Sci Clim Change, 2013. 4(5): p. 154-161. https://doi.org/10.4172/2157-7617.1000154 14. Patzelt, A., Photographic Field Guide to The Plants of the Western Hajar Mountains, Sultanate of Oman. Sultan Qaboos University, Muscat, 2015. 15. Patzelt, A., Synopsis of the flora and vegetation of Oman, with special emphasis on patterns of plant endemism. Abhandlungen der Braunschweigischen Wissenschaftlichen Gesellschaft, 2015. 282: p. 317. 16. Al-Jabri, T., A. Culham, and R. Ellis, Wild olive in Oman and its conservation a review. Journal of Agricultural and Marine Sciences, 2024. 29(1): p. 1-14. https://doi.org/10.53541/jams.vol29iss1pp1-14 17. Anthelme, F., A. Abdoulkader, and G. Besnard, Distribution, shape and clonal growth of the rare endemic tree Olea europaea subsp. laperrinei (Oleaceae) in the Saharan mountains of Niger. Plant Ecology, 2008. 198(1): p. 73-87. https://doi.org/10.1007/s11258-007-9386-6 18. Habib, N. A., Müller, M., Gailing, O., Patzelt, A., Al Issai, G., Krutovsky, K. V. and Wiehle, M. Genetic diversity and differentiation of Olea europaea subsp. cuspidata (Wall. & G. Don) Cif. in the Hajar Mountains of Oman. Genetic Resources and Crop Evolution, 2021. 68(3): p. 865-883. https://doi.org/10.1007/s10722-020-01030-2 19. Willing, E.-M., C. Dreyer, and C. Van Oosterhout, Estimates of genetic differentiation measured by FST do not necessarily require large sample sizes when using many SNP markers. 2012. https://doi:10.1371/journal.pone.0042649 20. Doyle, J.J. and J.L. Doyle, A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical bulletin, 1987. 21. Tel-Zur, N., Abbo, S., Myslabodski, D. and Mizrahi, Y. Modified CTAB procedure for DNA isolation from epiphytic cacti of the genera Hylocereus and Selenicereus (Cactaceae). Plant Molecular Biology Reporter, 1999. 17(3): p. 249-254. https://doi.org/10.1023/A:1007656315275 22. Yooprasert, S., Taxonomy and systematics of Urophyllum (Rubiaceae) in Thailand and Indochina. 2021, University of Reading. https://doi.org/10.48683/1926.0011002423. 23. Park, J.-S., Kang, M.-Y., Shim, E.-J., Oh, J., Seo, K.-I., Kim, K. S., Sim, S.-C., Chung, S.-M., Park, Y. and Lee, G. P. Genome-wide core sets of SNP markers and Fluidigm assays for rapid and effective genotypic identification of Korean cultivars of lettuce (Lactuca sativa L.). Horticulture Research, 2022. 9: p. uhac119. https://doi.org/10.1093/hr/uhac119 24. Bolger, A.M., M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 2014. 30(15): p. 2114-2120. https://doi.org/10.1093/bioinformatics/btu170 25. Johnson, M.G., et al., HybPiper: Extracting coding sequence and introns for phylogenetics from high‐throughput sequencing reads using target enrichment. Applications in plant sciences, 2016. 4(7): p. 1600016. https://doi.org/10.3732/apps.1600016 26. McLay, T.G., et al., New targets acquired: Improving locus recovery from the Angiosperms353 probe set. Applications in plant sciences, 2021. 9(7). https://doi.org/10.1002/aps3.11420 27. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. and Madden, T. L. BLAST+: architecture and applications. BMC bioinformatics, 2009. 10(1): p. 421. https://doi.org/10.1186/1471-2105-10-421 28. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S. and Daly, M. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome research, 2010. 20(9): p. 1297-1303. https://doi.org/10.1101/gr.107524.110 29. Slimp, M., Williams, L. D., Hale, H. and Johnson, M. G. On the potential of Angiosperms353 for population genomic studies. Applications in Plant Sciences, 2021. 9(7). https://doi.org/10.1002/aps3.11419 30. Johnson, M., Slimp, M., Williams, L. D., & Hale, H. Data from: On the potential of Angiosperm353 for population genomics studies. . Dryad Dataset. https://doi.org/10.5061/dryad.76hdr7sv3, 2021. https://doi.org/10.5061/dryad.76hdr7sv3 31. Linck, E. and C. Battey, Minor allele frequency thresholds strongly affect population structure inference with genomic data sets. Molecular Ecology Resources, 2019. 19(3): p. 639-647. https://doi:10.1111/1755-0998.12995 32. Weir, B.S. and C.C. Cockerham, Estimating F-statistics for the analysis of population structure. evolution, 1984: p. 1358-1370. 33. Lischer, H.E. and Excoffier L. PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics, 2012. 28(2): p. 298-299. https://doi.org/10.1093/bioinformatics/btr642 34. Pritchard, J.K., M. Stephens, and Donnelly P, Inference of population structure using multilocus genotype data. Genetics, 2000. 155(2): p. 945-959. https://doi.org/10.1093/genetics/155.2.945 35. Wang, J., Luo, M. C., Chen, Z., You, F. M., Wei, Y., Zheng, Y. and Dvorak, J. Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D‐genome genetic diversity and pinpoint the geographic origin of hexaploid wheat. New phytologist, 2013. 198(3): p. 925-937. https://doi.org/10.1111/nph.12164 36. Evanno, G., S. Regnaut, and Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular ecology, 2005. 14(8): p. 2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x 37. Francis, R. pophelper: an R package and web app to analyse and visualize population structure. Molecular ecology resources, 2017. 17(1): p. 27-32. https://doi.org/10.1111/1755-0998.12509 38. Jombart, T., adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 2008. 24(11): p. 1403-1405. https://doi.org/10.1093/bioinformatics/btn129 39. Kamvar, Z.N., J.F. Tabima, and Grünwald N.J. Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ, 2014. 2: p. e281. https://doi.org/10.7717/peerj.281 40. Knaus, B.J. and Grünwald N.J. vcfr: a package to manipulate and visualize variant call format data in R. Molecular ecology resources, 2017. 17(1): p. 44-53. https://doi.org/10.1111/1755-0998.12549 41. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., Maller, J., Sklar, P., De Bakker, P. I. and Daly, M. J. PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics, 2007. 81(3): p. 559-575. https://doi.org/10.1086/519795 42. Smouse, P. E., Long, J. C. and Sokal, R. R. Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Systematic zoology, 1986. 35(4): p. 627-632. https://doi.org/10.2307/2413122 43. Oksanen, J., Blanchet, F. G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., Minchin, P., O’Hara, R., Simpson, G. and Solymos, P. vegan: Community Ecology Package. R package version 2.5-3. 2018. 2018. https://CRAN.R-project.org/package=vegan 44. Ortiz, E.M. vcf2phylip v2. 0: convert a VCF matrix into several matrix formats for phylogenetic analysis. 2019. https://doi.org/10.5281/zenodo.2540861 45. Huson, D.H. and Bryant D. Application of phylogenetic networks in evolutionary studies. Molecular biology and evolution, 2006. 23(2): p. 254-267. https://doi.org/10.1093/molbev/msj030 46. Templeton, A.R., K.A. Crandall, and Sing C.F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics, 1992. 132(2): p. 619-633. https://doi.org/10.1093/genetics/132.2.619 47. Leigh, J.W., D. Bryant, and Nakagawa S. POPART: full-feature software for haplotype network construction. Methods in Ecology & Evolution, 2015. 6(9). https://doi.org/10.1111/2041-210X.12410 48. Omire, A., Neondo, J., Budambula, N. L., Wangai, L., Ogada, S. and Mweu, C. Genetic diversity and population structure of Doum Palm (Hyphaene compressa) using genotyping by sequencing. Frontiers in Genetics, 2022. 13: p. 762202. https://doi.org/10.3389/fgene.2022.762202 49. Besnard, G., R. Rubio de Casas, and Vargas P. Plastid and nuclear DNA polymorphism reveals historical processes of isolation and reticulation in the olive tree complex (Olea europaea). Journal of Biogeography, 2007. 34(4): p. 736-752. https://doi.org/10.1111/j.1365-2699.2006.01653.x 50. Fernández-Rodríguez, S., et al., Identification of potential sources of airborne Olea pollen in the Southwest Iberian Peninsula. International Journal of Biometeorology, 2014. 58(3): p. 337-348. https://doi.org/10.1007/s00484-012-0629-4 51. Besnard, G., et al., Contrasting genetic footprints among Saharan olive populations: potential causes and conservation implications. Plants, 2021. 10(6): p. 1207. https://doi.org/10.3390/plants10061207 52. Kassa, A., H. Konrad, and T. Geburek, Molecular diversity and gene flow within and among different subspecies of the wild olive (Olea europaea L.): A review. Flora, 2019. 250: p. 18-26. https://doi.org/10.1016/j.flora.2018.11.014 53. Al-Yahyai, R.A., et al., Genome-wide SNP analysis reveals genetic diversity and structure of wild and cultivated olives (Olea europaea L.) in Oman. Scientific Reports, 2026. https://doi.org/10.1038/s41598-026-40849-0 54. Dzialuk, A., Chybicki, I., Gout, R., Mączka, T., Fleischer, P., Konrad, H., Curtu, A. L., Sofletea, N. and Valadon, A. No reduction in genetic diversity of Swiss stone pine (Pinus cembra L.) in Tatra Mountains despite high fragmentation and small population size. Conservation Genetics, 2014. 15(6): p. 1433-1445. https://doi.org/10.1007/s10592-014-0628-6 55. Serrote, C. M. L., Reiniger, L. R. S., Silva, K. B. d. and Stefanel, C. M. Gene flow affects the genetic diversity of Copaifera langsdorffii Desf. in Cerrado. Acta Botanica Brasilica, 2022. 36: p. e20220007. https://doi.org/10.1590/1677-941X-ABB-2022-0007 56. Preston, G.W., et al., A multi-proxy analysis of the Holocene humid phase from the United Arab Emirates and its implications for southeast Arabia's Neolithic populations. Quaternary International, 2015. 382: p. 277-292. https://doi.org/10.1016/j.quaint.2015.01.054 57. Buschbom, J., Y. Yanbaev, and Degen B. Efficient long-distance gene flow into an isolated relict oak stand. Journal of Heredity, 2011. 102(4): p. 464-472. https://doi.org/10.1093/jhered/esr023 58. Chludil, D., Čepl, J., Steffenrem, A., Stejskal, J., Sagariya, C., Pook, T., Schueler, S., Korecký, J., Almqvist, C. and Chakraborty, D. A Pollen‐Based Assisted Migration for Rapid Forest Adaptation. Global Change Biology, 2025. 31(1): p. e70014. https://doi.org/10.1111/gcb.70014 59. Nassiry, M., A. Javanmard, and Reza Tohidi R.T. Application of statistical procedures for analysis of genetic diversity in domestic animal populations. 2009. https://doi.org/10.3844/ajavsp.2009.136.141 60. Besnard, G., Christin, P., Baali-Cherif, D., Bouguedoura, N. and Anthelme, F. Spatial genetic structure in the Laperrine's olive (Olea europaea subsp. laperrinei), a long-living tree from the central Saharan mountains. Heredity, 2007. 99(6): p. 649-657. https://doi.org/10.1038/sj.hdy.6801051 61. Besnard, G., Rubio de Casas, R., Christin, P.-A. and Vargas, P. Phylogenetics of Olea (Oleaceae) based on plastid and nuclear ribosomal DNA sequences: tertiary climatic shifts and lineage differentiation times. Annals of botany, 2009. 104(1): p. 143-160. https://doi.org/10.1093/aob/mcp105 62. Levy, E., Byrne, M., Coates, D., Macdonald, B., McArthur, S. and Van Leeuwen, S. Contrasting influences of geographic range and distribution of populations on patterns of genetic diversity in two sympatric Pilbara acacias. PLoS One, 2016. 11(10): p. e0163995. https://doi.org/10.1371/journal.pone.0163995 63. Grigoriadou Zormpa, O., Wilhelmi, S., Vucetic, B., Ciocîrlan, M.-I.-C., Mueller, M., Ciocîrlan, E., Curtu, A. L., Targem, M. B., Wildhagen, H. and Gailing, O. Genetic diversity and fine-scale spatial genetic structure of European beech populations along an elevational gradient. Heredity, 2025: p. 1-10. https://doi.org/10.1038/s41437-025-00776-8. 64. Cole, C.T., Genetic variation in rare and common plants. Annual Review of Ecology, Evolution, and Systematics, 2003. 34(1): p. 213-237. https://doi.org/10.1146/annurev.ecolsys.34.030102.151717 65. Su, Z., Lin, Z., Zhuo, L., Jiang, X. and Jiang, Q. Small Population Size and Low Levels of Genetic Diversity in an Endangered Species Endemic to the Western Tianshan Mountains. Plants, 2025. 14(19): p. 3105. https://doi.org/10.3390/plants1419310 66. Yoichi, W. and Tomaru, N. Patterns of geographic distribution have a considerable influence on population genetic structure in one common and two rare species of Rhododendron (Ericaceae). Tree Genetics & Genomes, 2014. 10(4): p. 827-837. https://doi.org/10.1007/s11295-014-0723-3 67. Zhu, X., Tang, J., Jiang, H., Yang, Y., Chen, Z., Zou, R., Xu, A., Luo, Y., Deng, Z. and Wei, X. Genomic evidence reveals high genetic diversity in a narrowly distributed species and natural hybridization risk with a widespread species in the genus Geodorum. BMC Plant Biology, 2023. 23(1): p. 317. https://doi.org/10.1186/s12870-023-04285-w 68. Godt, M. J. W. and Hamrick, J. Genetic divergence among infraspecific taxa of Sarracenia purpurea. Systematic Botany, 1998: p. 427-438. https://doi.org/10.2307/2419375 69. Kassa, A., H. Konrad, and Geburek T. Mating pattern and pollen dispersal in the wild olive tree (Olea europaea subsp. cuspidata). Tree Genetics & Genomes, 2018. 14(1): p. 3. https://doi.org/10.1007/s11295-017-1215-z 70. Hohenlohe, P.A., W.C. Funk, and O.P. Rajora, Population genomics for wildlife conservation and management. Molecular Ecology, 2021. 30(1): p. 62-82.