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Polic D, Yıldırım Y, Merilaita S, Franzén M, Forsman A. Genetic structure, UV-vision, wing coloration and size coincide with colour polymorphism in Fabriciana adippe butterflies. Mol Ecol 2024; 33:e17272. [PMID: 38240162 DOI: 10.1111/mec.17272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/18/2023] [Accepted: 01/08/2024] [Indexed: 02/22/2024]
Abstract
Colour polymorphisms have long served as model systems in evolutionary studies and continue to inform about processes involved in the origin and dynamics of biodiversity. Modern sequencing tools allow for evaluating whether phenotypic differences between morphs reflect genetic differentiation rather than developmental plasticity, and for investigating whether polymorphisms represent intermediate stages of diversification towards speciation. We investigated phenotypic and genetic differentiation between two colour morphs of the butterfly Fabriciana adippe using a combination of ddRAD-sequencing and comparisons of body size, colour patterns and optical properties of bright wing spots. The silvery-spotted adippe form had larger and darker wings and reflected UV light, while the yellow cleodoxa form displayed more green scales and reflected very little UV, showcasing that they constitute distinct and alternative integrated phenotypes. Genomic analyses revealed genetic structuring according to source population, and to colour morph, suggesting that the phenotypic differentiation reflects evolutionary modifications. We report 17 outlier loci associated with colour morph, including ultraviolet-sensitive visual pigment (UVRh1), which is associated with intraspecific communication and mate choice in butterflies. Together with the demonstration that the wings of the adippe (but essentially not the cleodoxa) morph reflect UV light, that UV reflectance is higher in females than males and that morphs differ in wing size, this suggests that these colour morphs might represent genetically integrated phenotypes, possibly adapted to different microhabitats. We propose that non-random mating might contribute to the differentiation and maintenance of the polymorphism.
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Affiliation(s)
- Daniela Polic
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Yeşerin Yıldırım
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Sami Merilaita
- Department of Biology, University of Turku, Turku, Finland
| | - Markus Franzén
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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Berggren H, Nordahl O, Yıldırım Y, Larsson P, Tibblin P, Forsman A. Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish. Proc Biol Sci 2023; 290:20231608. [PMID: 38113936 PMCID: PMC10730295 DOI: 10.1098/rspb.2023.1608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
Variation in the composition of skin-associated microbiomes has been attributed to host species, geographical location and habitat, but the role of intraspecific phenotypic variation among host individuals remains elusive. We explored if and how host environment and different phenotypic traits were associated with microbiome composition. We conducted repeated sampling of dorsal and ventral skin microbiomes of carp individuals (Cyprinus carpio) before and after translocation from laboratory conditions to a semi-natural environment. Both alpha and beta diversity of skin-associated microbiomes increased substantially within and among individuals following translocation, particularly on dorsal body sites. The variation in microbiome composition among hosts was significantly associated with body site, sun-basking, habitat switch and growth, but not temperature gain while basking, sex, personality nor colour morph. We suggest that the overall increase in the alpha and beta diversity estimates among hosts were induced by individuals expressing greater variation in behaviours and thus exposure to potential colonizers in the pond environment compared with the laboratory. Our results exemplify how biological diversity at one level of organization (phenotypic variation among and within fish host individuals) together with the external environment impacts biological diversity at a higher hierarchical level of organization (richness and composition of fish-associated microbial communities).
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Affiliation(s)
- Hanna Berggren
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Oscar Nordahl
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Yeşerin Yıldırım
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Per Larsson
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Petter Tibblin
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Anders Forsman
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
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Polic D, Yıldırım Y, Lee KM, Franzén M, Mutanen M, Vila R, Forsman A. Linking large-scale genetic structure of three Argynnini butterfly species to geography and environment. Mol Ecol 2022; 31:4381-4401. [PMID: 35841126 PMCID: PMC9544544 DOI: 10.1111/mec.16594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/17/2022] [Accepted: 06/29/2022] [Indexed: 12/04/2022]
Abstract
Understanding which factors and processes are associated with genetic differentiation within and among species remains a major goal in evolutionary biology. To explore differences and similarities in genetic structure and its association with geographical and climatic factors in sympatric sister species, we conducted a large‐scale (>32° latitude and >36° longitude) comparative phylogeographical study on three Argynnini butterfly species (Speyeria aglaja, Fabriciana adippe and F. niobe) that have similar life histories, but differ in ecological generalism and dispersal abilities. Analyses of nuclear (ddRAD‐sequencing derived SNP markers) and mitochondrial (COI sequences) data revealed differences between species in genetic structure and how genetic differentiation was associated with climatic factors (temperature, solar radiation, precipitation, wind speed). Geographical proximity accounted for much of the variation in nuclear and mitochondrial structure and evolutionary relationships in F. adippe and F. niobe, but only explained the pattern observed in the nuclear data in S. aglaja, for which mitonuclear discordance was documented. In all species, Iberian and Balkan individuals formed genetic clusters, suggesting isolation in glacial refugia and limited postglacial expansion. Solar radiation and precipitation were associated with the genetic structure on a regional scale in all species, but the specific combinations of environmental and geographical factors linked to variation within species were unique, pointing to species‐specific responses to common environments. Our findings show that the species share similar colonization histories, and that the same ecological factors, such as niche breadth and dispersal capacity, covary with genetic differentiation within these species to some extent, thereby highlighting the importance of comparative phylogeographical studies in sympatric sister species.
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Affiliation(s)
- Daniela Polic
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Yeşerin Yıldırım
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.,Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Kyung Min Lee
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Markus Franzén
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Anders Forsman
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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Berggren H, Tibblin P, Yıldırım Y, Broman E, Larsson P, Lundin D, Forsman A. Fish Skin Microbiomes Are Highly Variable Among Individuals and Populations but Not Within Individuals. Front Microbiol 2022; 12:767770. [PMID: 35126324 PMCID: PMC8813977 DOI: 10.3389/fmicb.2021.767770] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/13/2021] [Indexed: 12/31/2022] Open
Abstract
Fish skin-associated microbial communities are highly variable among populations and species and can impact host fitness. Still, the sources of variation in microbiome composition, and particularly how they vary among and within host individuals, have rarely been investigated. To tackle this issue, we explored patterns of variation in fish skin microbiomes across different spatial scales. We conducted replicate sampling of dorsal and ventral body sites of perch (Perca fluviatilis) from two populations and characterized the variation of fish skin-associated microbial communities with 16S rRNA gene metabarcoding. Results showed a high similarity of microbiome samples taken from the left and right side of the same fish individuals, suggesting that fish skin microbiomes can be reliably assessed and characterized even using a single sample from a specific body site. The microbiome composition of fish skin differed markedly from the bacterioplankton communities in the surrounding water and was highly variable among individuals. No ASV was present in all samples, and the most prevalent phyla, Actinobacteria, Bacteroidetes, and Proteobacteria, varied in relative abundance among fish hosts. Microbiome composition was both individual- and population specific, with most of the variation explained by individual host. At the individual level, we found no diversification in microbiome composition between dorsal and ventral body sites, but the degree of intra-individual heterogeneity varied among individuals. To identify how genetic and phenotypic characteristics of fish hosts impact the rate and nature of intra-individual temporal dynamics of the skin microbiome, and thereby contribute to the host-specific patterns documented here, remains an important task for future research.
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Affiliation(s)
- Hanna Berggren
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Petter Tibblin
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Yeşerin Yıldırım
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Per Larsson
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Daniel Lundin
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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Sunde J, Yıldırım Y, Tibblin P, Bekkevold D, Skov C, Nordahl O, Larsson P, Forsman A. Drivers of neutral and adaptive differentiation in pike (Esox lucius) populations from contrasting environments. Mol Ecol 2021; 31:1093-1110. [PMID: 34874594 DOI: 10.1111/mec.16315] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 01/28/2023]
Abstract
Understanding how eco-evolutionary processes and environmental factors drive population differentiation and adaptation are key challenges in evolutionary biology of relevance for biodiversity protection. Differentiation requires at least partial reproductive separation, which may result from different modes of isolation such as geographic isolation (allopatry) or isolation by distance (IBD), resistance (IBR), and environment (IBE). Despite that multiple modes might jointly influence differentiation, studies that compare the relative contributions are scarce. Using RADseq, we analyse neutral and adaptive genetic diversity and structure in 11 pike (Esox lucius) populations from contrasting environments along a latitudinal gradient (54.9-63.6°N), to investigate the relative effects of IBD, IBE and IBR, and to assess whether the effects differ between neutral and adaptive variation, or across structural levels. Patterns of neutral and adaptive variation differed, probably reflecting that they have been differently affected by stochastic and deterministic processes. The importance of the different modes of isolation differed between neutral and adaptive diversity, yet were consistent across structural levels. Neutral variation was influenced by interactions among all three modes of isolation, with IBR (seascape features) playing a central role, wheares adaptive variation was mainly influenced by IBE (environmental conditions). Taken together, this and previous studies suggest that it is common that multiple modes of isolation interactively shape patterns of genetic variation, and that their relative contributions differ among systems. To enable identification of general patterns and understand how various factors influence the relative contributions, it is important that several modes are simultaneously investigated in additional populations, species and environmental settings.
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Affiliation(s)
- Johanna Sunde
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Yeşerin Yıldırım
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Petter Tibblin
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Christian Skov
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Oscar Nordahl
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Per Larsson
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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Yesilkaya C, Arıcı M, Yıldırım Y, Agca A, Demircan A, Taskapılı M. Short and long term outcomes after small-incision lenticule extraction: A tertiary referral centre experience. J Fr Ophtalmol 2020; 43:753-760. [PMID: 32620412 DOI: 10.1016/j.jfo.2019.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/29/2019] [Accepted: 11/13/2019] [Indexed: 10/24/2022]
Abstract
PURPOSE The objective of this study is to evaluate the preoperative and short- and long-term postoperative results in terms of visual acuity, refractive error, and corneal wavefront aberrations in patients with myopia and myopic astigmatism undergoing small incision lenticule extraction (SMILE). METHODS Seventy-nine eyes of 52 myopes with or without astigmatism (41 right and 38 left) were enrolled in this retrospective study. The measurements included uncorrected distance visual acuity (UDVA), corrected distance visual acuity (CDVA), spherical equivalent (SE) and wavefront aberrations. All the measurements before and after SMILE surgery were systematically recorded. RESULTS Mean preoperative UDVA was 1.19±0.24 logMAR and improved to 0.06±0.17 logMAR at the 3-year postoperative follow-up. At the conclusion of the 3-year follow-up, UDVA was better than or equal to 20/20 and 20/25 in 73% and 84% of eyes, respectively. At 1 month postoperatively, CDVA was 0.05±0.23 logMAR and significantly lower than the preoperative CDVA, 0.02±0.04 log MAR (P>0.05). However, at 1 year and 3 years after surgery, CDVA showed a significant increase compared to preoperative CDVA. At the conclusion of the 3-year follow-up, SE was -0.47 D, and 69.6% and 83.5% of the eyes were within±0.50 D and±1.00 D, respectively, of the intended correction. HOA's, coma, and spherical aberration increased significantly. No significant change in trefoil was detected. CONCLUSION This study showed that SMILE produces a stable, safe outcome for surgical treatment of myopia and myopic astigmatism.
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Affiliation(s)
- C Yesilkaya
- Department of Ophthalmology, Health Sciences University, Beyoğlu Eye Research and Training Hospital, Istanbul, Turkey.
| | - M Arıcı
- Department of Ophthalmology, Health Sciences University, Beyoğlu Eye Research and Training Hospital, Istanbul, Turkey
| | - Y Yıldırım
- Department of Ophthalmology, Health Sciences University, Beyoğlu Eye Research and Training Hospital, Istanbul, Turkey
| | - A Agca
- Department of Ophthalmology, Health Sciences University, Beyoğlu Eye Research and Training Hospital, Istanbul, Turkey
| | - A Demircan
- Department of Ophthalmology, Health Sciences University, Beyoğlu Eye Research and Training Hospital, Istanbul, Turkey
| | - M Taskapılı
- Department of Ophthalmology, Health Sciences University, Beyoğlu Eye Research and Training Hospital, Istanbul, Turkey
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Sunde J, Yıldırım Y, Tibblin P, Forsman A. Comparing the Performance of Microsatellites and RADseq in Population Genetic Studies: Analysis of Data for Pike ( Esox lucius) and a Synthesis of Previous Studies. Front Genet 2020; 11:218. [PMID: 32231687 PMCID: PMC7082332 DOI: 10.3389/fgene.2020.00218] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/24/2020] [Indexed: 01/06/2023] Open
Abstract
Population genetic studies reveal biodiversity patterns and inform about drivers of evolutionary differentiation and adaptation, including gene flow, drift and selection. This can advance our understanding and aid decision making regarding management and conservation efforts. Microsatellites have long been used in population genetic studies. Thanks to the development of newer techniques, sequencing approaches such as restriction site associated DNA sequencing (RADseq) are on their way to replace microsatellites for some applications. However, the performance of these two marker types in population genetics have rarely been systematically compared. We utilized three neutrally and adaptively differentiated populations of anadromous pike (Esox lucius) to assess the relative performance of microsatellites and RADseq with respect to resolution and conclusiveness of estimates of population differentiation and genetic structure. To this end, the same set of individuals (N = 64) were genotyped with both RADseq and microsatellite markers. To assess effects of sample size, the same subset of 10 randomly chosen individuals from each population (N = 30 in total) were also genotyped with both methods. Comparisons of estimated genetic diversity and structure showed that both markers were able to uncover genetic structuring. The full RADseq dataset provided the clearest detection of the finer scaled genetic structuring, and the other three datasets (full and subset microsatellite, and subset RADseq) provided comparable results. A search for outlier loci performed on the full SNP dataset pointed to signs of selection potentially associated with salinity and temperature, exemplifying the utility of RADseq to inform about the importance of different environmental factors. To evaluate whether performance differences between the markers are general or context specific, the results of previous studies that have investigated population structure using both marker types were synthesized. The synthesis revealed that RADseq performed as well as, or better than microsatellites in detecting genetic structuring in the included studies. The differences in the ability to detect population structure, both in the present and the previous studies, are likely explained by the higher number of loci typically utilized in RADseq compared to microsatellite analysis, as increasing the number of markers will (regardless of the marker type) increase power and allow for clearer detection and higher resolution of genetic structure.
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Affiliation(s)
- Johanna Sunde
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Kalmar, Sweden
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Beşek NK, Tülü Aygün B, Yıldız BK, Er MO, Yıldırım Y, Genç S, Ağca A. Intraocular lens opacification following Triple-Descemet membrane endothelial keratoplasty surgery. J Fr Ophtalmol 2019; 43:e7-e10. [PMID: 31831275 DOI: 10.1016/j.jfo.2019.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 11/19/2022]
Affiliation(s)
- N K Beşek
- University of Health Sciences, Beyoğlu Eye Research and Training Hospital, Istanbul, Turkey.
| | - B Tülü Aygün
- University of Health Sciences, Beyoğlu Eye Research and Training Hospital, Istanbul, Turkey
| | - B K Yıldız
- University of Health Sciences, Beyoğlu Eye Research and Training Hospital, Istanbul, Turkey
| | - M O Er
- University of Health Sciences, Beyoğlu Eye Research and Training Hospital, Istanbul, Turkey
| | - Y Yıldırım
- University of Health Sciences, Beyoğlu Eye Research and Training Hospital, Istanbul, Turkey
| | - S Genç
- University of Health Sciences, Beyoğlu Eye Research and Training Hospital, Istanbul, Turkey
| | - A Ağca
- University of Health Sciences, Beyoğlu Eye Research and Training Hospital, Istanbul, Turkey
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Demir G, Sucu ME, Yıldırım Y, Tülü B, Özveren M, Kepez Yıldız B, Yaşa D, Karaağaç Günaydın Z, Demirok A. Long-term assessment of visual and refractive outcomes of laser in situ keratomileusis for hyperopia using the AMARIS ® 750S Excimer laser. J Fr Ophtalmol 2019; 42:703-710. [PMID: 31130390 DOI: 10.1016/j.jfo.2019.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/03/2019] [Accepted: 02/08/2019] [Indexed: 10/26/2022]
Abstract
PURPOSE To evaluate the long-term efficacy and safety of hyperopic laser in situ keratomileusis (LASIK) using the AMARIS® 750S (Schwind, Eye-tech-solutions, GmbH) excimer laser. METHODS The medical records of one hundred eleven eyes of 62 patients who underwent LASIK for hyperopia using the AMARIS® 750S excimer laser were reviewed retrospectively. Patients were divided into three groups based on preoperative spherical equivalent (SE) refraction: low hyperopia (less than +2.50 diopters [D]), moderate hyperopia (+2.75D to +4.00D), and high hyperopia (over +4.00D). Uncorrected and best corrected visual acuity (BCVA), long-term stability of refraction, and complications were evaluated. RESULTS Of the entire sample, the mean preoperative SE was +3.64D±1.22D. The mean age was 37.4±11.2 years (20-59). The mean follow-up for all eyes was 51 months. At the last visit, the mean SE was +0.85D±0.34D (SD) in the low hyperopia group, +1.09D±0.43D in the moderate hyperopia group, and +1.63D±0.47D in the high hyperopia group. (+1.15D±0.49D overall). Preoperative uncorrected visual acuity (UCVA) was 0.52±0.34 logMAR and increased to 0.18±0.15 logMAR at 4 years follow-up (P<0.01). There was no statistically significant difference between preoperative and postoperative BCVA. The UCVA was 0.30 logMAR or better in 100% of eyes in the low hyperopia group, 93.7% in the moderate hyperopia group, and 69.9% in the high hyperopia group (%89.2 overall). CONCLUSIONS LASIK is safe and effective for correcting hyperopia in the short term; however, the efficacy of the procedure is limited in the patients with high hyperopia and longer follow-up.
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Affiliation(s)
- G Demir
- The University of Health Sciences, Beyoglu Eye Training and Research Hospital, İstanbul, Turkey.
| | - M E Sucu
- The University of Health Sciences, Beyoglu Eye Training and Research Hospital, İstanbul, Turkey
| | - Y Yıldırım
- The University of Health Sciences, Beyoglu Eye Training and Research Hospital, İstanbul, Turkey
| | - B Tülü
- The University of Health Sciences, Beyoglu Eye Training and Research Hospital, İstanbul, Turkey
| | - M Özveren
- Edirne Sultan 1. Murat State Hospital, Edirne, Turkey
| | - B Kepez Yıldız
- The University of Health Sciences, Beyoglu Eye Training and Research Hospital, İstanbul, Turkey
| | - D Yaşa
- The University of Health Sciences, Beyoglu Eye Training and Research Hospital, İstanbul, Turkey
| | - Z Karaağaç Günaydın
- The University of Health Sciences, Beyoglu Eye Training and Research Hospital, İstanbul, Turkey
| | - A Demirok
- Department of Ophthalmology, Istanbul Medeniyet University, Goztepe Education and Research Hospital, İstanbul, Turkey
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Kara AV, Yıldırım Y, Ozcicek F, Aldemir MN, Arslan Y, Bayan K, Çelen MK. Effects of entecavir, tenofovir and telbivudine treatment on renal functions in chronic hepatitis B patients. Acta Gastroenterol Belg 2019; 82:273-277. [PMID: 31314188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
BACKGROUND AND STUDY AIMS The aim of this study was to enlighten the controversy about the renal safety of entecavir, tenofovir, and telbivudine treatments in chronic hepatitis B (CHB) patients by comparing these treatments in real-world conditions. PATIENTS AND METHODS We retrospectively enrolled 104 treatment-naive patients with CHB monoinfection into our study. Patients were treated with entecavir monotherapy (n=38), tenofovir monotherapy (n=35), or telbivudine monotherapy (n=31). We then compared and statistically analyzed the effects of these drugs on the estimated glomerular filtration rate (eGFR) over a 24-month follow-up period. RESULTS In the entecavir group, time-dependent change in eGFR was not statistically significant (p = 0.357). There was a statistically significant increase in eGFR in the telbivudine group at 12 months (p<0.001) and at 24 months (p<0.001) and, in contrast, a statistically significant decrease in the tenofovir group at 12 months (p<0.001) and at 24 months (p<0.001). There was no significant relationship between entecavir and eGFR change (p = 0.763). We found that tenofovir and telbivudine were independent predictors of eGFR change (decrease in eGFR, p<0.001 and increase in eGFR, p = 0.001, respectively). CONCLUSIONS We recommend close follow-up of renal functions, especially for patients treated with tenofovir. Telbivudine was superior to the other drugs in terms of renal function. We conclude that an individualized therapy program considering treatment efficacy and side effects is the best option for patients.
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Affiliation(s)
- A V Kara
- Department of Nephrology, Faculty of Medicine, Erzincan University, 24030, Erzincan, Turkey
| | - Y Yıldırım
- Department of Nephrology, Faculty of Medicine, Dicle University, 21200, Diyarbakır, Turkey
| | - F Ozcicek
- Department of Internal Medicine, Faculty of Medicine, Erzincan University 24030, Erzincan, Turkey
| | - M N Aldemir
- Department of Internal Medicine, Faculty of Medicine, Erzincan University 24030, Erzincan, Turkey
| | - Y Arslan
- Department of Biostatistics, Faculty of Medicine, Erzincan University, 24030, Erzincan, Turkey
| | - K Bayan
- Department of Gastroenterology, Private Sultan Hospital, 21200, Diyarbakır, Turkey
| | - M K Çelen
- Department of Infectious Disease and Clinical Microbiology, Faculty of Medicine, Dicle University, 21200, Diyarbakır, Turkey
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Yıldırım Y, Tinnert J, Forsman A. Contrasting patterns of neutral and functional genetic diversity in stable and disturbed environments. Ecol Evol 2018; 8:12073-12089. [PMID: 30598801 PMCID: PMC6303714 DOI: 10.1002/ece3.4667] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/01/2018] [Accepted: 10/05/2018] [Indexed: 01/05/2023] Open
Abstract
Genetic structure among and diversity within natural populations is influenced by a combination of ecological and evolutionary processes. These processes can differently influence neutral and functional genetic diversity and also vary according to environmental settings. To investigate the roles of interacting processes as drivers of population-level genetic diversity in the wild, we compared neutral and functional structure and diversity between 20 Tetrix undulata pygmy grasshopper populations in disturbed and stable habitats. Genetic differentiation was evident among the different populations, but there was no genetic separation between stable and disturbed environments. The incidence of long-winged phenotypes was higher in disturbed habitats, indicating that these populations were recently established by flight-capable colonizers. Color morph diversity and dispersion of outlier genetic diversity, estimated using AFLP markers, were higher in disturbed than in stable environments, likely reflecting that color polymorphism and variation in other functionally important traits increase establishment success. Neutral genetic diversity estimated using AFLP markers was lower in disturbed habitats, indicating stronger eroding effects on neutral diversity of genetic drift associated with founding events in disturbed compared to stable habitats. Functional diversity and neutral diversity were negatively correlated across populations, highlighting the utility of outlier loci in genetics studies and reinforcing that estimates of genetic diversity based on neutral markers do not infer evolutionary potential and the ability of populations and species to cope with environmental change.
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Affiliation(s)
- Yeşerin Yıldırım
- Ecology and Evolution in Microbial Model SystemsEEMISDepartment of Biology and Environmental ScienceLinnaeus UniversityKalmarSweden
| | - Jon Tinnert
- Ecology and Evolution in Microbial Model SystemsEEMISDepartment of Biology and Environmental ScienceLinnaeus UniversityKalmarSweden
| | - Anders Forsman
- Ecology and Evolution in Microbial Model SystemsEEMISDepartment of Biology and Environmental ScienceLinnaeus UniversityKalmarSweden
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Yıldırım Y, Anderson MJ, Hansson B, Patel S, Millar CD, Rainey PB. Genetic structure of the grey side-gilled sea slug (Pleurobranchaea maculata) in coastal waters of New Zealand. PLoS One 2018; 13:e0202197. [PMID: 30114275 PMCID: PMC6095540 DOI: 10.1371/journal.pone.0202197] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 07/30/2018] [Indexed: 01/09/2023] Open
Abstract
Pleurobranchaea maculata is a rarely studied species of the Heterobranchia found throughout the south and western Pacific-and recently recorded in Argentina-whose population genetic structure is unknown. Interest in the species was sparked in New Zealand following a series of dog deaths caused by ingestions of slugs containing high levels of the neurotoxin tetrodotoxin. Here we describe the genetic structure and demographic history of P. maculata populations from five principle locations in New Zealand based on extensive analyses of 12 microsatellite loci and the COI and CytB regions of mitochondrial DNA (mtDNA). Microsatellite data showed significant differentiation between northern and southern populations with population structure being associated with previously described regional variations in tetrodotoxin concentrations. However, mtDNA sequence data did not support such structure, revealing a star-shaped haplotype network with estimates of expansion time suggesting a population expansion in the Pleistocene era. Inclusion of publicly available mtDNA sequence sea slugs from Argentina did not alter the star-shaped network. We interpret our data as indicative of a single founding population that fragmented following geographical changes that brought about the present day north-south divide in New Zealand waters. Lack of evidence of cryptic species supports data indicating that differences in toxicity of individuals among regions are a consequence of differences in diet.
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Affiliation(s)
- Yeşerin Yıldırım
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Marti J. Anderson
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
| | - Selina Patel
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Craig D. Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Paul B. Rainey
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231, PSL Research University, Paris, France
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Yıldırım Y, Ouriachi T, Woehlbier U, Ouahioune W, Balkan M, Malik S, Tolun A. Linked homozygous BMPR1B and PDHA2 variants in a consanguineous family with complex digit malformation and male infertility. Eur J Hum Genet 2018; 26:876-885. [PMID: 29581481 DOI: 10.1038/s41431-018-0121-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 11/30/2017] [Accepted: 02/01/2018] [Indexed: 12/31/2022] Open
Abstract
In affected members of a consanguineous family, a syndrome, which is concurrence of set of medical signs, is often observed and commonly assumed to have arisen from pleiotropy, i.e., the phenomenon of a single gene variant affecting multiple traits. We detected six sibs afflicted with a unique combination of digit malformation that includes brachydactyly, symphalangism and zygodactyly plus infertility in males owing to azoospermia, sperm immotility or necrospermia, which we hypothesised to have arisen from a defect in a single gene. We mapped the disease locus and by exome sequencing identified in patients homozygous missense variants bone morphogenetic protein receptor type IB (BMPR1B) c.640C>T (p.(Arg214Cys)) and alpha-2 pyruvate dehydrogenase (PDHA2) c.679A>G (p.(Met227Val)). Structural protein modelling, protein sequence conservation and in silico analysis indicate that both variants affect protein function. BMPR1B is known to be responsible for autosomal dominant brachydactyly and autosomal recessive acromesomelic chondrodysplasia. Our findings show that also recessive complex digit malformation can be caused by BMPR1B variant and not all biallelic BMPR1B variants cause acromesomelic dysplasia. PDHA2 is a novel candidate gene for male infertility; the protein product is a mitochondrial enzyme with highest expression in ejaculated sperm. Our findings are a unique example of two linked variants, ~ 711 Kb apart, in different genes that together manifest as a novel syndrome. They demonstrate that exome sequencing and not candidate gene approach should be employed in disease gene hunt, defining new diseases and genetic testing, to rule out the coincidental presence of two variants contributing together to the phenotype, which may be discerned as a novel disease.
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Affiliation(s)
- Yeşerin Yıldırım
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Toufik Ouriachi
- Department of Pathology, University Hospital of Blida, Faculty of Medicine of Blida-1, Blida, Algeria
| | - Ute Woehlbier
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
| | - Wahiba Ouahioune
- Department of Pathology, University Hospital of Blida, Faculty of Medicine of Blida-1, Blida, Algeria
| | - Mahmut Balkan
- Department of Medical Biology and Genetics, Faculty of Medicine, Dicle University, Diyarbakır, Turkey
| | - Sajid Malik
- Human Genetics Program, Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
| | - Aslıhan Tolun
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey.
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Yıldırım Y, Patel S, Millar CD, Rainey PB. Microsatellite development for a tetrodotoxin-containing sea slug (Pleurobranchaea maculata). BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Tüysüz B, Tolun A, Yıldırım Y. Response to Kouwenberg et al. “Recognizable Phenotype With Common Occurrence of Microcephaly, Psychomotor Retardation, But No Spontaneous Bone Fractures in ARCL2B Due to PYCR1 Mutations”. Am J Med Genet A 2011. [DOI: 10.1002/ajmg.a.34151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Yıldırım Y, Orhan EK, Iseri SAU, Serdaroglu-Oflazer P, Kara B, Solakoğlu S, Tolun A. A frameshift mutation of ERLIN2 in recessive intellectual disability, motor dysfunction and multiple joint contractures. Hum Mol Genet 2011; 20:1886-92. [PMID: 21330303 DOI: 10.1093/hmg/ddr070] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We present a family afflicted with a novel autosomal recessive disease characterized by progressive intellectual disability, motor dysfunction and multiple joint contractures. No pathology was found by cranial imaging, electromyography and muscle biopsy, but electron microscopy in leukocytes revealed large vacuoles containing flocculent material. We mapped the disease gene by SNP genome scan and linkage analysis to an ∼0.80 cM and 1 Mb region at 8p11.23 with a multipoint logarithm of odds (LOD) score of 12. By candidate gene approach, we identified a homozygous two-nucleotide insertion in ERLIN2, predicted to lead to the truncation of the protein by about 20%. The gene encodes endoplasmic reticulum (ER) lipid raft-associated protein 2 that mediates the ER-associated degradation of activated inositol 1,4,5-trisphosphate receptors and other substrates.
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Affiliation(s)
- Yeşerin Yıldırım
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul 34342, Turkey
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Calikusu Z, Yıldırım Y, Sakalli H, Bal N, Akcali Z, Ozyilkan O. Role of c-erbb2 expression in non-small cell lung cancer. J Clin Oncol 2008. [DOI: 10.1200/jco.2008.26.15_suppl.22044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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