The genomic history of the Aegean palatial civilizations.

The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing ∼50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes.

Diversification in the mountains: Evolutionary history and molecular phylogeny of Anatolian rock lizards.

Mountains play a key role in forming biodiversity by acting both as barriers to gene flow among populations and as corridors for the migration of populations adapted to the conditions prevailing at high elevations. The Anatolian and the Zagros Mountains are located in the Alpine-Himalayan belt. The formation of these mountains has influenced the distribution and isolation of the animal population since the late Cenozoic. Apathya is a genus of lacertid lizards distributed along these mountains with two species, i.e., Apathya cappadocica and Apathya yassujica. The taxonomy status of lineages within the genus is complicated. In this study, we tried to collect extensive samples from throughout the distribution range, especially within the Zagros Mountains. Also, we used five genetic markers, two mitochondrial (COI and Cyt b) and three nuclear (C-mos, NKTR, and MCIR), to resolve the phylogenetic relationships within the genus and explain several possible scenarios that shaped multiple genetic structures. The combination of results in the current study indicated eight well-support monophyletic lineages that separated to two main groups; group 1 including A. c. cappadocica, A. c. muhtari and A. c. wolteri, group 2 contains four regional clades Turkey, Urmia, Baneh and Ilam, and finally a single clade belonging to the species A. yassujica. In contrast to previous studies, Apathya cappadocica urmiana was divided into four clades and three clades were recognized within Iranian boundaries. The clades have dispersed from Anatolia to adjacent regions in the south of Anatolia and the western Zagros Mountains. According to the evidence generated in this study this clade is paraphyletic. Based on our assumption, orogeny activities and also climate fluctuations in Middle Miocene and Pleistocene have influenced to formation of lineages. In this study we revisit the taxonomy of the genus and demonstrate that the species diversity was substantially underestimated. Our findings suggest that each of the eight clades corresponding to subspecies and distinct geographic regions deserve to be promoted to species level.

Evolution of hygrophytic plant species in the Anatolia-Caucasus region: insights from phylogenomic analyses of Cardamine perennials.

BACKGROUND AND AIMS: Southwestern Asia is a significant centre of biodiversity and a cradle of diversification for many plant groups, especially xerophytic elements. In contrast, little is known about the evolution and diversification of its hygrophytic flora. To fill this gap, we focus on Cardamine (Brassicaceae) species that grow in wetlands over a wide altitudinal range. We aimed to elucidate their evolution, assess the extent of presumed historical gene flow between species, and draw inferences about intraspecific structure. METHODS: We applied the phylogenomic Hyb-Seq approach, ecological niche analyses and multivariate morphometrics to a total of 85 Cardamine populations from the target region of Anatolia-Caucasus, usually treated as four to six species, and supplemented them with close relatives from Europe. KEY RESULTS: Five diploids are recognized in the focus area, three of which occur in regions adjacent to the Black and/or Caspian Sea (C. penzesii, C. tenera, C. lazica), one species widely distributed from the Caucasus to Lebanon and Iran (C. uliginosa), and one western Anatolian entity (provisionally C. cf. uliginosa). Phylogenomic data suggest recent speciation during the Pleistocene, likely driven by both geographic separation (allopatry) and ecological divergence. With the exception of a single hybrid (allotetraploid) speciation event proven for C. wiedemanniana, an endemic of southern Turkey, no significant traces of past or present interspecific gene flow were observed. Genetic variation within the studied species is spatially structured, suggesting reduced gene flow due to geographic and ecological barriers, but also glacial survival in different refugia. CONCLUSIONS: This study highlights the importance of the refugial regions of the Black and Caspian Seas for both harbouring and generating hygrophytic species diversity in Southwestern Asia. It also supports the significance of evolutionary links between Anatolia and the Balkan Peninsula. Reticulation and polyploidization played a minor evolutionary role here in contrast to the European relatives.

Evidence, hints and assumptions for late pregnancy in the Ancient Mediterranean and Near East.

Ancient women, who survived childhood mortality, received good and adequate nutrition, did not work hard and escaped death during childbirth could live fairly long lives. Girls started procreation after marriage, usually at 15 years, had on average seven children, childbearing lasted 14-21 or more years and could happen at the age of 35 or more years. Breastfeeding, usually with contraceptive effect, continued for 2-3 years. Limited actual facts, written evidence and findings, but several hints, assumptions and logical conclusions from secular texts, sacred books, narratives and myths suggest the possibility of late childbearing in the Mediterranean and Near-Eastern ancient world, particularly for the Jews.

Phenolic Constituents, Antioxidant and Antimicrobial Activity and Clustering Analysis of Propolis Samples Based on PCA from Different Regions of Anatolia.

This study aimed to evaluate the biochemical composition and biological activity of propolis samples from different regions of Türkiye to characterize and classify 24 Anatolian propolis samples according to their geographical origin. Chemometric techniques, namely, principal component analysis (PCA) and a hierarchical clustering algorithm (HCA), were applied for the first time to all data, including antioxidant capacity, individual phenolic constituents, and the antimicrobial activity of propolis to reveal the possible clustering of Anatolian propolis samples according to their geographical origin. As a result, the total phenolic content (TPC) of the propolis samples varied from 16.73 to 125.83 mg gallic acid equivalent per gram (GAE/g) sample, while the number of total flavonoids varied from 57.98 to 327.38 mg quercetin equivalent per gram (QE/g) sample. The identified constituents of propolis were phenolic/aromatic acids (chlorogenic acid, caffeic acid, p-coumaric acid, ferulic acid, and trans-cinnamic acid), phenolic aldehyde (vanillin), and flavonoids (pinocembrin, kaempferol, pinobanksin, and apigenin). This study has shown that the application of the PCA chemometric method to the biochemical composition and biological activity of propolis allows for the successful clustering of Anatolian propolis samples from different regions of Türkiye, except for samples from the Black Sea region.

Monitoring spatio-temporal changes in wetlands with harmonized image series in Google Earth Engine.

Study of rapidly changing lakes and wetlands with remote sensing methods is critical for understanding the climatic and anthropogenic effects. However, most of the studies search for the change of water body in specific time periods. Although this approach reduces the workload related to downloading and processing a large number of satellite images in computer environment, it actually causes ignoring some critical changes that occurred out of specified time periods. On the other hand, this situation reduces the data volume and the limited data causes problems for the management of water resources.  The Google Earth Engine (GEE) platform allows the opportunity to rapidly and practically process large-scale temporal data without downloading. In this study, areal changes in Lake Aksehir in Türkiye, from 1985 to 2020, were calculated and mapped by the GEE as a case. In order to calculate the changes, the Landsat 5 TM, 7 ETM + and 8 OLI&TIRS images were harmonized and created annual mosaics. The Normalized difference water index (NDWI) and the automated water extraction index (AWEI) were applied to these annual mosaics. By this approach, the change in the water area representing a shrank by 87% on average (according to the calculations 91% for the NDWI and 83% for the AWEI) from 1985 to 2020 was assessed practically and rapidly on annual mosaics created from all images between the studied period, instead of assessment based on images taken on only one date in the chosen years as in previous studies. Such an approach will provide time and labour savings and provide more meaningful and uninterrupted data for studies about changes in other wetland areas.

Religious and Cultural Practices of Muslims Living in Central Anatolia on Death and Mourning: A Qualitative Study from Turkey.

This study was conducted to determine the cultural practices of society regarding death and mourning. The sample of this qualitative study consisted of 31 adults who presented to a Family Health Center located in two different provincial centers in the Central Anatolia Region of Turkey. The main themes of "optimistic thinking", "pessimistic thinking" and "acceptance" emerged from the statements of the participants regarding death. It was determined that participants took part in cultural practices such as preparing for a burial and providing comfort to individuals who were about to die. This study sheds light on the cultural and religious practices of Muslim participants in Turkey regarding death and mourning.

Agricultural origins on the Anatolian plateau.

This paper explores the explanations for, and consequences of, the early appearance of food production outside the Fertile Crescent of Southwest Asia, where it originated in the 10th/9th millennia cal BC. We present evidence that cultivation appeared in Central Anatolia through adoption by indigenous foragers in the mid ninth millennium cal BC, but also demonstrate that uptake was not uniform, and that some communities chose to actively disregard cultivation. Adoption of cultivation was accompanied by experimentation with sheep/goat herding in a system of low-level food production that was integrated into foraging practices rather than used to replace them. Furthermore, rather than being a short-lived transitional state, low-level food production formed part of a subsistence strategy that lasted for several centuries, although its adoption had significant long-term social consequences for the adopting community at Boncuklu. Material continuities suggest that Boncuklu's community was ancestral to that seen at the much larger settlement of Çatalhöyük East from 7100 cal BC, by which time a modest involvement with food production had been transformed into a major commitment to mixed farming, allowing the sustenance of a very large sedentary community. This evidence from Central Anatolia illustrates that polarized positions explaining the early spread of farming, opposing indigenous adoption to farmer colonization, are unsuited to understanding local sequences of subsistence and related social change. We go beyond identifying the mechanisms for the spread of farming by investigating the shorter- and longer-term implications of rejecting or adopting farming practices.

Turcichondrostoma, a new genus for the Leuciscidae (Teleostei: Cypriniformes) from Southwestern Anatolia.

Turcichondrostoma, a new genus, from the Southwestern Anatolia is distinguished by having fewer gill rakers on first gill arch and morphologies of premaxilla and dentary bones. In addition, as a result of the phylogenetic analyses based on combine data set (mtDNA COI + Cytb) sequences (1706 bp.), Turcichondrostoma genus was recovered with high posterior probability value (BI PP:1.0) and strong-supported bootstrap value (ML BP: 100%) among the former Chondrostoma groups. Also, high K2P mean genetic distance values (more than 7.84%) differentiated genus Turcichondrostoma from the other genera of former Chondrostoma group. The results of both morphological-osteological and molecular analyses are congruent with each other. The results of this study revealed that the genus Turcichondrostoma is easily distinguished from the genera in Chondrostoma group.

Phylogenetic analysis of West Nile virus: first report of lineage 1 in donkey in Turkey.

West Nile virus (WNV), a member of the Flaviviridae, is a major arbovirus that causes West Nile fever. Previous data showed the prevalence of the WNV serologically and molecular in Turkey, and the presence of lineage 1 in horses and humans has been reported. This is the first notification of partial phylogeny of WNV detected in donkeys in the northeast of Turkey (on the Iranian border). Blood serum samples collected from 25 donkeys without clinical symptoms were tested by RT-PCR. Sequence analysis of the sample detected as positive was performed. Multiple sequence alignments of reference sequences taken from GenBank were performed using the ClustalW method using the MEGA6 program. Partial nucleotide sequences of the capsid gene coding region revealed that the strains are closely related to viruses of lineage 1, clade 1a. According to the phylogenetic tree, the TUR/Igdir/donkey strain was included in the same cluster as the strain (KJ958922) previously obtained from horses in Turkey and the strain (GQ851658) from the Central African Republic. This study is the first report to show the circulation of WNV lineage 1 in donkeys in Turkey.

Childhood-onset autosomal recessive ataxias: a cross-sectional study from Turkey.

Autosomal recessive ataxias (ARAs) are a heterogeneous group of inherited neurodegenerative disorders that affect the cerebellum, the spinocerebellar tract, and/or the sensory tracts of the spinal cord. This study is aimed at establishing molecular classification and phenotypic correlation of childhood-onset ARAs in Southeast Anatolia of Turkey. Sixty-five children (aged 0 to 18) from 40 unrelated families who were analyzed through hereditary ataxia NGS panel between the years of 2015-2018 were selected for the study. Seventeen different, clinically significant ARA-related pathogenic variants were detected in 33 of 40 families (82.5%), 12 of which were noted to be unreported variants. Among these 33 families, 24 had ATM-related (72.72%), four had SACS-related (12.12%), three had COQ8A-related (9.09%), and two had APTX-related (6.06%) pathogenic variants. The c.3576G>A (p.K1192=) was the most common homozygous pathogenic ATM variant (33.33%) that was associated with milder phenotype of ataxia telangiectasia (AT) with the onset of age of 3. Patients with SACS variants demonstrated developmental delay and progressive ataxia before the age of 3. Slowly progressive ataxia and intellectual disability were the common clinical manifestations of the patients with homozygous c.1396delG (p. E466Rfs*11) pathogenic variant in COQ8A. Homozygous APTX c.689T>G (p.V230G) pathogenic variant was identified in two patients who had chief complaint of ataxic gait onset after puberty. The most common types of ARAs in this region are AT- and Charlevoix-Saguenay-type spastic ataxia. ATM gene analysis should be performed foremost on children presenting early-onset ataxia from Southeastern Anatolia. If there is a concomitant peripheral neuron involvement, SACS gene analysis should be preferred. This valuable data will be a guide for the first step molecular diagnostic approach before requesting the NGS panel for ARA.

Molecular prevalence and genotyping of Giardia duodenalis in cattle in Central Anatolia Region of Turkey.

The molecular prevalence and genotypes of Giardia duodenalis in cattle were investigated. A total of 450 fecal samples were collected from cattle in three provinces of Central Anatolia from August 2017 to July 2019. Genomic DNA was extracted from the fecal samples and used in molecular analysis carried out by nested PCR analyses of the ß-giardin (bg) gene of G. duodenalis. Positive samples were further analyzed by nested PCR at two gene loci (triosephosphate isomerase (tpi) and glutamate dehydrogenase (gdh)) for genotyping of G. duodenalis isolates. PCR analyses of the bg gene indicated that the overall prevalence of G. duodenalis was 30.2%. However, lower rates were determined with PCR analyses for gdh and tpi loci. The sequence analyses of the bg, gdh, and tpi genes revealed the presence of zoonotic assemblage A and livestock-specific assemblage E. Combined-sequence analyses revealed that assemblage E was the most common in the study area. Our study provides the first data on the wide prevalence of livestock-specific assemblages E in cattle in Turkey. The prevalence of assemblage A in cattle also reveals the importance of cattle for zoonotic transmission of giardiasis in Turkey.

The importance of long-term well management in geothermal power systems using fuzzy control: A Western Anatolia (Turkey) case study.

Effective geothermal power generation depends on two main elements: geothermal reservoir management and maintenance of the power plant. Reservoir management consists of both the fluid production and reinjection of brine to the underground. The management of wells is important to ensure the sustainability of the reservoir. Thus, the flow rate control systems are essential to protect geothermal reservoirs under long-term power production. The second issue is the daily change in electricity prices and the load change process is complex because geothermal well controls are not flexible operations. The well management thus requires control approaches, and fuzzy control can be one effective solution. In this study, a fuzzy control system has been developed to control flow rates of the wells in Kizildere geothermal field and its performance has been compared with the real data taken from the Kizildere Power Plant. The results of comparison show that the fuzzy controllers achieved the target energy production in 2 h instead of 5 h, compared to the real data. Based on the real data, the reinjection was only able to stabilize at the end of the fourth hour and the process took only 2 h when using the fuzzy controllers.

A new species of trout from the northern drainages of Euphrates River, Turkey (Salmoniformes: Salmonidae).

Salmo fahrettini, a new species, is distributed in the northern tributaries of the Euphrates River. It differs from other Salmo species in adjacent waters by a combination of the following characters: a greyish body; one black spot behind the eye and on the cheek; three to six black spots on the opercle; numerous black spots on the back (missing on the predorsal area), flank and middle part of body, surrounded by a roundish white ring; red spots in the median part of the body, surrounded by a roundish white ring; short and narrow maxilla; increase in the number of black and red spots with an increase in size; adipose fin medium size, no or rarely one red spot at its posterior edge; 109-116 lateral line scales; 27-30 scale rows between dorsal-fin origin and lateral line; 20-23 scale rows between the lateral line and anal-fin origin; maxilla length 8.8-10.0% standard length in males, 8.8-9.6 in females.

Amino acid 15 N analysis reveals change in the importance of freshwater resources between the hunter-gatherer and farmer in the Neolithic upper Tigris.

OBJECTIVE: The inhabitants of several sites in the Upper Tigris Valley, such as Hakemi Use, domesticated animals and cereals during the Pottery Neolithic period, while the inhabitants in this valley were hunter-gatherers in the Pre-Pottery Neolithic period, consuming freshwater and terrestrial food resources. However, there is considerable uncertainty surrounding whether or not changes in dietary food composition accompanied the shift in food production away from foraging. In order to reveal the impact of the development of agriculture on the human diet over the Pre-Pottery and Pottery Neolithic periods in this region, we analyzed the isotopic compositions of amino acids from the farmers at the Hakemi Use Pottery Neolithic site, and compared them with those from the Pre-Pottery hunter-gatherers in the close region. MATERIALS AND METHODS: Herein, we report the nitrogen isotopic compositions of amino acids, as well as both carbon and nitrogen isotopic compositions of bulk collagen, from human and faunal remains collected from Hakemi Use. RESULTS: Whereas freshwater resources were consumed by hunter-gatherers in this region during the Pre-Pottery period, the δ15 N values of glutamic acid (δ15 NGlu ) and phenylalanine (δ15 NPhe ) suggest that freshwater food resources were rarely consumed by inhabitants following the development of agriculture. DISCUSSION: Despite living in similar settings by the Tigris as its inhabitants during the Pre-Pottery period, the farmers of the Pottery Neolithic period depended less on freshwater resources for their diets relative to the hunter-gatherers of the Pre-Pottery Neolithic period.

Early farmers from across Europe directly descended from Neolithic Aegeans.

Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.

Novel and emergent sandfly-borne phleboviruses in Asia Minor: a systematic review.

Sandfly-transmitted phleboviruses are globally spread agents causing febrile diseases and central nervous system infections. The activity of pathogenic phleboviruses, as well as several novel strains, has been reported from Turkey, a transboundary country connecting Asia, Europe, and Africa with suitable habitats for sandflies. This study overviews all published data on phleboviruses from Turkey and evaluates the impact from the virological, epidemiological, and public health perspectives. A systematic review of Web-based global and local resources was performed. Comparison and phylogenetic analyses of particular phlebovirus sequences were also undertaken. Through the evaluation of 1693 international and regional entries, 31 manuscripts providing data on case reports or outbreaks, serological surveillance, animal infections and exposure, virus characterization, vector surveillance, and/or diagnostics were accessed. Detailed information on 5 novel phleboviruses completely or partially characterized during 2008-2015 as well as on clinical and epidemiological features of major phleboviruses established as human pathogens such as Toscana virus and sandfly fever Sicilian virus has been compiled. The ongoing activity of these agents, as indicated by consistently reported symptomatic cases and confirmed exposure in vertebrates including humans, was noted. The circulation in the Anatolian peninsula of phleboviruses with surprising diversity as well as distinct virus species is documented. Specific phlebovirus strains constitute a public health threat for local populations and travelers and must be considered in the diagnostic workup of clinically compatible cases. Human health impact and epidemiological aspects of certain viruses require further investigation via intensive surveillance.

Mantle Sources of Recent Anatolian Intraplate Magmatism: A Regional Plume or Local Tectonic Origin?

We present an extensive study of rehomogenized olivine-hosted melt inclusions, olivine phenocrysts, and chromian spinel inclusions to explore the link between geodynamic conditions and the origin and composition of Pliocene-Quaternary intraplate magmatism in Anatolia at Kula, Ceyhan-Osmaniye, and Karacadag. Exceptional compositional variability of these products reveals early and incomplete mixing of distinct parental melts in each volcanic center, reflecting asthenospheric and lithospheric mantle sources. The studied primitive magmas consist of (1) two variably enriched ocean island basalt (OIB)-type melts in Kula; (2) both OIB-type and plume mid-ocean ridge basalt (P-MORB)-like melts beneath Toprakkale and Üçtepeler (Ceyhan-Osmaniye); and (3) two variably enriched OIB-type melts beneath Karacadag. Estimated conditions of primary melt generation are 23-9 kbar, 75-30 km, and 1415-1215 °C for Kula; 28-19 kbar, 90-65 km, and 1430-1350 °C for Toprakkale; 23-18 kbar, 75-60 km, and 1400-1355 °C for Üçtepeler; and 35-27 kbar, 115-90 km, and 1530-1455 °C for Karacadag, the deepest levels of which correspond to the depth of the lithosphere-asthenosphere boundary in all regions. Although magma ascent was likely facilitated by local deformation structures, recent Anatolian intraplate magmatism seems to be triggered by large-scale mantle flow that also affects the wider Arabian and North African regions. We infer that these volcanics form part of a much wider Arabian-North African intraplate volcanic province, which was able to invade the Anatolian upper plate through slab gaps.

Different types of multiethnic societies and different patterns of development and change in the prehistoric Near East.

After briefly examining the forms of cultural contact in pre- and protohistoric societies in relation to the problem of the varying perception of territories and their "borders" as well as of "membership" in those societies, and after a brief reconsideration of the concept of culture and ethnicity in such archaic contexts, this paper then examines three examples of multiethnic societies in the Near East, and specifically in Upper Mesopotamia and Southeast Anatolia, in the fifth, fourth, and at the beginning of the third millennia before the common era (BCE), respectively. These examples are dealt with as emblematic cases of different models of society, types of interaction with alien groups, levels of integration, and development dynamics. Each of these cases is examined with respect to its socioeconomic context, the archeological evidence of "multiethnicity," the types of interaction between different components, the degree of cultural integration achieved, and the effects on the dynamics of change and the development of the societies examined. By analyzing and comparing these examples, the paper aims to show how interethnic contact impacted differently on different societies according to their types, the reasons and purposes of the interaction, and the degree of integration achieved.

Atmospheric pollen spectrum in Stone City, Mardin; the northern border of Mesopotamia/SE-Turkey.

Airborne pollen distribution in Mardin city was measured volumetrically during three consecutive years, 2014-2016. Three thousand eight hundred fifty-seven pollen grains as a mean value belonging to 44 taxa were recorded annually during the study period, and pollen grains from woody plant taxa had the more substantial atmospheric contribution with 62.66% and with 23 taxa. Despite the differences between years, the highest pollen concentration was recorded in April. The main pollen producers of the pollen spectrum were Cupressaceae (27.79%), Poaceae (21.21%), Platanus (10.29%), Morus (6.19%), Olea europaea (5.01%), Quercus (4.91%), Pinus (3.84%), and Amaranthaceae (3.73%) and almost all dominant pollen types in the city atmosphere were previously stated to be allergic. The atmospheric sampling data was characterized by the high presence of woody plants in spring, as well as the high presentation of herbaceous plants in late spring to early winter. The main pollen season (MPS) and durations of dominated pollen types were analyzed and mostly found a little bit earlier or parallel with similar studies in Mediterranean basin, but found earlier than the east. Statistical analyses were performed to compare years with each other and for correlating daily pollen concentrations of dominated pollen types concurrent with the data of meteorological parameters; a number of significant correlations were found.