Makale Koleksiyonu

Bu koleksiyon için kalıcı URI

https://hdl.handle.net/20.500.12587/18856

Listeleniyor 1 - 20 / 569

Whole-genome analyses disentangle reticulate evolution of primroses in a biodiversity hotspot
(Wiley, 2023) Stubbs, Rebecca L.; Theodoridis, Spyros; Mora-Carrera, Emiliano; Keller, Barbara; Yousefi, Narjes; Potente, Giacomo; Leveille-Bourret, Etienne
Biodiversity hotspots, such as the Caucasus mountains, provide unprecedented opportunities for understanding the evolutionary processes that shape species diversity and richness. Therefore, we investigated the evolution of Primula sect. Primula, a clade with a high degree of endemism in the Caucasus. We performed phylogenetic and network analyses of whole-genome resequencing data from the entire nuclear genome, the entire chloroplast genome, and the entire heterostyly supergene. The different characteristics of the genomic partitions and the resulting phylogenetic incongruences enabled us to disentangle evolutionary histories resulting from tokogenetic vs cladogenetic processes. We provide the first phylogeny inferred from the heterostyly supergene that includes all species of Primula sect. Primula. Our results identified recurrent admixture at deep nodes between lineages in the Caucasus as the cause of non-monophyly in Primula. Biogeographic analyses support the 'out-of-the-Caucasus' hypothesis, emphasizing the importance of this hotspot as a cradle for biodiversity. Our findings provide novel insights into causal processes of phylogenetic discordance, demonstrating that genome-wide analyses from partitions with contrasting genetic characteristics and broad geographic sampling are crucial for disentangling the diversification of species-rich clades in biodiversity hotspots.
Web Structure and Silk Spinning Apparatus Morphology of Uloborus walckenaerius Latreille 1806 (Araneae, Uloboridae) Spider
(Hard, 2024) Öcal, İlkay Çorak; Kayhan, Nazife Yiğit; Aktaş, Ümmügülsüm Hanife
The web- building skills of spiders made them strong from the evolutionary aspect. Spider webs are used in hunting, building nests, setting traps, and movement. The structure of web architecture, that of adhesive materials being produced, and that of cribellate offer important clues in order to understand their hunting behaviors. Spiders have different silk -spinning apparatuses, allowing them to produce different types of silk fibrils. While some spider species rely on webs for survival in nature, others can survive without them. Even though basic taxonomic features remain constant, the silk -spinning apparatuses of spiders might be subjected to adaptive variations. In the present study, the structural organization of the silk -spinning apparatus and the web architecture of the web -maker spider Uloborus walckenaerius Latreille, 1806 were observed by making use of scanning electron microscopy (SEM). The web structure of U. walckenaerius, the characteristics of the spinnerets, especially the posterior spinneret, and the arrangement of the spigots are reported in this study. Adaptations of the silk -spinning apparatus, which has provided an evolutionary success to U. walckenaerius, were also analyzed. It was determined that the web structure consisted of very fine nanofibers and, differing from other groups, there also were crimped silk fibrils.
Unveiling the Genome-Wide Consequences of Range Expansion and Mating System Transitions in Primula vulgaris
(Oxford Univ Press, 2024) Mora-Carrera, Emiliano; Stubbs, Rebecca L.; Potente, Giacomo; Yousefi, Narjes; Aeschbacher, Simon; Keller, Barbara; Choudhury, Rimjhim Roy
Genetic diversity is heterogeneously distributed among populations of the same species, due to the joint effects of multiple demographic processes, including range contractions and expansions, and mating systems shifts. Here, we ask how both processes shape genomic diversity in space and time in the classical Primula vulgaris model. This perennial herb originated in the Caucasus region and was hypothesized to have expanded westward following glacial retreat in the Quaternary. Moreover, this species is a long-standing model for mating system transitions, exemplified by shifts from heterostyly to homostyly. Leveraging a high-quality reference genome of the closely related Primula veris and whole-genome resequencing data from both heterostylous and homostylous individuals from populations encompassing a wide distribution of P. vulgaris, we reconstructed the demographic history of P. vulgaris. Results are compatible with the previously proposed hypothesis of range expansion from the Caucasus region approximately 79,000 years ago and suggest later shifts to homostyly following rather than preceding postglacial colonization of England. Furthermore, in accordance with population genetic theoretical predictions, both processes are associated with reduced genetic diversity, increased linkage disequilibrium, and reduced efficacy of purifying selection. A novel result concerns the contrasting effects of range expansion versus shift to homostyly on transposable elements, for the former, process is associated with changes in transposable element genomic content, while the latter is not. Jointly, our results elucidate how the interactions among range expansion, transitions to selfing, and Quaternary climatic oscillations shape plant evolution.
Two new spider species of the family Dysderidae (Araneae) from Turkey
(Amer Entomol Soc, 2018) Varol, İsmail; Danışman, Tarık
Two new species of the spider family Dysderidae, Harpactea forceps sp. n. and Dysdera furcatus sp. n. are described from the west Black Sea region of Turkey. Detailed morphological descriptions and diagnoses are presented. Photographs and electron micrographs are included. The two new species are compared with closely related species.
Two new species of Dysdera (Aranei: Dysderidae) from Turkey
(Kmk Scientific Press Ltd, Moscow State Univ, 2024) Coşar, İlhan; Yağmur, Ersen Aydın; Danışman, Tarik; Özkütük, Recep Sulhi; Kunt, Kadir Bogaç
Two new species of Dysdera Latreille, 1804, D. yigitakcai sp.n. (male female; Kahramanmara & scedil;) and D. mehmeti sp.n. (male female; Gaziantep), are described from the eastern Mediterranean region of Turkey. Of these, D . mehmeti sp.n. belongs to the asiatica species-group. Dysdera yigitakcai sp.n. possesses characteristics of different species-groups but appears closest to the longirostris-group.-group. In addition, photographs of the palp of D. neocretica Deeleman-Reinhold, 1988; D. fragaria Deeleman-Reinhold, 1988; and the vulva of D. argaeica Nosek, 1905 are included for comparison.
Two new species belonging to Coreodrassus and Poecilochroa (Aranei: Gnaphosidae) from Anatolia with comments on taxonomy of both genera
(Kmk Scientific Press Ltd, Moscow State Univ, 2024) Coşar, İlhan; Danışman, Tarık; Marusik, Yuri M.
Two new species are described from Anatolia: Coreodrassus recepsahini sp.n. (male female) and Poecilochroa ilkerakkusi sp.n. (male). Coreodrassus recepsahini sp.n. differs from the sibling C. semidesertus Ponomarev et Tsvetkov, 2006 (re-illustrated here) by the shape of copulatory organs. Poecilochroa ilkerakkusi sp.n. well differs from P. hamipalpis (Kroneberg, 1875) by contrast leg colouration. Coreodrassus Paik, 1892 is split in two species groups and diagnoses are provided. Poecilochroa Westring, 1874 species known from males are also split in two groups, of which the senilis-group may represent a separate genus. The type locality of the new species of Coreodrassus represents the westernmost record of the genus in the entire range. Coreodrassus boldgivi Jargalsaikhan, Fomichev et Nergui, 2023 syn.n. from Mongolia was found to be a junior synonym of C. murphyi Liu et Zhang, 2023. All distribution records of Coreodrassus species are mapped. The northernmost distribution limits of two genera are briefly discussed as well as Gnaphosidae species endemic and subendemic to Turkey.
Turkocranum gen. n., a new genus of Liocranidae (Arachnida: Araneae) from Turkey
(Taylor & Francis Ltd, 2022) Danışman, Tarık; Coşar, İlhan
A new genus of Liocranidae, Turkocranum gen. n., is described which can be distinguished from the other genera of Liocraninae by the spination pattern of the legs, the male palp with large lanceolate retrolateral tibial apophysis and the epigyne including triangular septum covered with setae. The genus is regarded as monobasic with T. bosselaersi sp. n. being the only species.
Tissue expression of glutathione S transferase isoenzymes in vitiligo
(Taylor & Francis Ltd, 2022) Uzunçakmak, Tuğba Kevser; Özkanlı, Şeyma; Koçdoğan, Arzu Kaya; Oğuztüzün, Serpil; Karadağ, Ayşe Serap; Özlü, Emin; Akdeniz, Necmettin
The association of glutathione S-transferase (GST) enzymes with vitiligo is inconclusive. To evaluate tissue expressions of GST isoenzymes in vitiligo patients and to compare these expressions with healthy controls, we used 26 active depigmented patches on the trunk of vitiligo patients and 20 healthy sex and age matched controls. Punch biopsies were taken from the lesioned or normal skin. Tissue expression of GST isoenzymes were analyzed immunohistochemically. Tissue expression of GSTT1, GSTA1 and GSTP1 was significantly higher in the patient group than controls. Tissue expression of GSTM1 was not significantly different between the two groups. The increased tissue expression of GSTT1, GSTA1 and GSTP1 may represent a response to excess free radical formation in vitiligo and may support the role of oxidative stress in the pathogenesis of vitiligo.
Three new Zodarion species (Araneae: Zodariidae) from Southeastern Turkey
(Magnolia Press, 2021) Coşar, İlhan; Danışman, Tarık
Three new species of zodariid spiders are described from Turkey: Zodarion ozkutuki spec. nov., Zodarion turkesi spec. nov. and Zodarion yagmuri spec. nov. New photographs of genitalia are provided for Zodarion van Bosmans 2009.
The Steppe Vegetation of Dinek Mountain (Kırıkkale)
(Gazi Univ, 2005) Hamzaoğlu, Ergin
In this study, the steppe vegetation of Dinek Mountain (Kirikkale) was analysed by Braun-Blanquet's method. All the associations described in the area, were included in the alliance of Arenario ledebouriana-Astragalion plumosi Akman 1990 regarding to their ecological and floristic peculiarities. This alliance includes the order of Onobrychido armenae-Thymetalia leucostomi Akman, Ketenoglu & Quezel 1985, and the class of Astragalo microcephali-Brometea tomentelli Quezel 1973.
The taxonomic significance of leaf epidermal micromorphological characters of some Brassicaceae species in Turkey
(Pakistan Botanical Soc, 2023) Erden, Ayşe; Menemen, Yusuf
Leaf epidermal micromorphological characters were examined using light and scanning electron microscopes in 43 taxa belonging to 30 genera of Brassicaceae. The cell curvature of the periclinal wall has an important influence on the surface roughness and stands out as an important character in the separation of some closely related species. The course of the anticlinal cell wall can be straight or uneven. Uneven anticlines could be further divided into arched, straight to arched, repand, sinuous, and undulate. Undulations of anticlinal cell walls could increase the mechanical stability of the epidermis tissue. Epicuticular surface ornamentation comprised 4 types: smooth, striate, wrinkled, and ridged. In general, wrinkled and ridged were the most common types. Different types of wax layers were found in different taxa growing in the same climatic conditions. Therefore, wax diversification may be is an important feature at all taxonomic hierarchy from species to tribal level. The stomata were amphistomatic, and anisocytic in all the species, while anomocytic stomata were found in some species too. It was revealed that the low stomatal index values of some species growing on high, stony-rocky areas are directly related to the climatic conditions and habitat that the plant is exposed to. It was also observed that the stomatal index was higher in species growing in lower areas and prefer moist soil. As a result, this study showed that the shape, measurement, surface curvature, anticlinal cell wall, stomata type, stomatal index, epicuticular surface ornamentation and waxy cover of the leaf epidermis cells could be important characters for distinguishing the species, genera and tribes within the familly.
The genomes of Darwin's primroses reveal chromosome-scale adaptive introgression and differential permeability of species boundaries
(Wiley, 2024) Stubbs, Rebecca L.; Theodoridis, Spyros; Mora-Carrera, Emiliano; Keller, Barbara; Potente, Giacomo; Yousefi, Narjes; Jay, Paul
Introgression is an important source of genetic variation that can determine species adaptation to environmental conditions. Yet, definitive evidence of the genomic and adaptive implications of introgression in nature remains scarce. The widespread hybrid zones of Darwin's primroses (Primula elatior, Primula veris, and Primula vulgaris) provide a unique natural laboratory for studying introgression in flowering plants and the varying permeability of species boundaries. Through analysis of 650 genomes, we provide evidence of an introgressed genomic region likely to confer adaptive advantage in conditions of soil toxicity. We also document unequivocal evidence of chloroplast introgression, an important precursor to species-wide chloroplast capture. Finally, we provide the first evidence that the S-locus supergene, which controls heterostyly in primroses, does not introgress in this clade. Our results contribute novel insights into the adaptive role of introgression and demonstrate the importance of extensive genomic and geographical sampling for illuminating the complex nature of species boundaries.
The comparative protein profiles of venom and venom gland extracts of Agelena labyrinthica (Araneae: Agelenidae)
(Gazi Univ, 2005) Yiğit, Nazife
Spider venoms are biologically active substances which affect a variety of vital physiological functions in both insects and mammals. The major constituents of spider venoms are protein, polypeptide and polyamine neurotoxins, enzymes, nucleic acids, free amino acids, monoamines and inorganic salts. The identification of the proteins in spider venoms is an essential step for identification of venom. In this study, we compared with protein profiles of Agelena labyrinthica venom obtained by electrostimulation of the prosoma and extracted directly from gland. There were seven components identified in whole venom, when whole venom and venom gland extracts composition of A. labyrinthica were compared by SDS-PAGE.
The Administration of Steroids and its Impact on Caspase-3 Expression in Pediatric Adenoid Hypertrophy
(Springer India, 2024) Apaydin, Emre; Yaşar, Buse; Şimşek, Gülçin; Kaygın, Pınar; Sarıaltın, Sezen Yılmaz; Dirican, Onur; Çetin, Hazal Eylem
ObjectiveAdenoid hypertrophy is a prevalent pediatric condition, often necessitating surgical intervention. Intranasal steroid administration shows promise as a conservative treatment, particularly by inducing apoptosis in adenoidal cells, leading to a reduction in adenoid size and inflammation. This study aims to characterize the expression profile of caspase-3 as an apoptotic inducer protein in inflammatory and epithelial adenoid tissues and explore its association with steroid administration. MethodsWe performed immunohistochemical staining for caspase-3 proteins in adenoid tissues obtained from 51 pediatric patients aged between 2.5 and 12 years (mean age: 6.09 +/- 2.1 years) who underwent adenoid surgery. A retrospective analysis of clinical data was conducted, categorizing participants into steroid treatment receivers (n = 25) and non-receivers (n = 26). Subsequently, the lymphoid inflammatory tissue and epithelial tissue from the adenoid were compared in terms of caspase-3 protein expression, and associated clinical variables were assessed. ResultsImmunohistochemical analysis revealed significant caspase-3 expression in inflammatory tissues. The expression levels were scored, and no significant correlation was observed between inflammation and epithelium based on caspase-3 expression (correlation coefficient = 0.143; p > 0.05). Furthermore, demographic and clinical characteristics did not show a statistically significant difference in caspase-3 expression levels. ConclusionCaspase-3 expression was significant in inflammatory adenoid tissue, but it showed no association with nasal steroid administration.
Synopsis of the Central Asian Salvia species with identification key
(Magnolia Press, 2022) Turdiboev, Obidjon A.; Shormanova, Aijamal A.; Sheludyakova, Mariya B.; Akbarov, Feruz; Drew, Bryan T.; Celep, Ferhat
The genus Salvia is comprised of about 1000 species and has diversity hotspots in the Americas, East Asia, southwest Asia and the Mediterranean region. Central Asia also possesses considerable Salvia species diversity but is understudied relative to the aforementioned diversity hotspots. To help remedy this deficiency, we present a synopsis of Central Asian Salvia species based on extensive fieldwork, herbarium consultation, and literature surveys focusing on Uzbekistan, Kyrgyzstan, Tajikistan, Kazakhstan, and Turkmenistan (i.e., Central Asia). According to our final taxonomic revision, there are 41 species of native Salvia in the flora of Central Asia, 24 of which are endemic. Salvia ariana from Tajikistan and S. spinosa from Kazakhstan are documented from the respective countries for the first time, and the presence of S. tianschanica from Tajikistan and S. verticillata from Kazakhstan has been confirmed. In addition, the neotypification of S. deserta and three lectotypifications (Perovskia abrotanoides, S. bucharica and S. trautvetterii) are provided. Furthermore, we synonymized six species of Salvia that were previously reported from Central Asia, including S. intercedens, S. kopetdaghensis, S. linczevskii, S. lipskyi, S. semilanata and S. stepposa. Finally, a new species identification key for Central Asian Salvia is presented based on the new nomenclature changes and our taxonomic revision.
Stigma shape shifting in sages (Salvia: Lamiaceae): hummingbirds guided the evolution of New World floral features
(Oxford Univ Press, 2022) Kriebel, Ricardo; Drew, Bryan T.; Gonzalez-Gallegos, Jesus G.; Celep, Ferhat; Antar, Guilherme M.; Pastore, Jose Floriano Barea; Uria, Rolando
A fundamental question in evolutionary biology is how clades of organisms exert influence on one another. The evolution of the flower and subsequent plant/pollinator coevolution are major innovations that have operated in flowering plants to promote species radiations at a variety of taxonomic levels in the Neotropics. Here we test the hypothesis that pollination by Neotropical endemic hummingbirds drove the evolution of two unique stigma traits in correlation with other floral traits in New World Salvia (Lamiaceae). We examined morphometric shapes of stigma lobing across 400 Salvia spp., scored presence and absence of a stigma brush across Salvia, and used a suite of phylogenetic comparative methods to detect shape regime shifts, correlation of trait shifts with BayesTraits and phylogenetic generalized least square regressions, and the influence of scored pollinators on trait evolution using OUwie. We found that a major Neotropical clade of Salvia evolved a correlated set of stigma features, with a longer upper stigma lobe and stigmatic brush, following an early shift to hummingbird pollination. Evolutionary constraint is evident as subsequent shifts to bee pollination largely retained these two features. Our results support the hypothesis that hummingbirds guided the correlative shifts in corolla, anther connective, style and stigma shape in Neotropical Salvia, despite repeated shifts back to bee pollination.
Some new findings of the genus Zodarion (Aranei: Zodariidae) from Turkey
(Kmk Scientific Press Ltd, Moscow State Univ, 2022) Coşar, İlha; Danışman, Tarık; Kunt, Kadir Bogaç
A new species of Zodarion similar to Z. van Bosmans, 2009, Z. cYrewsae sp.n. (male female), from Osmaniye, Turkey is described. Zodarion spinibarbe Wunderlich, 1973 (male) a species previously know from Cyprus found in Turkey for the first time. Three species arc arc illustrated and their distribution arc mapped, This study increases the number of Zodarion species in Turkey to 30.
Size-selective microplastic uptake by freshwater organisms: Fish, mussel, and zooplankton
(Elsevier Sci Ltd, 2023) Kankılıç, Gökben Başaran; Koraltan, Idris; Erkmen, Belda; Çağan, Ali Serhan; Çırak, Tamer; Özen, Mihriban; Seyfe, Melike
Microplastics, as an emergent pollutant, have garnered substantial attention within aquatic environments, yet a significant knowledge gap persists regarding the interplay of organism size and pollution impacts on microplastic uptake in freshwater ecosystems. The main aim of the current study is to assess the microplastic ingestion by aquatic organisms across diverse trophic levels. To achieve this objective, zooplankton, mussels (Anodonta anatina), and fish (Carassius gibelio) were collected from the highly polluted Susurluk River Basin in Turkiye. The size distribution encompassed 160.8 & PLUSMN; 56.9 & mu;m for the prevailing zooplankton, 6.9 & PLUSMN; 2.2 cm for mussel, and 20.4 & PLUSMN; 3.1 cm for fish, respectively. While no microplastic ingestion was observed among zooplankton, the finding highlights the influence of body-size and pollution on microplastic ingestion. In contrast, A. anatina and C. gibelio contained 617 and 792 microplastic particles, respectively. Predominantly, fibers emerged as the most prevalent microplastic type across trophic levels (except zooplankton) followed by films. Notably, only fish exhibited fragments within their gastrointestinal tract. A substantial correlation emerged between microplastic abundance and mussel size and weight, but no such correlation manifested for fish. The study also revealed a positive link between microplastic count and turbidity (phosphate and high Chl a level), impacting mussel ingestion capacity due to the variability in the food availability and potential shifts in feeding preferences. Conversely, no distinct pattern emerged for fish concerning water quality parameters and ingested microplastics. Consequently, our study underscores diverse microplastic uptake patterns in freshwater ecosystems, with a predominant frequency of microplastics falling with the 0.3 mm-3.0 mm range, emphasizing the significance of size-selective uptake by organisms.
Scenedesmus regularis: An alternative biosorbent for the efficient and fast removal of methylene blue
(Global Network Environmental Science & Technology, 2022) Kankılıç, Gökben Başaran
This study focused on removing methylene blue (MB) from aqueous solutions using microalga Scenedesmus regularis as a biosorbent. The biomass was characterized by Fourier transform infrared spectroscopy (FT-IR) and field emission scanning electron microscopy (FE-SEM). The difference in thermal properties of the biomass was investigated by thermogravimetric analysis (TGA). The adsorption capacity of S. regularis was tested with different environmental key parameters (pH, temperature, biosorbent dosage, dye concentration, and contact time) in batch system experiments. The maximum adsorption capacity was 341.34 mg/g at a pH of 6.8, a temperature of 25 degrees C, a dye concentration of 250 mg/L, and a biosorbent concentration of 5 mg. Approximately 92% of the dye was removed within two minutes, and the removal efficiency reached 99% within 15 minutes. MB adsorption equilibrium data fit well with the Langmuir (R2=0.994) and Dubinin-Radushkevich (R2=0.993) isotherm models. The kinetic model of adsorption followed pseudo-second-order kinetics. Thermodynamic parameters showed that the adsorption process was endothermic and physical, favorable, and spontaneous. The results showed that S. regularis is an eco-friendly biosorbent with efficient performance that may be used for MB removal without any modification.
Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes
(Frontiers Media Sa, 2021) Rose, Jeffrey P.; Kriebel, Ricardo; Kahan, Larissa; DiNicola, Alexa; Gonzalez-Gallegos, Jesus G.; Celep, Ferhat; Lemmon, Emily M.
Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with similar to 1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia. We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia, are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia. Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation.

Güncel Gönderiler