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Q. coccifera L. İçerisindeki Genetik Varyasyonların Analizi ve Populasyonlar Arasındaki İlişkilerde Coğrafik Farklılıkların Etkisi

Year 2024, Volume: 24 Issue: 3, 302 - 311

Aykut Yılmaz , Orcan Demircan , Ramazan Tutuş

https://doi.org/10.17475/kastorman.1599983

Abstract

Çalışmanın amacı: Bu çalışma, Q. coccifera içerisindeki varyasyonları ve populasyonlar arasındaki varyasyonlar üzerine coğrafik farklılıkların etkisini belirlemeyi amaçlamaktadır.
Çalışma alanı: Akdeniz ülkelerinin Q. coccifera populasyonlarını içeren bu çalışmaya ait örnekler, NCBI veri tabanından temin edilmiştir.
Materyal ve yöntem: Bu çalışmada, matK geni-kısmi trnK gen intronu ve rbcL gen sekansları temelinde, Q. coccifera ve Q. calliprinos’a ait tüm populasyonlar, NCBI veri tabanından toplandı. Popülasyonların ilişkilerini ve varyasyonlarını ortaya çıkarma yetenekleri açısından barkodlama bölgelerini değerlendirmek ve popülasyonların filogenetik ilişkileri hakkında daha bilgilendirici sonuçları belirlemek amaçlandı. Moleküler Evrimsel Genetik Analiz (MEGA11) bu amaçla kullanıldı.
Temel sonuçlar: Barkodlama bölgelerinin her ikisi için, Doğu Akdeniz bölgesinde daha yüksek varyasyonlu örneklerin varlığı açık bir şekilde gözlenmiştir. Bununla birlikte Q. coccifera populasyonları arasında dikkat çekici varyasyonlar ayırt edildi.
Araştırma vurguları: Levant olarak adlandırılan bölgeden örnekler, oldukça olası bir şekilde Q. coccifera ve Q. calliprinos olarak iki farklı türün veya Q. coccifera subsp coccifera ve Q. coccifera subsp calliprinos olarak iki tür içi taksonun varlığını güçlendirmektedir. Ancak, bu durumun Türkiye’nin Doğu Akdeniz bölgesinden Mısır’a, Q. calliprinos ve Q. coccifera örnekleri içeren çalışmalarla desteklenmesi gerekmektedir.

Keywords

Q. coccifera Q. calliprinos matK Geni-partial trnK Gen İntronu rbcL Geni

References

  • Arnold, M.L. (1997). Natural Hybridization and Evolution. New York. USA: Oxford University Press.
  • Bacilieri, R., Ducousso, A., Petit, R.J. & Kremer, A. (1996). Mating system and asymetric hybridization in a mixed stand of european oaks. Evolution, 50(2), 900-908.
  • Blondel, J. & Aronson, J. (1999). Biology and wildlife of the Mediterranean region. Oxford University Press, Oxford.
  • Borazan, A. & Babaç, M.T. (2003). Morphometric leaf variation in oaks (Quercus) of Bolu, Turkey. Annales Botanici Fennici, 40, 233-242.
  • Candolle, A.D. (1864). Prodromus systematis naturalis regni vegetabilis sive enumeratio contracta ordinum, generum specierumque plantarum huc usque cognitarum, juxta methodi naturalis normas digesta sumptibus sociorum, 16(2). Treuttel et Würtz, Paris. doi: 10.5962/bhl.title.286
  • Charalambos, N., Filippos, A. A., Siegfried, F. & Aikaterini, D. (2011). Interfertile oaks in an island environment. II. Limited hybridization between Quercus alnifolia Poech and Q. coccifera L. in a mixed stand. European Journal of Forest Research, 130, 623-635.
  • Denk, T. & Grimm, G. W. (2010). The oaks of western Eurasia: traditional classifications and evidence from two nuclear markers. Taxon, 59(2), 351-366.
  • Douaihy, B., Saliba, C., Stephan, J., Simeone, M.C., Cardoni, S., et al. (2020). Tracking diversity and evolutionary pathways of Lebanese oak taxa through plastome analyses. Botany Letters, 167(3), 315-330.
  • Hokanson, S. C., Isebrands, J. G., Jensen, R. J. & Hancock, J. F. 1993. Isozyme variation in oaks of the Apostle Islands in Wisconsin: Genetic structure and levels of inbreeding in Quercus rubra and Quercus ellipsoidalis (Fagaceae). American Journal of Botany, 80, 1349-1357.
  • Hubert, F., Grimm, G. W., Jousselin, E., Berry, V., Franc, A. & Kremer, A. (2014). Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus. Systematics and Biodiversity, 12(4), 405-423.
  • Kasapligil, B. (1981). Past and present oaks of Turkey I. Phytologia, 49, 95-146.
  • Kremer, A. & Petıt, R.J. (1993). Gene diversity in natural populations of oak species. Annals of Forest Science, 50, 186-202.
  • Manos, P. S., Zhou, Z. & Cannon, C.H. (2001). Systematics of Fagaceae: phylogenetic tests of reproductive trait evolution. International Journal of Plant Sciences, 162, 1361-1379.
  • NCBI, National Centre of Biotechnology Information, https://www.ncbi.nlm.nih.gov/ genbank.
  • Neophytou, C., Aravanopoulos, F. A., Fink, S. & Dounavi, A. (2010). Detecting interspecific and geographic differentiation patterns in two interfertile oak species (Quercus petraea (Matt.) Liebl. and Quercus robur L.) using small sets of microsatellite markers. Forest Ecology and Management, 259, 2026-2035.
  • Ngoc, N. V., Duy, N. V., Phuong, N.T.M. & Binh, H. T. (2022). Evaluation of DNA Barcodes in Discriminating Quercus species from Lam Dong, Vietnam. Vietnam Journal of Biotechnology, 20(4), 621-631.
  • Ozturk, M. & Altay, V. (2021). Role of Quercus coccifera (=Q. calliprinos) in the light of climate change scenarios in the Mediterranean Basin. Plant & Fungal Research, 4(2), 8-20.
  • Öztürk, S. & Özdemir, Z. (2013). The effects of urban open and green spaces on life quality; a case study of Kastamonu. Kastamonu Univ., Journal of Forestry Faculty, 13(1), 109-116.
  • Petit, R. J., Bodenes, C., Ducousso, A., Roussel, G. & Kremer, A. (2004). Hybridization as a mechanism of invasion in oaks. New Phytologist, 161, 151-164.
  • Piredda, R., Simeone, M. C., Attimonelli, M., Bellarosa, R. & Schirone, B. (2011). Prospects of barcoding the Italian wild dendroflora: oaks reveal severe limitations to tracking species identity. Molecular Ecology Resources, 11, 72-83.
  • Rieseberg, L. H. & Willis, J. H. (2007). Plant Speciation. Science, 317, 910-914.
  • Salvatore, G. & Paola, G. (1976). ‘‘Quercus calliprinos’’ Webb e ‘‘Quercus coccifera’’L.: Ricerche sull’anatomia fogliare e valutazioni tassonomiche e corologiche. Gıornale Botanico Italliano, 110, 89-115.
  • Simeone, M.C., Piredda, R., Papini, A., Vessella, F. & Schirone, B. (2013). Application of plastid and nuclear markers to DNA barcoding of Euro-Mediterranean oaks (Quercus, Fagaceae): problems, prospects and phylogenetic implications. Botanical Journal of the Linnean Society, 172(4), 478-499.
  • Tamura, K., Stecher, G. & Kumar, S. (2021). MEGA 11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution, 38(7), 3022-3027.
  • Toumı, L. & Lumaret, R. (2001). Allozyme characterization of four Mediteranean evergreen oak species. Biochemical Systematics and Ecology, 29, 799-817.
  • Tutin, T. G., Heywood, V. H., Burges, N. A., Valentine, D. H., Walters, S. M., et al. (2010). Flora Europaea. Vol. 1, second edition. Cambridge University Press, London.
  • Vázquez, F. M., Coombes, A. J., Garcia, D., Márquez F., Pinto-Gomes, C., et al. (2018). Anotaciones a la nomenclatura del género Quercus L. (Fagaceae) en la Península Ibérica y NW de África. Folia Botánica Extremadurensis, 12, 5-79.
  • Vila-Viçosa, C., Capelo, J., Alves, P., Almeida, R. & Vazquez, F.M. (2023). New annotated checklist of the Portuguese oaks (Quercus, Fagaceae). Mediterranean Botany, 44, e79286.
  • Vila-Viçosa, C., Vieira, C., Márquez, F., Almeida, R. & Vázquez, F. (2022). Notes on the original materials of the three western Mediterranean oaks (Quercus, Fagaceae) described by Desfontaines. Mediterranean Botany, 43, e76648.
  • Webb, P. (1838). Iter Hispaniense. Béthune and Plon, Paris. doi: 10.5962/bhl.title.59218
  • Yılmaz, A. (2016). Phylogenetic relationships of the genus Quercus L. (Fageceae) from three different sections. African Journal of Biotechnology, 15(40), 2265-2271.
  • Yılmaz, A. (2017). Cytotaxonomic study of Quercus L. species from Section Quercus in Turkey. Caryologia: International Journal of Cytology, Cytosystematics and Cytogenetics, 70(2), 141-146.
  • Yılmaz, A. (2018a). Karyomorphology of some Quercus L. species from section Quercus and Cerris in Turkey. Caryologia: International Journal of Cytology, Cytosystematics and Cytogenetics, 71(3), 210-216.
  • Yılmaz, A. (2018b). Cytogenetic Relationships of Turkish Oaks. Cytogenetics- Past, Present and Further Perspectives, Chapter 2.
  • Yılmaz, A. (2020a). The importance in DNA barcoding of the regions which is covering rRNA genes and ITS sequences in the genus Quercus L. Bangladesh Journal of Plant Taxonomy, 27(2), 261-271.
  • Yılmaz, A. (2020b). Quercus L. Cinsine Ait Türlerde Kloroplast DNA’ya Ait psbA-trnH IGS Bölgesinin Kullanılarak Filogenetik İlişkilerin Değerlendirilmesi. Düzce Üniversitesi Bilim ve Teknoloji Dergisi, 8, 1185-1192.
  • Yılmaz, A. Uslu, E. & Babaç, M.T. (2017). Morphological Variability of Evergreen Oaks (Quercus) in Turkey. Bangladesh Journal of Plant Taxononomy, 24(1), 39-47.
  • Yılmaz, A., Uslu, E. & Babaç, M.T. (2013). Molecular diversity among Turkish oaks (QUERCUS) using random amplified polymorphic DNA (RAPD) analysis. African Journal of Biotechnology, 12(45), 6358-6365.
  • Zohary, M. (1966). Flora Palaestina. Jerusalem Academic Press. Israel.

Analysis of Genetic Variations within Q. coccifera L. and the Effects of Geographical Differences in Relationships among Populations

Year 2024, Volume: 24 Issue: 3, 302 - 311

Aykut Yılmaz , Orcan Demircan , Ramazan Tutuş

https://doi.org/10.17475/kastorman.1599983

Abstract

Aim of study: This study aims to determine the variations within Q. coccifera and the effects of geographical differences on the variations among populations.
Area of study: Samples in this study containing Q. coccifera populations of Mediterranean countries were obtained from National Center for Biotechnology Information (NCBI) database.
Material and method: In this study, all populations belonging to Q. coccifera and Q. calliprinos based on rbcL gene and matK gene-partial trnK gene intron sequences, were collected from NCBI database. It is aimed to determine more informative results about the phylogenetic relations of populations and to evaluate the barcoding regions in terms of their abilities to reveal the relationships and variations of populations. For this purpose, Molecular Evolutionary Genetics Analysis (MEGA 11) was performed.
Main results: For both barcoding regions, the presence of the samples with higher variations in the Eastern Mediterranean region was clearly observed. Moreover, remarkable variations were recognized among Q. coccifera populations.
Research highlights: The samples from region called Levant quite possibly strengthen the presence of two different species as Q. coccifera and Q. calliprinos or two intraspecific taxa such as Q. coccifera subsp coccifera and Q. coccifera subsp calliprinos. However, this needs to be supported by studies including Q. calliprinos and Q. coccifera samples from East Mediterranean region of Türkiye to Egypt.

Keywords

Q. coccifera Q. calliprinos matK Gene-partial trnK Gene Intron rbcL Gene

References

  • Arnold, M.L. (1997). Natural Hybridization and Evolution. New York. USA: Oxford University Press.
  • Bacilieri, R., Ducousso, A., Petit, R.J. & Kremer, A. (1996). Mating system and asymetric hybridization in a mixed stand of european oaks. Evolution, 50(2), 900-908.
  • Blondel, J. & Aronson, J. (1999). Biology and wildlife of the Mediterranean region. Oxford University Press, Oxford.
  • Borazan, A. & Babaç, M.T. (2003). Morphometric leaf variation in oaks (Quercus) of Bolu, Turkey. Annales Botanici Fennici, 40, 233-242.
  • Candolle, A.D. (1864). Prodromus systematis naturalis regni vegetabilis sive enumeratio contracta ordinum, generum specierumque plantarum huc usque cognitarum, juxta methodi naturalis normas digesta sumptibus sociorum, 16(2). Treuttel et Würtz, Paris. doi: 10.5962/bhl.title.286
  • Charalambos, N., Filippos, A. A., Siegfried, F. & Aikaterini, D. (2011). Interfertile oaks in an island environment. II. Limited hybridization between Quercus alnifolia Poech and Q. coccifera L. in a mixed stand. European Journal of Forest Research, 130, 623-635.
  • Denk, T. & Grimm, G. W. (2010). The oaks of western Eurasia: traditional classifications and evidence from two nuclear markers. Taxon, 59(2), 351-366.
  • Douaihy, B., Saliba, C., Stephan, J., Simeone, M.C., Cardoni, S., et al. (2020). Tracking diversity and evolutionary pathways of Lebanese oak taxa through plastome analyses. Botany Letters, 167(3), 315-330.
  • Hokanson, S. C., Isebrands, J. G., Jensen, R. J. & Hancock, J. F. 1993. Isozyme variation in oaks of the Apostle Islands in Wisconsin: Genetic structure and levels of inbreeding in Quercus rubra and Quercus ellipsoidalis (Fagaceae). American Journal of Botany, 80, 1349-1357.
  • Hubert, F., Grimm, G. W., Jousselin, E., Berry, V., Franc, A. & Kremer, A. (2014). Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus. Systematics and Biodiversity, 12(4), 405-423.
  • Kasapligil, B. (1981). Past and present oaks of Turkey I. Phytologia, 49, 95-146.
  • Kremer, A. & Petıt, R.J. (1993). Gene diversity in natural populations of oak species. Annals of Forest Science, 50, 186-202.
  • Manos, P. S., Zhou, Z. & Cannon, C.H. (2001). Systematics of Fagaceae: phylogenetic tests of reproductive trait evolution. International Journal of Plant Sciences, 162, 1361-1379.
  • NCBI, National Centre of Biotechnology Information, https://www.ncbi.nlm.nih.gov/ genbank.
  • Neophytou, C., Aravanopoulos, F. A., Fink, S. & Dounavi, A. (2010). Detecting interspecific and geographic differentiation patterns in two interfertile oak species (Quercus petraea (Matt.) Liebl. and Quercus robur L.) using small sets of microsatellite markers. Forest Ecology and Management, 259, 2026-2035.
  • Ngoc, N. V., Duy, N. V., Phuong, N.T.M. & Binh, H. T. (2022). Evaluation of DNA Barcodes in Discriminating Quercus species from Lam Dong, Vietnam. Vietnam Journal of Biotechnology, 20(4), 621-631.
  • Ozturk, M. & Altay, V. (2021). Role of Quercus coccifera (=Q. calliprinos) in the light of climate change scenarios in the Mediterranean Basin. Plant & Fungal Research, 4(2), 8-20.
  • Öztürk, S. & Özdemir, Z. (2013). The effects of urban open and green spaces on life quality; a case study of Kastamonu. Kastamonu Univ., Journal of Forestry Faculty, 13(1), 109-116.
  • Petit, R. J., Bodenes, C., Ducousso, A., Roussel, G. & Kremer, A. (2004). Hybridization as a mechanism of invasion in oaks. New Phytologist, 161, 151-164.
  • Piredda, R., Simeone, M. C., Attimonelli, M., Bellarosa, R. & Schirone, B. (2011). Prospects of barcoding the Italian wild dendroflora: oaks reveal severe limitations to tracking species identity. Molecular Ecology Resources, 11, 72-83.
  • Rieseberg, L. H. & Willis, J. H. (2007). Plant Speciation. Science, 317, 910-914.
  • Salvatore, G. & Paola, G. (1976). ‘‘Quercus calliprinos’’ Webb e ‘‘Quercus coccifera’’L.: Ricerche sull’anatomia fogliare e valutazioni tassonomiche e corologiche. Gıornale Botanico Italliano, 110, 89-115.
  • Simeone, M.C., Piredda, R., Papini, A., Vessella, F. & Schirone, B. (2013). Application of plastid and nuclear markers to DNA barcoding of Euro-Mediterranean oaks (Quercus, Fagaceae): problems, prospects and phylogenetic implications. Botanical Journal of the Linnean Society, 172(4), 478-499.
  • Tamura, K., Stecher, G. & Kumar, S. (2021). MEGA 11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution, 38(7), 3022-3027.
  • Toumı, L. & Lumaret, R. (2001). Allozyme characterization of four Mediteranean evergreen oak species. Biochemical Systematics and Ecology, 29, 799-817.
  • Tutin, T. G., Heywood, V. H., Burges, N. A., Valentine, D. H., Walters, S. M., et al. (2010). Flora Europaea. Vol. 1, second edition. Cambridge University Press, London.
  • Vázquez, F. M., Coombes, A. J., Garcia, D., Márquez F., Pinto-Gomes, C., et al. (2018). Anotaciones a la nomenclatura del género Quercus L. (Fagaceae) en la Península Ibérica y NW de África. Folia Botánica Extremadurensis, 12, 5-79.
  • Vila-Viçosa, C., Capelo, J., Alves, P., Almeida, R. & Vazquez, F.M. (2023). New annotated checklist of the Portuguese oaks (Quercus, Fagaceae). Mediterranean Botany, 44, e79286.
  • Vila-Viçosa, C., Vieira, C., Márquez, F., Almeida, R. & Vázquez, F. (2022). Notes on the original materials of the three western Mediterranean oaks (Quercus, Fagaceae) described by Desfontaines. Mediterranean Botany, 43, e76648.
  • Webb, P. (1838). Iter Hispaniense. Béthune and Plon, Paris. doi: 10.5962/bhl.title.59218
  • Yılmaz, A. (2016). Phylogenetic relationships of the genus Quercus L. (Fageceae) from three different sections. African Journal of Biotechnology, 15(40), 2265-2271.
  • Yılmaz, A. (2017). Cytotaxonomic study of Quercus L. species from Section Quercus in Turkey. Caryologia: International Journal of Cytology, Cytosystematics and Cytogenetics, 70(2), 141-146.
  • Yılmaz, A. (2018a). Karyomorphology of some Quercus L. species from section Quercus and Cerris in Turkey. Caryologia: International Journal of Cytology, Cytosystematics and Cytogenetics, 71(3), 210-216.
  • Yılmaz, A. (2018b). Cytogenetic Relationships of Turkish Oaks. Cytogenetics- Past, Present and Further Perspectives, Chapter 2.
  • Yılmaz, A. (2020a). The importance in DNA barcoding of the regions which is covering rRNA genes and ITS sequences in the genus Quercus L. Bangladesh Journal of Plant Taxonomy, 27(2), 261-271.
  • Yılmaz, A. (2020b). Quercus L. Cinsine Ait Türlerde Kloroplast DNA’ya Ait psbA-trnH IGS Bölgesinin Kullanılarak Filogenetik İlişkilerin Değerlendirilmesi. Düzce Üniversitesi Bilim ve Teknoloji Dergisi, 8, 1185-1192.
  • Yılmaz, A. Uslu, E. & Babaç, M.T. (2017). Morphological Variability of Evergreen Oaks (Quercus) in Turkey. Bangladesh Journal of Plant Taxononomy, 24(1), 39-47.
  • Yılmaz, A., Uslu, E. & Babaç, M.T. (2013). Molecular diversity among Turkish oaks (QUERCUS) using random amplified polymorphic DNA (RAPD) analysis. African Journal of Biotechnology, 12(45), 6358-6365.
  • Zohary, M. (1966). Flora Palaestina. Jerusalem Academic Press. Israel.
There are 39 citations in total.

Details

Primary Language English
Subjects Forest Industry Engineering (Other)
Journal Section Articles
Authors

Aykut Yılmaz

Orcan Demircan

Ramazan Tutuş

Early Pub Date December 14, 2024
Publication Date
Submission Date January 24, 2024
Acceptance Date August 5, 2024
Published in Issue Year 2024 Volume: 24 Issue: 3

Cite

APA Yılmaz, A., Demircan, O., & Tutuş, R. (2024). Analysis of Genetic Variations within Q. coccifera L. and the Effects of Geographical Differences in Relationships among Populations. Kastamonu University Journal of Forestry Faculty, 24(3), 302-311. https://doi.org/10.17475/kastorman.1599983
AMA Yılmaz A, Demircan O, Tutuş R. Analysis of Genetic Variations within Q. coccifera L. and the Effects of Geographical Differences in Relationships among Populations. Kastamonu University Journal of Forestry Faculty. December 2024;24(3):302-311. doi:10.17475/kastorman.1599983
Chicago Yılmaz, Aykut, Orcan Demircan, and Ramazan Tutuş. “Analysis of Genetic Variations Within Q. Coccifera L. And the Effects of Geographical Differences in Relationships Among Populations”. Kastamonu University Journal of Forestry Faculty 24, no. 3 (December 2024): 302-11. https://doi.org/10.17475/kastorman.1599983.
EndNote Yılmaz A, Demircan O, Tutuş R (December 1, 2024) Analysis of Genetic Variations within Q. coccifera L. and the Effects of Geographical Differences in Relationships among Populations. Kastamonu University Journal of Forestry Faculty 24 3 302–311.
IEEE A. Yılmaz, O. Demircan, and R. Tutuş, “Analysis of Genetic Variations within Q. coccifera L. and the Effects of Geographical Differences in Relationships among Populations”, Kastamonu University Journal of Forestry Faculty, vol. 24, no. 3, pp. 302–311, 2024, doi: 10.17475/kastorman.1599983.
ISNAD Yılmaz, Aykut et al. “Analysis of Genetic Variations Within Q. Coccifera L. And the Effects of Geographical Differences in Relationships Among Populations”. Kastamonu University Journal of Forestry Faculty 24/3 (December 2024), 302-311. https://doi.org/10.17475/kastorman.1599983.
JAMA Yılmaz A, Demircan O, Tutuş R. Analysis of Genetic Variations within Q. coccifera L. and the Effects of Geographical Differences in Relationships among Populations. Kastamonu University Journal of Forestry Faculty. 2024;24:302–311.
MLA Yılmaz, Aykut et al. “Analysis of Genetic Variations Within Q. Coccifera L. And the Effects of Geographical Differences in Relationships Among Populations”. Kastamonu University Journal of Forestry Faculty, vol. 24, no. 3, 2024, pp. 302-11, doi:10.17475/kastorman.1599983.
Vancouver Yılmaz A, Demircan O, Tutuş R. Analysis of Genetic Variations within Q. coccifera L. and the Effects of Geographical Differences in Relationships among Populations. Kastamonu University Journal of Forestry Faculty. 2024;24(3):302-11.

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