Browsing by Author "Kaya, Zeki"

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A Molecular Phylogeny of Salvia Euphratica Sensu Lato (Salvia L., Lamiaceae) and Its Closely Related Species With a Focus on the Section Hymenosphace
(Springer Wien, 2015) Dizkirici, Ayten; Celep, Ferhat; Kansu, Cigdem; Kahraman, Ahmet; Dogan, Musa; Kaya, Zeki
To investigate the phylogenetic relationships of Salvia euphratica sensu lato and its closely related species with a focus on the section Hymenosphace, we screened five different regions; one nuclear ribosomal DNA region (Internal Transcribed Spacer, ITS) and four chloroplast DNA regions [trnT-trnL intergenic spacer (IGS), trnL intron, trnL-trnF IGS and trnV intron]. Based on 19 sequences of 7 Salvia taxa produced in the study and different number of sequences obtained from GenBank, our results supported latest taxonomic treatments on Salvia pseudeuphratica and S. cerino-pruinosa as they are resurrected and accepted different species from S. euphratica. The results confirmed the latest phylogenetic findings as "the section Hymenosphace is a non-monophyletic group, originated thick textured, non-expanding ancestral group, and expanding calyces with widely diverging lips in fruiting stage evolved several times in parallel, not only in Salvia but also in the Iranian genus Zhumeria". The species of the sect. Hymenosphace are mostly distributed in three different geographic regions [(1) Southwest Asia, Turkey, Russia and Iran, (2) Canary Islands, (3) Southern Africa] with different morphological characters. The results showed that ITS had the highest resolution power for discriminating studied taxa and the highest number of haplotypes was also observed in this region. The resolutions of the chloroplast regions were too low for taxa native to Turkey, but quite enough to discriminate species from the different clades whose sequences were obtained from database.
Phylogenetic Relationships Among Native Oxytropis Species in Turkey Using the Trnl Intron, Trnl-F Igs, and Trnv Intron Cpdna Regions
(Tubitak Scientific & Technological Research Council Turkey, 2016) Tekpinar, Ayten; Erkul, Seher Karaman; Aytac, Zeki; Kaya, Zeki
We tested the phylogenetic utility of three chloroplast DNA loci, i.e. the trnL((UAA)) intron,trnL((UAA))-F-(GAA) intergenic spacer (IGS), and trnV((UAC)) intron, across thirteen native Oxytropis species. Our objective was to determine whether any of these chloroplast DNA markers could be beneficial to figure out phylogenetic relationships among Oxytropis species. To increase the interspecific sampling, nine sequences of the trnL intron and trnL-F regions were retrieved from GenBank and included in the analyses. No sequence of the trnV intron region was available in the database and so only sequences of the native species were used for the analyses. Phylogenies derived from maximum likelihood and maximum parsimony analyses indicated that the trnL intron and trnV intron regions provided better resolution for relationships among species with respect to the trnL-F region. The highest variable and parsimony informative sites were observed in the trnL intron region, while the lowest sites were seen in the trnV intron. Less variable sites for the trnV intron region were expected since no foreign sequences could be included in the analysis. Oxytropis lazica was phylogenetically separated from native species and clustered with foreign ones when the trnL intron and trnL-F regions were analyzed. The result obtained from the trnV intron region proved that Oxytropis engizekensis Duman and Vural may be a synonym of O. persica Boiss. A previous study that used morphological characters arrived at a similar conclusion.
Phylogenetic Relationships Among Triticum L. and Aegilops L. Species as Genome Progenitors of Bread Wheat Based on Sequence Diversity in Trnt-F Region of Chloroplast Dna
(Springer, 2013) Dizkirici, Ayten; Kansu, Cigdem; Onde, Sertac; Birsin, Melahat; Ozgen, Murat; Kaya, Zeki
Cultivated wheat, (Triticum aestivum L.), is one of the most important food crops in the world. The Aegilops L. genus is frequently utilized by plant breeders for improving the current wheat cultivars due to their close relationships. Therefore, understanding the phylogenetic relationships among the species of these genera is not only valuable for plant taxonomy, but also for plant breeding efforts. The presented phylogenetic analysis was based on the sequences of trnT-F chloroplast DNA containing three non-coding sub-regions. Twelve genotypes belonging to four species of Triticum L. genus and twenty-four genotypes belonging to eight species of Aegilops genus were used in the current study. The results postulated a close genetic relationship between diploid Aegilops species containing the BB genome and polyploid Triticum species. With the exception of Aegilops cylindrica Host (CCDD), all other Aegilops species having the CC genome were alienated from Aegilops speltoides Tausch (BB) and clustered together. These two clusters joined by a third cluster including the AA genome containing diploid Triticum species.
Phylogenetic Relationships Between Oxytropis Dc. and Astragalus L. Species Native To an Old World Diversity Center Inferred From Nuclear Ribosomal Its and Plastid Matk Gene Sequences
(Tubitak Scientific & Technological Research Council Turkey, 2016) Tekpinar, Ayten Dizkirici; Erkul, Seher Karaman; Aytac, Zeki; Kaya, Zeki
Oxytropis and Astragalus represent one of the largest angiosperm genera complexes. Although phylogenetic studies of this complex exist, the evolutionary relationships among Astragalus and Oxytropis species sharing similar habitats in the Old World have not been studied in detail. The phylogenetic relationships among 13 Oxytropis and 56 Astragalus species native to Turkey were inferred from nucleotide sequence variations in the nuclear ribosomal internal transcribed spacer (ITS) and chloroplast maturase-like protein (matK) gene regions. In addition to our samples, 36 Oxytropis ITS and 6 Oxytropis matK sequences were retrieved from GenBank and included in the analysis. Phylogenies derived from a maximum likelihood analysis of the sequences indicated that Oxytropis and Astragalus genera are more likely monophyletic. However, the results suggest that New World Oxytropis species did not evolve by a single adaptive radiation in the genus, but rather from different Old World lineages. The genetic divergence between genera was less when the matK region was analyzed. Although the Oxytropis species did not show high genetic diversity, one subcluster of the genus was always distinctly separated in both trees. This subcluster was formed by the species Oxytropis engizekensis Duman & Vural and O. persica Boiss., which are also regarded as synonyms in regard to several morphological characters of the genus.
Phylogeography and Phylogeny of Genus Quercus L. (Fagaceae) in Turkey Implied by Variations of Trnt(ugu)-L(uaa)< (Gaa) Chloroplast Dna Region
(Springer Heidelberg, 2021) Tekpinar, Ayten Dizkirici; Aktas, Caner; Kansu, Cigdem; Duman, Hayri; Kaya, Zeki
The genus Quercus L. is one of the most abundant and important genera of woody plants in the Northern Hemisphere as well as in Turkey. In the current study which is the most comprehensive study dealing with Turkish oaks, sequence variations of three noncoding regions (trnT((UGU))-L-(UAA) IGS, trnL((UAA))intron, trnL((UAA))-F-(GAA) IGS) of chloroplast DNA (cpDNA) were used for phylogeographic and phylogenetic analysis on 319 individuals representing 23 taxa (17 species). The trnT((UGU))-L-(UAA) region was found to be the most variable and parsimony informative region. Twenty-eight cpDNA haplotypes were identified based on 34 substitutions and 22 indels. High number of haplotypes and h(T) > v(T) observed in populations of oaks in Turkey indicated that the Anatolian Peninsula might have been a refugium at Glacial Periods. Phylogeographic construction and molecular variance analysis revealed that Quercus cpDNA haplotypes were geographically structured. Although local haplotype sharing among species from same infrageneric clades was common, levels of hybridization differ between species pairs. Haplotype analysis revealed four infrageneric clades, namely Section Quercus, Section Cerris and two clades corresponding to Section Ilex, namely "Ilex" and "Coccifera." Furthermore, a Section Cerris haplotype was detected in the Aegean members of Q. ilex and Q. coccifera. Section Ponticae was placed in the Section Quercus cluster. In contrast to the phylogenetic reconstructions based on the nuclear DNA sequence data, Group Ilex seems to be polyphyletic based on plastome phylogeny. Chloroplast phylogeny of oaks reflects the traces of recent and ancient introgression events during diversification of species. In addition to this, incomplete linkage sorting may also explain this polymorphic assemblage. Therefore, further investigation is required to clarify the cpDNA phylogeny of oaks, especially for Section Ilex.
Updated-Extended Molecular Time and Molecular Phylogeny of Gundelia Species Native To Turkey
(Springer Wien, 2021) Ates, M. Alev; Firat, Mehmet; Kaya, Zeki
Generally, Gundelia tournefortii is considered as the sole representative of the genus and the other species of Gundelia as synonyms. Recent studies suggest that the genus is rich with 22 species. Off these, thirteen are endemic to Turkey. To date, no comprehensive molecular study dealing with speciation exists in the genus. To address the speciation at the molecular level, fresh leaves from 57 samples representing 15 species from their natural ranges in Turkey were obtained by sampling over several years and studied with respect to nrDNA (ITS) and the cpDNA (ndhF) gene regions. Molecular data from cpDNA and nrDNA revealed that there were two major clades. One of these clades consists of G. anatolica, G. glabra and G. asperrima when the ndhF data were used (or just G. anatolica based on ITS data) while the other major clade included the remaining species with subclades. Divergence time and geographical phylogenetic reconstruction analysis indicated that there may be 3 major ancestral associations existing in the studied Gundelia species. Based on ndhF data, the oldest ancestral group included G. anatolica, G. glabra and G. asperrima with the divergence time about 21.27 MYA, while G. tournefortii var. tenuisecta and G. dersim were the most recently diverged group (about 4.66 MYA). Ancestral history of diversity analysis suggested that the dispersal and vicariance events involved in the speciation in the genus Gundelia with complex events of natural hybridization, introgression, geographical isolations or some other weak isolation mechanisms.