Browsing by Author "Yigit, Oktay"

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Molecular Phylogenetics of Some Orchis Species (Orchidaceae) Native To Turkey Using Nuclear and Chloroplast Dna Sequences
(Gazi Univ, 2017) Dizkirici, Ayten; Isler, Sinan; Yigit, Oktay
Phylogenetic relationships among nine Turkish Orchis species were inferred from variation in the internal transcribed spacer and maturase Kinase regions. Foreign sequences were also retrieved from NCBI to increase interspecific sampling. The topology of ITS tree was broadly congruent to that of matK tree. The trees showed two major clades; the first one included species from Orchis and Neotinea subgenera and the second included species of Anacamptis subgenus. Phylogenetic separation of some species found in Neotinea and Anacamptis subgenera were previously reported, and the current study also indicated that moving these species into Neotinea and Anacamptis genera could be reasonable.
Molecular Phylogeny of Muscari (Asparagaceae) Inferred From Cpdna Sequences
(Springer, 2019) Dizkirici, Ayten; Yigit, Oktay; Pinar, Mesut; Eroglu, Huseyin
In this study, we tried to figure out phylogenetic relationships and taxonomical positions of closely related Muscari species. Four different cpDNA regions including both coding and non-coding ones, namely, matK, trnT((UGU))-trnL((UAA)) intergenic spacer (IGS), trnL((UAA)) intron and trnL((UAA))-F-(GAA) IGS, were employed to determine the exact circumscription of three subgenera, Muscari, Leopoldia and Botryanthus. Seventy Muscari accessions representing 31 Muscari species and different number of previously published sequences retrieved from NCBI database were analyzed. The concatenated and matK data alone were observed to be informative while none of the used non-coding regions was suitable to determine phylogeny of Muscari. Concatenated alignment gave almost the same tree topology with matK sequence. Muscari azureum and M. coeleste phylogenetically separated from all other species of Botryanthus and four main clades were observed in both of the trees even though three subgenera are accepted by Flora of Turkey. After discussing the phylogenetic positions and morphological characters in detail, moving of these two species from Botryanthus to Pseudomuscari subgenus was suggested. Thus, this study proposes that the number of Muscari subgenera should be increased from three to four in Flora of Turkey. The position of M. mirum was also remarkable; it always located distantly to its relatives of Leopoldia. Although this species may also be distinguished based on morphological features such as quite shorter plant length, one or sometimes two relatively wider leaves, and a larger fruit, it needs further studies to resolve its position reliably. Interesting positions of other species were also discussed in detail based on morphological characters in the text.
Understanding Taxonomic Position of Local Endemic Agropyron Deweyi (Poaceae) Using Morphological Characters and Sequences of Nuclear and Chloroplast Dna Regions
(Springer, 2015) Pinar, Mesut S.; Dizkirici, Ayten; Yigit, Oktay
In this study, both morphological characters and molecular techniques were used to determine the taxonomic position of the local endemic Agropyron deweyi within the genus. Plant length, inflorescence type, flower, leaf, spike, spikelet, indumentum and lemma structures were studied as morphological characters. DNA sequences of the nuclear ribosomal DNA internal transcribed spacer region (nrDNA ITS) and four chloroplast DNA regions [trnT-trnL intergenic spacer (IGS), trnL intron, trnL-trnF IGS and matK gene] were analyzed as part of molecular investigations. The results demonstrated that no remarkable morphological differences exist among studied specimens of A. deweyi and A. cristatum complex. Based on 12 sequences of 4 Agropyron taxa produced from the current study and different numbers of sequences obtained from GenBank, our results support the conclusion that the taxonomic status of Agropyron deweyi is synonymous to that of the species A. cristatum. Sequence divergences were estimated using Kimura two-parameter model, and the phylogenetic analyses were performed using the maximum parsimony (MP) and maximum likelihood (ML) methods. No genetic variation was observed among samples of native A. deweyi and A. cristatum complex regardless of the analyzed region. Agropyron deweyi was especially very similar to A. cristatum subsp. pectinatum var. pectinatum in terms of morphological characters such as inflorescence rachis tough at maturity, spikelets with distinct gaps, indumentum glabrous, and lemma glabrous. Therefore, when all morphological and molecular results are taken into account, A. deweyi and A. cristatum subsp. pectinatum var. pectinatum should be considered as synonym.