LEE-Yer Sistem Bilimi-Yüksek Lisans

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http://hdl.handle.net/11527/19500

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Yayın Türü "Master Thesis" ile LEE-Yer Sistem Bilimi-Yüksek Lisans'a göz atma
  • Öge
    Analysis of global climate change on the hydrography of the Black Sea using CMIP6 climate models
    (Graduate School, 2023-01-06) Çetin, Derin Ülger ; Ilıcak, Mehmet ; 601191004 ; Earth System Science
    Climate change has numerous impacts on Earth from past to today. Specially after industrial revolution, the impact of climate change on Earth has been increasing and therefore has been focus of interest by scientists. The study of climate change has become important in terms of examining the negative effects such as drought, floods, the increase in the frequency and impact of severe hurricanes, as well as the increase of ocean and sea water levels, pH changes, salinity and temperature changes, and the melting of glaciers. The models used in this paper created using the close relationship between the ocean and the atmosphere and the use of past climate parameters, with an aim of modeling the ocean parameters for the next century. In this study, the behavior of the Black Sea water in different climate models for the next century was tried to be understood by considering the sea surface water temperature, salinity and heat exchange with the atmosphere, and comparisons between the models were included. In this study, we have analyzed the spatial and temporal variations of sea surface temperature (SST) and sea surface salinity (SSS) in the Black Sea using nine different climate models from the CMIP6 database. We have also examined the net heat flux (Qnet) and the heat transport through the Bosporus Strait, as well as the frequency and duration of marine heatwaves (MHWs) in the Black Sea. Our results show that the Black Sea is expected to experience significant warming and changes in salinity in the 21st century, with SST increasing by an average of 4.5 °C and SSS increasing by an average of 2.25 psu. These changes are expected to have significant impacts on the Black Sea ecosystem, as well as on human populations and industries in the region. Our analysis of SST and SSS using the nine CMIP6 models reveals a spatially asymmetrical pattern, with the western part of the Black Sea expected to experience greater warming than the eastern part. The multi-model mean also shows that the warming trend in the Black Sea is expected to continue in a nearly monotonic, corresponding to the increase phase of global climate change due to anthropogenic activities. Our analysis of Qnet and heat transport through the Bosporus Strait reveals that the asymmetrical warming pattern in the Black Sea is not due to heat transport from the Bosporus, but rather to net heat flux. We also found that the Rim Current system may play a role in this asymmetrical warming pattern. Our analysis of MHWs in the Black Sea shows that there is expected to be a regime shift in SST, with the frequency and duration of MHWs increasing significantly in the 21st century. In some models, the total number of days considered MHWs is projected to reach over 300 days per year by the end of the century. In conclusion, our study provides new insights into the expected impacts of global climate change on the Black Sea, highlighting the need for further research and efforts to mitigate and adapt to these changes. The asymmetrical warming pattern and the expected increase in MHWs have significant implications for the Black Sea ecosystem, as well as for human populations and industries in the region. Further research is needed to better understand the mechanisms driving these changes and to develop strategies for addressing their impacts.
  • Öge
    Assessing the Bosphorus as a migratory corridor for Pipistrellus nathusii using acoustic monitoring methods
    (Graduate School, 2024-07-02) İlbaş, Tuğçe Nur ; Çoraman, Emrah ; 601211009 ; Earth System Science
    Türkiye has one of the richest bat diversity in the Mediterranean region. However, essential ecological information about bat species, such as population sizes, distributions and their migration behaviour is lacking. This information gap is primarily due to the elusive behavior of bats. Most of the bat research in Türkiye is about cave-dwelling species, which are relatively easier to study. Studies on other species, on the other hand, are generally based on opportunistic and non-systematic surveys. In this context, acoustic ecology methods offer an effective approach to investigating bats. This study aims to conduct a systematic acoustic ecology investigation in İstanbul, Türkiye, with a specific focus on the role of Bosphorus as a migratory corridor for bats. In particular, the migration patterns of Pipistrellus nathusii, a long-distance migratory bat species, were investigated. Additionally, the relationship between bat activity and meteorological parameters, as well as moon phases were explored to assess their impact on migration. Ultrasonic sound recordings were collected from four different locations along the Bosphorus, spanning from north to south, between April and November 2022. Recordings were preliminary analysed with Kaleidoscope Pro software and then processed manually. Analysis revealed that bat activity was positively related to temperature. Wind speed and direction affect bat activity in different ways depending on the season. In particular, light winds are positively associated with bat activity. When the effect of moon phases on bat activity was examined, it was found that the P. nathusii activity level in Yıldız City Park and ITU Campus was more affected by the moon phases, and especially the Nathusius Pipistrelle acoustic group activity decreased during the full moon phase. Pipistrellus nathusii activity in Yıldız City Park increased from mid-August and decreased towards the end of October. Activity on the ITU Campus started to increase in mid-August, peaked towards the end of September, and decreased at the end of October. Activity in the Atatürk City Forest started to increase in mid-August, peaked in September, and continued to decrease slightly in the autumn. In the Sarıyer Forest, there was an increase in August, the highest activity was seen in September and decreased with the end of the autumn. These findings show that the Bosphorus is a migratory corridor for P. nathusii. The insights gained from this study will contribute to the conservation of migratory bat routes between Europe and Asia.
  • Öge
    Ecological niche modeling of Myotis davidii
    (Graduate School, 2022-06-09) Aksakal, Emre Can ; Çoraman, Emrah ; 601181012 ; Earth System Science
    Myotis davidii is a whiskered bat species distributed in large areas of the Western Palaearctic. It has a cryptic sister species, Myotis mystacinus, which also has a similar distribution range in Europe and western Asia. The distribution of M. davidii extends from the Balkans to the Far East Asia, whereas M. mystacinus is found in Europe, Anatolia, and the Caucasus. They have a sympatric range in an area extending from the Balkans to the Transcaucasia via Anatolia. In this sympatric area, the populations of M. davidii had discordant patterns of mitochondrial and nuclear DNA, indicating that there were gene exchange between these species in the past. In this study, it was aimed to investigate the effects of the past climatic conditions on the evolutionary history of M. davidii and its cryptic sister species, M. mystacinus. The particular aims of this thesis are: 1) to construct the bioclimatic niches of M. davidii and M. mystacinus; 2) to identify their putative refugial areas during the last glacial period; and 3) to assess their responses to current climate change. In order to investigate these aims, ecological niche models were utilized. Ecological niche models aims to predict the distribution range of species by matching the environmental factors with species occurence points. Ecological niche modeling approach has become a common and practical application in conservation and biogeography study, especially with the advent of computer sciences and essential databases. In this study, ecological niche models are constructed by using the R programming language, as implemented in the BIOMOD2 package. A maximum entrophy appoach was used, which is a machine learning method developed for ecological niche modelling applications. The constructed models captured the current range of M. davidii but failed for M. mystacinus. For Myotis mystacinus, the lack of data from the Balkans and Anatolia was the likely reason for the unsuccessful model projections. The models for M. davidii suggest that inaccordance with the genetic lineages there might be to separate ecological units. Past projections suggest that Anatolia and the Balkans might have acted as refugial areas for both of the species during the Last Glacial Maximum. For M. davidii, the coastal regions of the Black Sea and the Mediterranean regions of Anatolia were likely refugial areas. These findings highlights the importance of Anatolia as a glacial refugium. Finally, the future projections suggested that there will major range shifts in the distribution of these species, especially for M. mystacinus moving towards norther Europe.
  • Öge
    Effects on the transportation of pollen grains and inorganic particles in sedimentological processes
    (Graduate School, 2024-06-12) Acar, Dursun ; Biltekin, Demet ; Kalenderli, Özcan ; 601191017 ; Earth System Science
    Sedimentary particles can be inorganic or organic origin. While these materials are the size of clay or sand, the environments they are transported in are solid, liquid, gases or their mixtures. These sedimentary particles, no larger than grains of sand or clay, come from both inorganic and organic sources. Remarkably, they travel with forces that propel them through a surprising variety of environments, not just water or air, but also solids, and even mixtures of these states. Their transportation takes place in the form of creep movement under tectonics or gravity in solids, laminar flow, density flow, or discrete partial bulk or fully discrete granular, depending on the types of physical forces in gases and liquids. These forces, originating from inorganic or biological sources as same as particles, act on the particles with or without significantly altering the surrounding environment. For example, while the interactions of pollen grains with each other during their movements in the air and the interactions coming from the atmosphere are in question, today it has been understood that the bees flying in the air have gained a positive charge and accordingly, they collect and carry the pollen with a negative charge in the plant by static electricity attraction. Secondly atmospheric electric and other carrier environments such as wind, water, density currents understanding these interactions between themselves is essential for various fields at natural sciences.
  • Öge
    Endless tug-of-war: impact of social media on science communication of climate change
    (Graduate School, 2023-06-21) Altan, Derin ; Yetemen, Ömer ; 601201006 ; Earth System Science
    The pervasiveness of social media in contemporary society necessitates a comprehensive, particularly by climate scientists, an understanding of social media's undeniable impact on the mass communication and perception of climate change by the "commons". This thesis provides an in-depth exploration into the multifaceted role that social media plays in the dissemination of, and – of course, most importantly – the public understanding of the incredibly complex issue of climate change. The study also further delves into the trajectory of science communication and climate change communication, providing a historical backdrop against which the emerging role of social media is investigated thoroughly. The undeniable capability of modern social media platforms to either augment public comprehension of climate change or contribute to misinformation and misunderstanding is critically evaluated, with a particular emphasis on the phenomenon of online polarization – an agonizing development that can dangerously shackle even the most careful climate communicator. An analysis of various polarized climate change topics on social media uncovers key actors and narratives that significantly shape the public discourse surrounding this critical issue. Parallel to this, the research contrasts the strategies adopted by mainstream media with the logic of effective climate change communication. The examination uncovers inherent contradictions between the two, largely driven by differing business models and journalistic practices that had lead mainstream media platforms for decades, which can ultimately impact public perception and action towards climate change. Moreover, the study sheds light on current trends in climate change communication across different social media platforms. It scrutinizes their potential and the challenges they pose in fostering widespread climate change awareness and inspiring public action. The findings underscore the complexity and multi-dimensionality of climate change communication in the digital age. A nuanced understanding of these dynamics offers scientists, communicators, and policymakers vital insights to develop more effective strategies for engaging the public in climate change discussions and inciting action. In summation, this thesis emphasizes the pressing need to navigate the challenges and seize the opportunities presented by social media. On one hand, the social media platforms provide an incredible opportunity: the ability to reach millions of people with the click of a button. On the other hand, the deep polarization probability of such communication rings the alarm bells, constantly. Regardless, an effective use of the social media platforms by climate change communicators (mostly climate scientists), is expected to enhance the public's general understanding of climate change science, reduce polarization that diminishes public discourse, and stimulate informed action towards developing effective mitigation, adaptation and resilience strategies, all of which are crucial steps in confronting the climate crisis.
  • Öge
    Estimation of PM10 variations in the Southeastern and Eastern Anatolia regions of Türkiye using remote sensing and statistical models
    (Graduate School, 2024-07-25) Murzaeva, Sultanay ; Ünal, Alper ; 601211016 ; Earth System Science
    The significance of air quality extends to both indoor and outdoor settings, with poor air quality directly impacting the quality of life. Particulate Matters smaller than 10 μm in diameter (PM10) are of particular concern. Penetration to the airways is easier with these types of particles. Particulate Matters (PMs) can contribute to both respiratory and cardiovascular diseases (i.e. asthma, emphysema, and lung cancer). Air quality in Türkiye is affected by dust coming from Sahara Desert and Arabian Peninsula. Our study aims to research PM10 variations in the Southeastern and Eastern Anatolia regions of Türkiye from 2014 to 2016 using remote sensing and statistical models. The Moderate Resolution Imaging Spectroradiometer (MODIS) derived Level-3 Aerosol Optical Depth (AOD) data, air quality data and meteorological variables of 15 ground-observed stations present in the Southeastern and Eastern Anatolia regions of Türkiye were used in this study to assess PM10 estimations in the study area. The PM10 ground observations used in the study for the years 2014, 2015 and 2016 were received from the Republic of Türkiye Ministry of Environment and Urbanization and Climate Change. Hourly PM10 and meteorological data were converted to daily data and days having more than 30% missing values were not included into the study in order to find out PM10 variations. Moreover, statistical methods such as Multiple Linear Regression (MLR) model, Linear Mixed Effect (LME) model and Machine Learning (ML) techniques were used to anticipate the Particulate Matter (PM) concentration in the region using satellite-based AOD and meteorological variables such as temperature, wind speed, relative humidity, precipitation and atmospheric pressure. Since some cities are located on the same grid in the AOD study area map obtained from MODIS in the PM10 estimation studies, 12 out of 15 stations were included in the statistical analysis to avoid extra PM10 calculations. The results indicated that aerosol pollution in the region as a result of transported dust from the Arabian Peninsula in spring time was high enough and the PM10 concentration in the cities close to the borders of Iraq and Suria such as Hakkari and Mardin was observed more than 200 µg/m3 in spring of 2015. Both local heating emissions and long-range dust transport could have significantly impact on PM10 levels in Southeastern Anatolia in study period. In addition, stubble burning in those years may also be effective in the high PM10 levels in the region in the fall. Significant amounts of dust, pollution, or biomass combustion make contribution to higher atmospheric aerosol concentrations. MODIS data from the AOD maps of 2014, 2015 and 2016 show that the Southeastern and Eastern Anatolia regions were exposed to aerosol pollution. The results of statistical models for prediction of PM10 indicated that PM10 was very dependent on AOD and temperature. The statistical parameters such as Correlation Coefficient (R), R-Squared (R2) and Root Mean Square Error (RMSE) were calculated to understand performances of models applied in the study. In the MLR method, PM10 was estimated by including only one meteorological factor other than AOD. Each meteorological factor was used with AOD in the equation respectively in the MLR method. When PM10 was predicted by using all meteorological factors respectively, it showed that among these parameters, temperature affected PM10 values more. Based on the outcomes, performance of all statistical models was improved when AOD values with all meteorological parameters were used in estimating PM10. For example, the R, R2 and RMSE values of MLR for averaged data for summer season were calculated about 0.69, 0.47 and 8.21 with best performance in the study period, while winter accounted to the lower performance with R, R2 and RMSE values of 0.40, 0.16 and 25.10, respectively. MLR for all 12-station data gave its best result in autumn season with an R, R2 and RMSE values of 0.57, 0.33 and 42.46 respectively. For the LME model, the random effect parameter selected AOD enabled the model to have R, R2 and RMSE values of 0.51, 0.26 and 36.60, respectively for all study period. Atmospheric pressure also had a random effect in the LME model, with R, R2 and RMSE values of 0.86, 0.73 and 28.26, respectively for all studied years. AOD and atmospheric pressure had a significant impact on improving the LME model results. For whole study period Extreme Gradient Boosting (XGBoost) having 0.73, 0.54 and 17.88 values as R, R2 and RMSE, respectively for averaged data and having 0.69, 0.44 and 32.13 values as R, R2 and RMSE, respectively for non-averaged data making a moderate performance in estimating PM10 levels. Among all statistical methods, Random Forest performed the best in terms of fitting the regression line, with R, R2 and RMSE values of 0.97, 0.93 and 17.90, respectively, when averaged variables are included in the model, and R, R2 and RMSE values of 0.97, 0.93 and 29.26, respectively, when all variables are included in the model. While MLR depended on factors like quantity of meteorological variables included, its performance also was affected by which meteorological variable is chosen with AOD in PM10 estimation. In this study, the LME model also showed variability in performance depending on which meteorological variable was selected as a random effect for PM10 estimation. XGBoost's performance was moderate and it also had better results than MLR method for overall. In conclusion, satellite data with meteorological variables gives us the best performance when it is introduced to the Random Forest Model in order to forecast PM10 in study area. The correlation between PM10 and AOD is influenced by weather conditions, local pollutant emissions and the chemical composition of aerosols. Ground-based monitoring data is commonly used in health effect research. Because satellite data is readily available and inexpensive, AOD images can be used to estimate PM10 via using Machine Learning methods which processes factors that affect abundance of PM10.
  • Öge
    The impact of climate change on future extreme precipitation in Turkey
    (Graduate School, 2021-08-06) Albayrak, Derya ; Şen, Ömer Lütfi ; 601191005 ; Earth System Science ; Yer Sistem Bilimi
    This study investigates the impact of climate change on extreme precipitation in Turkey with the aid of both historical and model-based future projection data. Firstly, we have applied the equidistant quantile matching method and generated bias-adjusted extreme precipitation daily and sub-daily time series of 73 stations in Turkey from a 14 member CMIP6 ensemble. The resulting data are utilized for deriving the Intensity-Duration-Frequency curves for two future periods (2020-2050 and 2070-2100) and results are spatially presented. Thus, annual extreme precipitation with 1-hr, 2-hr, 6-hr, 12-hr, and 24-hr durations over Turkey are examined for 10-yr, 25-yr, 50-yr, and 100-yr return periods in two future periods through a CMIP6 ensemble-based analysis. The impacts of climate change on annual extreme precipitation in the regions of Turkey are estimated. Our CMIP6-ensemble analyses reveal that for the reference period 1970-2000 the highest impacts over Turkey are estimated for shorter duration (≤ 6-hr) generally higher-frequent annual extreme precipitation which may be attributed to the thermal enhancement due to the mean temperature increase in Turkey. Moreover, for all durations and frequencies covered here, till the mid-century, change in regional medians varies between 4.6-10.4% in the Marmara region, 4.9-8.4% in south-eastern Anatolia, 7.4-10.4% in the Aegean region, -1.8-0.8% in central Anatolia, 6.8-12.1% in eastern Anatolia, 5.2-7.2% in Black Sea region, 4-14.2% in Mediterranean region. Due to the high spatial variability of the extreme precipitation, both decreasing and increasing relative changes occur in the regions. However, by the end-century, the impact of annual extreme precipitation in the regions noticeably intensifies, relative regional medians raise to 18.5-21.7% in Marmara region, 14.8-18.7% in south-eastern Anatolia, 10.2-13.9% in Aegean region, 13.4-16.6% in central Anatolia, 19.3-23.3% in eastern Anatolia, 16.2-20.7% in Black Sea region, 15.1-21.1% in Mediterranean region. Coastal regimes in Turkey receive a higher amount of annual extreme precipitation than the continental parts, especially local extremes that are noticeable on the coastal line, which is projected for all future periods and extreme precipitation durations presented in this study. Moreover, according to the median of the relative changes among the regions, the south and north coasts of Turkey are subject to the impact of different annual extreme precipitation durations. Northern coastal regimes are projected to have the highest impact by the intensification of the short-duration annual extremes (≤ 2-hr annual extreme precipitation). Southern coastal regimes are estimated to have the highest impact by the longer duration (≥ 6-hr) annual extreme precipitation events. Central Anatolia, the only region with persistent decreasing median changes till the mid-century, experiences a substantial increase in the impact of the 1-hr and 2-hr high-frequent convective precipitation extremes at the end-century. Crucial for adaptation and mitigation strategies, our current practice of deriving and implementing Intensity-Duration-Frequency curves rely on the historical data, which may be insufficient for capturing the variable impacts of climate change. Consequently, underestimating the impact of climate change on extreme precipitation may result in a decrease in the capacity of the numerous hydrological systems to deliver the required services at their optimum. Thus, decision and policymakers should evaluate and consider the intensification of different extreme precipitation durations among both the regions and the future periods to eliminate the exacerbated vulnerability of the hydrological systems to climate change-related extreme precipitation events and manage adverse socio-economic consequences.
  • Öge
    Investigating the genomic differentiation landscape of the large mouse-eared bats
    (Graduate School, 2024-05-23) Şensoy, Bengisu ; Çoraman, Emrah ; 601211001 ; Earth System Science
    Interspecific gene flow, through shaping the evolution of species over time, plays a pivotal role in evolutionary biology. Often complex and multifaceted, this process presents a rich area to explore the intricate dynamics that drive the evolution of species. The large mouse-eared bats, specifically Myotis myotis and M. blythii, present a particularly intriguing species complex for studying interspecific gene flow. Myotis myotis and M. blythii have substantially overlapping ranges across Europe and Anatolia. These species also exhibit evidence of gene flow, identified in the previous studies. Their shared mitochondrial lineage suggests past hybridization events. Additionally, nuclear marker based analyses identified evidence of recent gene flow events. Despite their sympatric distribution coupled with past and present hybridization events, the mechanism underlying the maintenance of separate gene pools remains an intriguing question. This study aims to contribute in the understanding of the evolutionary history of the large Myotis bats through a whole-genome approach. In this regard, genomic differentiation landscapes were considered within and between Large Myotis bats. For the genomic analysis, whole-genome shotgun sequencing data was generated from a total of thirty-four samples, representing M. myotis, M. blythii, and their closely related species, M. punicus. To assess the population structures and differentiation levels, Principal Component and Admixture analyses were conducted. Both analyses identified three distinct clusters in accordance with the three large Myotis taxa. Within M. blythii, a further split separating the individuals from Kyrgyzstan and Mongolia from the rest was present. Genomic landscapes of differentiation were explored through Manhattan plots of fixation index, nucleotide diversity and genomic divergence. The genomic differentiation assessments supported the nuclear divergence of M. myotis and M. blythii. Within M. blythii, East and West populations exhibited a significant divergence, although not to a level comparable to the divergence seen between two different species. Potentially introgressed genomic regions were investigated. Although a slightly increased gene flow signal was observed across the entire genome between M. myotis and Eastern M. blythii, localized introgression regions that would indicate recent hybridization could not be detected. Further exploration of introgressed genomic regions may reveal the genomic basis for species differentiation. This study contributes to future studies on large Myotis bats and other cryptic species complexes, while also demonstrating the power of whole-genome data in unraveling the complex processes that shape the evolution of species.
  • Öge
    Phylogeography of the Savi's pipistrelle (Vespertilionidae, chiroptera) complex based on whole mitochondrial genome analysis
    (Graduate School, 2024-07-01) Ergöl, Yeliz ; Çoraman, Emrah ; 601211010 ; Earth System Science
    Understanding the phylogeography of species provides insight into the historical processes that lead the formation of their current geographic distributions and also how they evolve and adapt to variable environments over time. Intraspecific and interspecific genetic variations stand as a great indicator for elucidation of the evolutionary history of organisms in diverged phylogeographical patterns. Bats represent an immensely diverged group among mammals. They inhabit a wide variety of ecosystems, with the tropical belt hosting the highest number of bat species, similar to many other life forms. While the oldest known fossil of Chiroptera is approximately 52 million years old, they are hypothesized to be evolved around the Cretaceous-Tertiary boundary. During their evolution, they settled to the nocturnal niche. Echolocation and flight capabilities have affected the phylogenetic classification in the era of morphological and physiological taxonomy. However, the taxonomic classification of Chiroptera is a more complex phenomenon. The developments of modern genetic techniques transformed the historical perception of taxonomy. The introduction of high-throughput sequencing, which enables the sequencing of an organism's whole genetic material, has made genomic studies increasingly popular in biodiversity research. This powerful technique has revealed that organisms can exhibit significant genetic variation, even when their phenotypic characteristics do not reflect this diversity. Cryptic species, which arise from the discordance between morphological similarity and genetic divergence, exemplify this phenomenon. Resolving cryptic diversity is cruicial for identying evolutionary significant units and provides a new dimension for investigating the ecological dynamics of species. Furthermore, it is a significant concept in biodiversity assessment and monitoring, essential for inforimg conservation actions. Past studies have showned that the Palearctic Region hosts a rich fauna with signifacnt cryptic diversity, including among bats. Savi's Pipistrelle, Hypsugo savii, is a small-sized, vespertilionid bat species with a broad distribution range across various ecoregions in Europe, Asia, and North Africa. The accumulation of studies showing intraspecific variation within the species has drawn attention to the investigation of possible divergence within the taxon. Several studies idenfied deeply diverged mitochondrial lineages of H. savii. Two of such lineages have been proposed as distinct species statuses, H. darwinii and H. stubbei, based on their significant divergence from H.savii. Hypsugo savii hosts possibly further cryptic diversity. It is composed of deeply diverged clades, with sympatric occurences in Northwestern Africa, the Iberian Peninsula, Italy, and some Mediterranean islands (Sardinia, Sicily, and Malta). These studies, however, are based on limited sampling from a very broad geographical range. Furthermore, they utilize realtively short mitochondrial markers and marker selection is not usually consistent among studies. This study aims to invesitage the whole mitogemones of the previously identified H. savii lineages and the recently suggested related species. There are three main objectives: 1) establishing a reproducible workflow to de novo assemble mitogenome from whole genome sequencing data; 2) de novo assembling complete mitogenome of H. savii and the related species; and 3) reconstructing their phylogenetic relationships based on whole mitogenome sequences. Thirty samples from various regions including Central Asia, Sinai Peninsula, North Africa, continental Europea, and Mediterranean islands were analysed. High-throughput shotgun sequencing data was used for the analysis. The analysis workflow covers data filtering, de novo assembling of complete mitogenomes, and annotating the obtained mitogenomes. Complete mitochondrial genomes were succesfully de novo assembled for thirty samples, representing all of the previously identified lineages, as well as the closely related species, H. stubbei and H. alaschanicus. Mitochondrial genes were annotated on the assembled genomes. The read pool of each sample was mapped to the assembled mitogenomes to assess their coverage and also to edit possible misallignments and gaps. The samples which had uncircular genomes were manual edited and circularized. The tRNA profiles were analyzed with tRNAscan-SE. Phylogenetic relations of the analysed samples were investigated reconstructing phylogenetic trees. The sequences were aligned and the pairwise distance of the sequences were calculated with MEGA11. The phylogenies were obtained with Maximum-Likelihood model with IQ-TREE and RAxML tools. The trees were visualized with FigTree abd iTOL WebServer. The alignments were analysed with PopArt for a haplotype network analysis. The highly variable non-coding D-loop regions were removed from the sequences for all these analysis . All thirty-seven mitochondrial genes were annotated: two of them were ribosomal RNAs; twenty-two were transfer RNAs; and thirteen were protein-coding genes. D-loop regions of mitogenomes were also annotated. The secondary stuctures of the tRNA profiles were calculated and illustrated. The tRNA for serine amino acid was lacking the D- arm in the secondary stucture, which had no significant impact on its functionality. Phylogenetic analysis revealed that there are three main H. savii lineages in the Western Palearctic region. The related species, H. ariel, H.alaschanicus, and H. stubbei, also formed three distinct clusters. The latter was identified in Kyrgyzstan, which is outside of its known range. The distribution of Hypsugo savii lineages were in three main regions: Eastern Mediterranean, Western Mediterranean, and North African-Southwestern Mediterranean. In Sardinia, the latter of these three lineages were found together. The pairwise genetic distance between the clades in Europe were between 8 and 10%, close to the difference observed between H. alaschanicus and the other species. Similar levels of divergences were also found between newly proposed species, H. stubbei, and the European clades. These observed high levels of mitogenomic differences suggest that the H. savii complex probably harbours further cryptic diversity.
  • Öge
    Potential implications of sea-level rise in Türkiye and its vicinity
    (Graduate School, 2022-10-08) Alabay, Ebru ; Karaca, Mehmet ; Baykara, Metin ; 601201007 ; Earth System Sciences
    In the last century, the sea-level rise has accelerated due to anthropogenic climate change. With the growing population, the consequences of climate change have become more adverse. As in the rest of the world, the population pressure is high on the Turkish Coasts, where 45 million people live in. Türkiye, which has a long shoreline with 8333 km covered with seas on three sides will be affected adversely by the consequences of accelerated sea-level rise (e.g. flooding, salt intrusion, erosion, etc.). In addition to physical hazards, also socio-economic losses will have consequences. The purpose of this study is to determine the potential implications of the sea-level rise on Turkish coasts. For this purpose, the monthly sea-level data in the Turkish Seas (the Black Sea, the Marmara Sea, the Aegean Sea, and the Mediterranean Sea) are received from the Permanent Service for Mean Sea Level. However, some tide gauge stations have data gaps and insufficient data for determining long-term sea-level change. Therefore, cubic interpolation was applied to eliminate the data gaps, also the tide gauge station data in the same sea are combined to create a longer time series of sea-level change. Thus, the mean sea-level rise rates in the Black Sea, the Marmara, the Aegean, and the Mediterranean Sea are calculated at 5,31 mm/yr in 1874-2018, 8,79 mm/yr in 1984-2009, 0,844 mm/yr in 1969-2019, 0,8455mm/yr in 1923-2019, respectively. It is determined that sea-level rise has accelerated in recent decades. The accelerated sea-level rise causes the increasing frequency and intensity of disaster floods, inundations, coastal erosion, landslides, saltwater intrusion, and even storm surges. The main economic activities in this region are tourism, agriculture, fishing, port, and industry sectors. In Turkey, the coastal low-lying delta areas (i.e. Cukurova, Bafra, Carsamba, Meric, Goksu, etc.) are important in agricultural production. Especially one-third of Samsun is covered with agricultural lands its agricultural contribution to the economy is approximately $1 billion. Thanks to their long sandy beaches, the Mediterranean and the Aegean are among the destinations that attract a lot of international tourists and play an important role in the development of the region locally and nationally. Another popular destination for international tourists is Istanbul with its natural beauty, rich culture, and historical places. Hence, the socio-economic factors on the Turkish coast were examined. The contribution of the coastal region is estimated at two-thirds of the Turkish Gross Domestic Product (GDP): the Marmara, the Aegean, the Mediterranean, and the Black Sea coastal regions' contributions are 44.5%, 8.3%, 8.4%, and %4.7 respectively. As a result, these economically active regions are essential to be protected against sea-level rise. In this study, adaptation strategies have been determined for the protection of coastal areas from the destructive consequences of sea-level rise. In addition, the adaptation costs for agricultural areas (Bafra and Carsamba) in Samsun, and the sandy beaches are also examined.
  • Öge
    Sparse identification of non-linear dynamics (SINDy) of landscape evolution model simulations
    (Graduate School, 2024-07-01) Birol, Özgür Doğan ; Yetemen, Ömer ; 601211007 ; Earth System Science
    This study, titled "Sparse Identification of Nonlinear Dynamics (SINDy) of Landscape Evolution Model (LEM) Simulations" explores the linear inference of differential physical processes simulated by the LEM called Landlab by using the SINDy toolkit. The research aims to enable LEM researchers to incorporate data trained models to explain nonlinear phenomena alongside the traditional approach of physical equations. The study employed an iterative approach to investigate explanation of the non-linear Taylor diffusion process from simulation data using a sparse, linear model. The data was collected from the simulations run by the LEM model Landlab which incorporated a non-linear hillslope and a fluvial flux process. Results suggest that the underlying nonlinear dynamic could be identified with a trained SINDy model in a relatively sparse manner with a median average percentage error as low as 0.097%. Although, the simulations ran with the trained model exhibited drift from the original course of model data. This is expected due to stochasticity of non-linear models. The findings of this study reveal that soil elevation at a node in a spatial grid can be inferred using the elevation values of the neighboring nodes as model features. This has important implications for LEM modelling providing viable employable alternatives to representative physical equations. Additionally, this study contributes to the existing body of knowledge in earth sciences by showing that it is possible to linearize a process in spatial domain simulations when treated as a dynamical system. Furthermore, the study highlights the challenge of reducing number of terms in a linear model to just a few, which can contribute to further research in this area. In conclusion, this study sheds light on treating differential physical processes in a spatial domain as sparse linear models and providing valuable insights for researchers who design or employ LEM's in their studies.
  • Öge
    Studying the ancient settlement of Hacılar Büyük Höyük with integrated methods
    (Graduate School, 2022) Özdoğru, İnci Nurgül ; Arıkan, Bülent ; Küçükdemirci, Melda ; 714414 ; Earth System Science Programme
    Archaeology has great potential to illustrate the long-term human-environment interactions especially when it is supported by other disciplines and computational modeling. This holistic perspective provides a detailed analysis of landscape with a multidisciplinary framework that might provide an understanding of complex systems, including land use, interactions of the elements, and adaptation. The Hacılar Büyük Höyük, a major Early Bronze Age-I (ca. 3100 – 2900 BC) site in Burdur, (Turkey), has been the focus of this thesis. It has significant contribution to the knowledge of the Early Bronze Age-I (EBA-I, hereafter) and II phases in Southwest Anatolia with its settlement plan, defense system, archaeological remains, and its material culture. The primary goal of this research is to assess the long-term human-environment interactions at the site from an interdisciplinary perspective. In this research, three different digital-computational approaches have been used to assess the long-term changes in landscape around the site; GIS-based morphometric analysis, Ground Penetrating Radar (GPR, hereafter), and Agent Based Modelling (ABM, hereafter). Data was collected via unmanned aerial vehicle (UAV, hereafter) photography, and sub-surface geophysical measurements. Through the use of GPR and GIS-based morphometric analyses, I will calculate the scale of settlement and its agro-pastoral (i.e., farming and herding) catchment areas. I will then integrate cultural, economic, and environmental parameters into an agent-based modeling platform where I will visualize the spatio-temporal impacts of human activities (e.g., de-vegetation, erosion, deposition) at the site. The geomorphometric analysis is used to figure out how geomorphological features on and around the settlement are distributed. To gain a better understanding of the landscape, the sky-view factor (SVF, hereafter) map and red relief image mapping (RRIM, hereafter) approaches were applied. A combination of morphometric analysis and field observation provides complementary information about the site, land, and surroundings. Then, GPR data were implemented and results analyzed. The geomorphic units are mapped and the estimated agricultural catchment area is identified based on the slope of the area and distance from the settlement as the flat area limited by the river considering the geomorphic units were similar with modern data. Based on the site's layout, it is possible to calculate the approximate population of the settlement considering that the casemates surround the mound. ABM is used to evaluate the effects of land use on surface processes as well as to calculate agricultural catchment areas based on precipitation and population data. The Macrophysical climate model (MCM) results were used in the model as the input climate data. The ABM used in this study is Medland Modeling Laboratory (MML, hereafter) to simulate how dry farming and ovicaprid-based, site-tethered pastoralism affected the landscape around the site. As a result of the study, possible archaeological structures buried underground were determined by using GPR. Then, model results show agricultural exploitation of the landscape and husbandry practices between 3100-2900 BC had varying degrees of impact on the environment and that population density is the most critical factor. Within the scope of the study, GPR and geomorphological analyses enabled to visualize to combine incorporate unearthed archaeological remains in the ABM for calculating the approximate human and animal population of the settlement. Then, four scenarios have been tested by changing the climate and increasing population variables for 200 years. The cumulative changes in the woodland vegetation, erosion, and deposition provide critical information about the land use patterns and anthropogenic impacts around the Hacılar Büyük Höyük during EBA-I. This thesis study illustrates that integrating the existing archaeological and anthropological data with the numerical models can benefit the interpretation of social structure at the settlement.