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    Conflicting signals in phylogenetic relationships and taxonomy of Anatolian endemic Silene sordida (Caryophyllaceae)
    (Magnolia Press, 2022) Toprak, Zeynep; Yildiz, Kemal
    Silene sordida is a Southwest Anatolian endemic that shows highly contradicting signals regarding its actual classification. Using morphological, molecular, and palynological data we here investigate phylogeny and taxonomy of S. sordida. Morphological and palynological features of S. sordida are compared to the species known as very closely related to S. sordida. In addition, we generated DNA sequences of three nuclear and one plastid loci from S. sordida and some allied species belonging to several sections and analyzed these data together with the available sequence data of corresponding taxa. Our findings strongly support the unrelatedness of S. sordida with the section Atocion. The relationship between S. sordida and the section Cryptoneurae and S. odontopetala remains unstable among the four loci analyzed. Both morphological and molecular evidence suggest the recognition of a new monotypic section (here named ???Sordidae???).
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    Convergent Morphological Evolution in Silene Sect. Italicae (Caryophyllaceae) in the Mediterranean Basin
    (Frontiers Media Sa, 2022) Naciri, Yamama; Toprak, Zeynep; Prentice, Honor C.; Hugot, Laetitia; Troia, Angelo; Burgarella, Concetta; Lluis Gradaille, Josep
    Recent divergence can obscure species boundaries among closely related taxa. Silene section Italicae (Caryophyllaceae) has been taxonomically controversial, with about 30 species described. We investigate species delimitation within this section using 500 specimens sequenced for one nuclear and two plastid markers. Despite the use of a small number of genes, the large number of sequenced samples allowed confident delimitation of 50% of the species. The delimitation of other species (e.g., Silene nemoralis, S. nodulosa and S. andryalifolia) was more challenging. We confirmed that seven of the ten chasmophyte species in the section are not related to each other but are, instead, genetically closer to geographically nearby species belonging to Italicae yet growing in open habitats. Adaptation to chasmophytic habitats therefore appears to have occurred independently, as a result of convergent evolution within the group. Species from the Western Mediterranean Basin showed more conflicting species boundaries than species from the Eastern Mediterranean Basin, where there are fewer but better-delimited species. Significant positive correlations were found between an estimation of the effective population size of the taxa and their extent of occurrence (EOO) or area of occupancy (AOO), and negative but non-significant correlations between the former and the posterior probability (PP) of the corresponding clades. These correlations might suggest a lower impact of incomplete lineage sorting in species with low effective population sizes and small distributional ranges compared with that in species inhabiting large areas. Finally, we confirmed that S. italica and S. nemoralis are distinct species, that S. nemoralis might furthermore include two different species and that S. velutina from Corsica and S. hicesiae from the Lipari Islands are sister species.
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    Investigation of the occurrence of silene fuscata in Anatolia based on molecular analysis
    (ABADER (Adıyaman Bilimsel Arastırmalar Dernegi), 2023) Toprak, Zeynep
    Silene fuscata is an annual species distributed to a wide geography including Eastern Mediterranean, Northern Africa, and Southern Europe. The native range of this species is known as the Mediterranean Region. Presence of S. fuscata in Anatolia is reported by several comprehensive botanical literatures; however, the actual situation has never been investigated thoroughly. This study focuses on the occurrence of S. fuscata in Anatolia. In order to determine the existence of this species in the aforementioned area, nuclear and chloroplast-DNA sequence data from a wide range of Silene samples were analyzed. DNA sequence analyses and other available evidence display no support for the presence of S. fuscata in Anatolia.
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    Katı-faz fermentasyon (solid state fermentation) tekniğiyle alkalin proteaz eldesi
    (2016) Toprak, Zeynep; Uyar, Fikret
    Katı-Faz Fermentasyon (SSF) tekniğiyle alkalin proteaz üretiminin incelendiği bu çalışmada Bacillus sp. 'nin hangi substrat varlığında daha iyi alkalin proteaz ürettiğini tespit etmek için ; muz kabuğu, pirinç kabuğu ve darı bitkisi kullanıldı. Yapılan deneyler sonucunda en yüksek enzim üretimi muz kabuğunda 72 saat inkübasyon süresi ve 1500 um parçacık büyüklüğünde görüldü. Mikroorganizma için uygun substrat belirlendikten sonra katı-faz fermentasyon (SSF) sistemlerinde enzim üretimini etkileyen İnkübasyon süresi, pH, sıcaklık, ekim miktarı, azot ve karbon kaynağı ilavesi gibi bazı parametrelerin etkileri incelendi. Yapılan inhibisyon çalışmasında PMSF ile inhibe olan enzimin Alkalin Serin Proteaz olduğu saptandı. Ca iyonlarının enzimin termal stabilitesi üzerine etkisi belirlendi. Enzimin Km değeri 3,8.10"2 olarak hesaplandı. Anahtar Kelimeler: Bacillus sp., Katı faz fermentasyon, Alkalin serin proteaz, Muz kabuğu.
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    New insights into the Usnea cornuta aggregate (Parmeliaceae, lichenized Ascomycota): Molecular analysis reveals high genetic diversity correlated with chemistry
    (Academic Press Inc Elsevier Science, 2019) Lima Gerlach, Alice da Cruz; Toprak, Zeynep; Naciri, Yamama; Araujo Caviro, Elena; Borges da Silveira, Rosa Mara; Clerc, Philippe
    Biological processes such as hybridization, incomplete lineage sorting and gene flow can obscure the recognition of distinct evolutionary lineages, particularly in groups of organisms that have recently diverged. Therefore, compiling pieces of evidence from diverse data sources is critical to accurately assess species boundaries in such groups. The increasing availability of DNA sequence data allows for a much deeper understanding of diversification and speciation processes and their consequences on biodiversity. In this study, we applied an integrative approach based on DNA sequence, chemical, geographic and morphological data to attempt to define species boundaries in the lichen-forming genus Usnea (Parmeliaceae), particularly the U. cornuta aggregate, a cosmo-politan species group. We provide the first species delimitation for this group in the neotropics based on the multispecies coalescent (MSC) model. Using ITS rDNA and two protein-coding genes, Mcm7 and RPB1, we estimated the species tree under the MSC model in a Bayesian framework using STACEY. Our results indicate that at least nine strongly supported distinct lineages coexist in the U. cornuta aggregate, which are well chemically characterized. Additionally, we found evidence for the polyphyly of three morphospecies, Usnea brasiliensis, U. cornuta and U. dasaea.
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    Recombination provides evidence for ancient hybridisation in the Silene aegyptiaca (Caryophyllaceae) complex
    (Springer Verlag, 2017) Pfeil, Bernard E.; Toprak, Zeynep; Oxelman, Bengt
    Recombination events among distinct alleles complicate phylogenetic estimation. Various in vivo and in vitro processes can bring distinct alleles into the same genome to then undergo recombination, which may subsequently mislead phylogenetic inference if not assessed properly. Among the processes bringing divergent alleles together, hybridisation is perhaps the simplest and most likely, but alternatives need to be considered before hybridisation can be accepted as the underlying cause. Such alternatives include the presence of paralogues or deeply coalescing alleles, as well as amplification artefacts. Here, we document a recombination event that apparently took place between two divergent lineages of the Silene aegyptiaca complex in the flowering plant family Caryophyllaceae. We evaluate several possible mechanisms that might be responsible for the observed pattern. An ancient introgressive hybridisation event was the simplest explanation for the observations, compatible with geographic proximity of the affected lineages, whereas paralogy and deep coalescence are difficult to reconcile with the evidence obtained from a species tree of the group based on six different, non-recombinant genes and gene trees inferred using two partitions of the recombinant locus.
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    Species delimitation without prior knowledge: DISSECT reveals extensive cryptic speciation in the Silene aegyptiaca complex (Caryophyllaceae)
    (Academic Press Inc Elsevier Science, 2016) Toprak, Zeynep; Pfeil, Bernard E.; Jones, Graham; Marcussen, Thomas; Ertekin, Alaattin Selcuk; Oxelman, Bengt
    Species delimitation is a major focus of biosystematics. In recent years, considerable progress has been achieved with the development of the multispecies coalescent (MSC) model, where species constitute the branches of the species tree or network. However, researchers are faced with the limitation that the MSC method of choice often requires a priori assignment of individuals to species. This not only introduces subjectivitiy into the analyses, but may also lead to meaningless species tree hypotheses, if the allele-to-species assignments are inaccurate. DISSECT is a recently introduced method that does not require a priori allele-to-species assignments, but instead examines the posterior probabilities of groupings (clusterings) of individuals under study. Using the DISSECT approach, we analysed genetic data from 75 individual plants belonging to the Silene aegyptiaca species complex that has previously been divided into 3-5 species. Marginal likelihood estimates from *BEAST analyses, run with predefined species classifications, strongly favour those compatible with the DISSECT result over those from morphology- and geography-based taxonomy. We found at least nine species, including several cryptic ones, for which no clear geographical or morphological patterns are correlated. However, the limited data and the possibility of unmodelled processes mean there is still much uncertainty about the true number of MSC species, and for taxonomic purposes, other criteria might be relevant. Nevertheless, we argue that the approach signifies an important step towards objective and testable species delimitations in any organismal group. In particular, it makes it possible to avoid biologically irrelevant species classifications. (C) 2016 Elsevier Inc. All rights reserved.