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Molecular phylogeny of beech (Fagus) populations in Turkey

Year 2016, Volume: 1 Issue: 4 A, 69 - 79, 24.12.2016
https://doi.org/10.17568/oad.84722

Abstract

Fagus orientalis Lipsky (Oriental beech) indigenously grows in the west from Balkans through Anatolia, to the east Caucasus, northern Iran and Crimea. In Turkey there is also natural distribution of Fagus sylvatica L. (European beech).
In this study molecular divergence of Oriental beech and European beech was investigated by ITS-5 region. Oriental beech and European beech samples were collected from 11 different natural populations. During sampling, populations were selected from four seed transfer zones of distributional area in Turkey. In addition to different zones, marginal populations were also sampled. For each population, leaves from 5 single-trees were harvested for DNA isolation. Nuclear ribosomal ITS-5 region sequences didn’t show different grouping in European and Oriental beech populations.

References

  • Alvarez, I., Mendel, J.F. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet.Evol. 29: 417-434.
  • Anonim, 1985. Kayın. OAE El kitabı dizisi no:1. Muhtelif yayınlar serisi:42. Ankara
  • Anonim, 2015. Orman Varlığımız. OGM yayını ANKARA.
  • Anşin, R., Özkan, Z. C. 1997. Tohumlu bitkiler. Odunsu taksonlar. KTÜ Or. Fak. Yayın no:19. Trabzon.
  • Atalay, İ. 1992. Kayın ormanlarının ekolojisi ve tohum transfer yönünden bölgelere ayrılması. OATIAM Yayın no:5. 209 sayfa, ANKARA.
  • Aydınözü, D. 2008. Avrupa kayınının Yıldız Dağlarındaki yayılış alanı Coğrafya Dergisi (İstanbul Üniversitesi Edebiyat Fakültesi Coğrafya Bölümü) Sayı17, sayfa 44-56.
  • Baldwin, B. G. 1992. Phylogenetic utility of the Internal Transcribed Spacers of Nuclear Ribosomal DNA in PLants: An example from the Compositae. Molecular Phylogenetics and Evolution
  • Conkle, M.T. 1980. Amount and Distribution of Isozyme Variation in Various Conifers Species. In: Proceeding of the 7th Meeting. Canadian For. Ser. page: 109-117.
  • Çalıkoğlu, M. Kavgacı, A. 2001. Biyolojik çeşitliliğin sürekliliği ve arttırılması açısından baltalıkların koruya dönüştürülmesi. İO Fak Der. Seri B, Cilt 51. sayı 1. 111-121.
  • Cossalter, C. 1989. Genetic Conservation: A cornerstone of breeding strategies: Breeding Tropical Trees. Population Structure and Gene Improvement Strategies in Clonal and Seedling Forestry. (Proc. IUFRO Conference Pattaya, Thailand, November 1988). Gibson, G.J. Grıffın, A.R. Matheson, A.C. (Ed.) Oxford Forestry Institute, Oxford, U.K. 28-38.
  • Davis, P. H. 1982. Flora of Turkey and the East Aegean Island, Edinburg Uni. Pres. Volume VII.
  • Demesure, B., Comps, B. Petit, J. 1996. Chloroplast DNA phylogeography of the common beech (Fagus sylvatica L.) in Europe. Evolution 50: 2515-2520.
  • Denk, T.H. 1999.The taxonomy of Fagus in Eurasia. 2: Fagus sylvatica subs. Sylvatica. Feddes Repertorium 11: 5-6, 381-412.
  • Denk, T.Grimm, G., Stögerer, K., Langer, M., Hemleben, V. 2002. The evolutionary history of Fagus in western Eurasia: evidence from genes, morphology and the fossil record. Plant Systematics and Evolution 232: 213–236.
  • Dirik, H. 1994. Genetik çeşitlilik orman gen kaynalarının korunması. İ.Ü. Orman Fakültesi Dergisi, Seri B, Cilt 44, Sayı 3-4, Sayfa 13-121, İstanbul.
  • Doyle, J.J., Doyle, J.L. 1990. Isolation of plant DNA from fresh tissue. Focus 12: 13-15.
  • El-Kasaby, Y. A. 1995. Evaluation of the tree improvement delivery system: Factors affecting genetic potential. Tree Physiol.15:545-550.
  • Feliner, G. N., Rossello, J. A. 2007. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Molecular Phylogenetics and Evolution 44:911-919.
  • Gailling, O., Wuehlisch, V.G. 2004. Nuclear markers (AFLPs) and chloroplast microsatellites differ between Fagus sylvatica and Fagus orientalis. Silvae Genetica, 53, 3.105-110.
  • Gielly, L., Tabarlet, P. 1994. The use of chloroplast DNA to resolve plant phylogenies: Noncoding versus rbcL sequences. Molecular Biology and Evolution. 11(5):769-777.
  • Graham, S.W., Olmstead, R.G. 2000.Systematics utility of 17 chloroplast genes for inferring the phylogeny of the Angiosperms. American Journal of Botany, 11: 87-97.
  • Gömöry, D., Paulo, L., Brus, P., Zhelev, Z., Tomovic,Z., Gracans, J. 1999. Genetic differentiation and phylogeny of beech on Balkan Peninsula. J. Evol. Biol. 12, 748-754.
  • Gömöry, D., Paulo, L., Vysyn, J. 2007. Patterns of allozyme variation in western Eurasian Fagus Botanical Journal of the Linnean Society Volume 154, Issue 2, pages 165–174, June 2007.
  • Hatziskakis, S., Papageorgiou, A.C., Gailing, O. Finkeldey, R. 2009. High chloroplast haplotype diversitiy in Greek populations of beech. Plant Biology 11, 425-433.
  • Hatziskakis, S., Tsiripidis, I., Papageorgiou, A. C. 2011. Leaf morphological variation in beech (Fagus sylvatica L.) populations in Greece and its relation to their post-glacial origins. Botanical Journal of the Linnean Society, 165: 422-436.
  • Hughes, C.E, Eastwood, R.J., Bailey, C.D. 2006. From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction. Phil. Trans. R. Soc.B. 361:211-225.
  • Kandemir, G.E. 2010. COST Action E52, Genetic resources of beech in Europe-current strate, vol 25, pp 256-264.
  • Kandemir, G. 2013 http://www.fao.org/3/a-i3825e/i3825e71.pdf.
  • Kandemir, G., Kaya, Z. 2009. Technical guidelines of EUFORGEN. Fagus orientalis, Lipsky.
  • Kimura, M., Crow, J.F. 1964. The number of alleles that can be maintained in a finite population. Genetics 49:725-38.
  • Kimura, M. 1980."A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences". Journal of Molecular Evolution 16 (2): 111–120.
  • Koski, V., Antola, J. 1993. Türkiye Milli Ağaç Islahı ve Tohum Üretimi Programı. Ankara.
  • Li, D-Z, Gaoa, L-M., Lia, H-T., Gea, X-J., Liu, J-Q., Chena, Z. D., Zhoua, S-L., Yanga, J-B., Fua, C-X, Zenga, C-X., Yana, H-F., Zhua, Y-J., Suna, Y-S., Chena, S-Y., Zhoa, L., Wanga, K., Yanga, T. and Duana, G-W. 2011. Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. PNAS, vol. 108 no 149, p19641-19646.
  • Magri, D., Vendramin, G. G., Comps, B., Dupanloup, I., Geburek, T., Gömöry, D., Latalowa, M., Litt, T., Paule, L., Roure, J.M., Tantau, I., Van Der Knap, W. O., Petit, R. J., Beaulieu, J. L. 2006. A new scenario for the Quaternary history of European beech populations: palaebotanical evidence and genetic consequences. New Phytologist 171: 199-221.
  • Nei, M. 1972. Genetic distance between populations. American Naturalist, 106:283-292.
  • Papageorgiou, A. C., Vidalis, A., Gailing, O., Tsiripidis, I. Hatziskakis, S., Boutsios, S. Galatsidas, S., Finkeldey, R. 2008. Genetic variation of beech (Fagus sylvatica) in Rodopi (N.E. Greece). European Journal of Forestry Research 127: 81-88.
  • Paule, L. 1995. Gene conservation in European beech (Fagus sylvatica L.) For. Genet. 2 (3): 161-170.
  • Shanjani, P., Vettori, C. Giannini, R., Khavari-Nejad, R. A. 2004. Intraspecific variation and geographic patterns of Fagus orientalis Lipsky chloroplast DNA. Silvae Genetica 53, 5-6 page 193-197.
  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution doi: 10.1093/molbev/msr121.
  • Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G. 1997. The CLUSTAL –X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (24): 4876-4882.
  • Vettori, C., Pafetti, D., Paule, L. Giannini, R. 2004. Identification of the Fagus sylvatica L. and Fagus orientalis L. species and intraspecific variability. Forest Genetics 11(3-4):223-230.
  • White, T.J., Bruns T., Lee S., Taylor, J.W. 1990. Amplification and Direct Sequencing of Fungal Ribosomal RNA Genes For Phylogenetics. Pp. 315-322 In: PCR Protocols: A Guide to Methods and Applications, eds. Innis, M. A., D. H. Gelfand, J. J. Sninsky, and T. J. White. Academic Press, Inc., New York.
  • Zobel, B., Talbert, S. 1984. Applied forest tree improvement. North Carolina State University. Wiley and Sons. Inc. NY.

Türkiye’de yayılış gösteren kayın (Fagus) populasyonlarının moleküler filogenisi

Year 2016, Volume: 1 Issue: 4 A, 69 - 79, 24.12.2016
https://doi.org/10.17568/oad.84722

Abstract

Fagus orientalis Lipsky (Doğu kayını) Balkanlar'dan Batı Anadolu üzerinden Doğu Kafkasya, Kuzey İran ve Kırım'a kadar yetişen yerli türlerdendir. Türkiye’de ayrıca Fagus sylvatica L. (Avrupa kayını) da yayılış göstermektedir.

Bu çalışmada, Türkiye’de doğal olarak yayılış gösteren on bir Doğu kayını ve Avrupa kayını populasyonu çekirdek ITS-5 bölgesi incelenerek tür farkı belirlenmeye çalışılmıştır. Çalışmada on bir farklı Avrupa ve Doğu kayını populasyonundan örnekleme yapılmıştır. Örnekleme yapılırken dört tohum transfer zonu dikkate alınmıştır. Bu zonların dışında örnekleme yaparken yükselti olarak marjinal populasyonlar da dikkate alınmıştır. Her bir populasyondan beşer ağacın yaprakları DNA izolasyonu için kullanılmış ve populasyonların çekirdek ribozomal ITS-5 bölgesi dizi analizleri yapılmıştır.  Populasyonların ITS-5 bölgesi incelendiğinde, bu bölge DNA dizilerinde Doğu kayını ve Avrupa kayını dizileri farklı bir gruplaşma göstermemiştir.

References

  • Alvarez, I., Mendel, J.F. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet.Evol. 29: 417-434.
  • Anonim, 1985. Kayın. OAE El kitabı dizisi no:1. Muhtelif yayınlar serisi:42. Ankara
  • Anonim, 2015. Orman Varlığımız. OGM yayını ANKARA.
  • Anşin, R., Özkan, Z. C. 1997. Tohumlu bitkiler. Odunsu taksonlar. KTÜ Or. Fak. Yayın no:19. Trabzon.
  • Atalay, İ. 1992. Kayın ormanlarının ekolojisi ve tohum transfer yönünden bölgelere ayrılması. OATIAM Yayın no:5. 209 sayfa, ANKARA.
  • Aydınözü, D. 2008. Avrupa kayınının Yıldız Dağlarındaki yayılış alanı Coğrafya Dergisi (İstanbul Üniversitesi Edebiyat Fakültesi Coğrafya Bölümü) Sayı17, sayfa 44-56.
  • Baldwin, B. G. 1992. Phylogenetic utility of the Internal Transcribed Spacers of Nuclear Ribosomal DNA in PLants: An example from the Compositae. Molecular Phylogenetics and Evolution
  • Conkle, M.T. 1980. Amount and Distribution of Isozyme Variation in Various Conifers Species. In: Proceeding of the 7th Meeting. Canadian For. Ser. page: 109-117.
  • Çalıkoğlu, M. Kavgacı, A. 2001. Biyolojik çeşitliliğin sürekliliği ve arttırılması açısından baltalıkların koruya dönüştürülmesi. İO Fak Der. Seri B, Cilt 51. sayı 1. 111-121.
  • Cossalter, C. 1989. Genetic Conservation: A cornerstone of breeding strategies: Breeding Tropical Trees. Population Structure and Gene Improvement Strategies in Clonal and Seedling Forestry. (Proc. IUFRO Conference Pattaya, Thailand, November 1988). Gibson, G.J. Grıffın, A.R. Matheson, A.C. (Ed.) Oxford Forestry Institute, Oxford, U.K. 28-38.
  • Davis, P. H. 1982. Flora of Turkey and the East Aegean Island, Edinburg Uni. Pres. Volume VII.
  • Demesure, B., Comps, B. Petit, J. 1996. Chloroplast DNA phylogeography of the common beech (Fagus sylvatica L.) in Europe. Evolution 50: 2515-2520.
  • Denk, T.H. 1999.The taxonomy of Fagus in Eurasia. 2: Fagus sylvatica subs. Sylvatica. Feddes Repertorium 11: 5-6, 381-412.
  • Denk, T.Grimm, G., Stögerer, K., Langer, M., Hemleben, V. 2002. The evolutionary history of Fagus in western Eurasia: evidence from genes, morphology and the fossil record. Plant Systematics and Evolution 232: 213–236.
  • Dirik, H. 1994. Genetik çeşitlilik orman gen kaynalarının korunması. İ.Ü. Orman Fakültesi Dergisi, Seri B, Cilt 44, Sayı 3-4, Sayfa 13-121, İstanbul.
  • Doyle, J.J., Doyle, J.L. 1990. Isolation of plant DNA from fresh tissue. Focus 12: 13-15.
  • El-Kasaby, Y. A. 1995. Evaluation of the tree improvement delivery system: Factors affecting genetic potential. Tree Physiol.15:545-550.
  • Feliner, G. N., Rossello, J. A. 2007. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Molecular Phylogenetics and Evolution 44:911-919.
  • Gailling, O., Wuehlisch, V.G. 2004. Nuclear markers (AFLPs) and chloroplast microsatellites differ between Fagus sylvatica and Fagus orientalis. Silvae Genetica, 53, 3.105-110.
  • Gielly, L., Tabarlet, P. 1994. The use of chloroplast DNA to resolve plant phylogenies: Noncoding versus rbcL sequences. Molecular Biology and Evolution. 11(5):769-777.
  • Graham, S.W., Olmstead, R.G. 2000.Systematics utility of 17 chloroplast genes for inferring the phylogeny of the Angiosperms. American Journal of Botany, 11: 87-97.
  • Gömöry, D., Paulo, L., Brus, P., Zhelev, Z., Tomovic,Z., Gracans, J. 1999. Genetic differentiation and phylogeny of beech on Balkan Peninsula. J. Evol. Biol. 12, 748-754.
  • Gömöry, D., Paulo, L., Vysyn, J. 2007. Patterns of allozyme variation in western Eurasian Fagus Botanical Journal of the Linnean Society Volume 154, Issue 2, pages 165–174, June 2007.
  • Hatziskakis, S., Papageorgiou, A.C., Gailing, O. Finkeldey, R. 2009. High chloroplast haplotype diversitiy in Greek populations of beech. Plant Biology 11, 425-433.
  • Hatziskakis, S., Tsiripidis, I., Papageorgiou, A. C. 2011. Leaf morphological variation in beech (Fagus sylvatica L.) populations in Greece and its relation to their post-glacial origins. Botanical Journal of the Linnean Society, 165: 422-436.
  • Hughes, C.E, Eastwood, R.J., Bailey, C.D. 2006. From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction. Phil. Trans. R. Soc.B. 361:211-225.
  • Kandemir, G.E. 2010. COST Action E52, Genetic resources of beech in Europe-current strate, vol 25, pp 256-264.
  • Kandemir, G. 2013 http://www.fao.org/3/a-i3825e/i3825e71.pdf.
  • Kandemir, G., Kaya, Z. 2009. Technical guidelines of EUFORGEN. Fagus orientalis, Lipsky.
  • Kimura, M., Crow, J.F. 1964. The number of alleles that can be maintained in a finite population. Genetics 49:725-38.
  • Kimura, M. 1980."A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences". Journal of Molecular Evolution 16 (2): 111–120.
  • Koski, V., Antola, J. 1993. Türkiye Milli Ağaç Islahı ve Tohum Üretimi Programı. Ankara.
  • Li, D-Z, Gaoa, L-M., Lia, H-T., Gea, X-J., Liu, J-Q., Chena, Z. D., Zhoua, S-L., Yanga, J-B., Fua, C-X, Zenga, C-X., Yana, H-F., Zhua, Y-J., Suna, Y-S., Chena, S-Y., Zhoa, L., Wanga, K., Yanga, T. and Duana, G-W. 2011. Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. PNAS, vol. 108 no 149, p19641-19646.
  • Magri, D., Vendramin, G. G., Comps, B., Dupanloup, I., Geburek, T., Gömöry, D., Latalowa, M., Litt, T., Paule, L., Roure, J.M., Tantau, I., Van Der Knap, W. O., Petit, R. J., Beaulieu, J. L. 2006. A new scenario for the Quaternary history of European beech populations: palaebotanical evidence and genetic consequences. New Phytologist 171: 199-221.
  • Nei, M. 1972. Genetic distance between populations. American Naturalist, 106:283-292.
  • Papageorgiou, A. C., Vidalis, A., Gailing, O., Tsiripidis, I. Hatziskakis, S., Boutsios, S. Galatsidas, S., Finkeldey, R. 2008. Genetic variation of beech (Fagus sylvatica) in Rodopi (N.E. Greece). European Journal of Forestry Research 127: 81-88.
  • Paule, L. 1995. Gene conservation in European beech (Fagus sylvatica L.) For. Genet. 2 (3): 161-170.
  • Shanjani, P., Vettori, C. Giannini, R., Khavari-Nejad, R. A. 2004. Intraspecific variation and geographic patterns of Fagus orientalis Lipsky chloroplast DNA. Silvae Genetica 53, 5-6 page 193-197.
  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution doi: 10.1093/molbev/msr121.
  • Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G. 1997. The CLUSTAL –X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (24): 4876-4882.
  • Vettori, C., Pafetti, D., Paule, L. Giannini, R. 2004. Identification of the Fagus sylvatica L. and Fagus orientalis L. species and intraspecific variability. Forest Genetics 11(3-4):223-230.
  • White, T.J., Bruns T., Lee S., Taylor, J.W. 1990. Amplification and Direct Sequencing of Fungal Ribosomal RNA Genes For Phylogenetics. Pp. 315-322 In: PCR Protocols: A Guide to Methods and Applications, eds. Innis, M. A., D. H. Gelfand, J. J. Sninsky, and T. J. White. Academic Press, Inc., New York.
  • Zobel, B., Talbert, S. 1984. Applied forest tree improvement. North Carolina State University. Wiley and Sons. Inc. NY.
There are 43 citations in total.

Details

Journal Section Tree Breeding
Authors

Gaye Eren Kandemir

Yasemin Tayanç This is me

Burcu Çengel This is me

Ercan Velioğlu

Publication Date December 24, 2016
Submission Date March 11, 2016
Published in Issue Year 2016 Volume: 1 Issue: 4 A

Cite

APA Eren Kandemir, G., Tayanç, Y., Çengel, B., Velioğlu, E. (2016). Türkiye’de yayılış gösteren kayın (Fagus) populasyonlarının moleküler filogenisi. Ormancılık Araştırma Dergisi, 1(4 A), 69-79. https://doi.org/10.17568/oad.84722
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