Geographical structure of the Y-chromosomal genetic landscape of the Levant: a coastal-inland contrast.
Ontology highlight
ABSTRACT:
SUBMITTER: El-Sibai M
PROVIDER: S-EPMC3312577 | biostudies-literature | 2009 Nov
REPOSITORIES: biostudies-literature
Publications
Geographical structure of the Y-chromosomal genetic landscape of the Levant: a coastal-inland contrast.
El-Sibai Mirvat M Platt Daniel E DE Haber Marc M Xue Yali Y Youhanna Sonia C SC Wells R Spencer RS Izaabel Hassan H Sanyoura May F MF Harmanani Haidar H Bonab Maziar Ashrafian MA Behbehani Jaafar J Hashwa Fuad F Tyler-Smith Chris C Zalloua Pierre A PA
Annals of human genetics 20090816 Pt 6
We have examined the male-specific phylogeography of the Levant and its surroundings by analyzing Y-chromosomal haplogroup distributions using 5874 samples (885 new) from 23 countries. The diversity within some of these haplogroups was also examined. The Levantine populations showed clustering in SNP and STR analyses when considered against a broad Middle-East and North African background. However, we also found a coastal-inland, east-west pattern of diversity and frequency distribution in sever ...[more]
Similar Datasets
Project description:Climate change threatens global mangroves, which are already among the world's most impacted ecosystems. Vulnerability components of exposure, sensitivity and adaptive capacity were evaluated on mangroves of atoll settings on Jaluit Atoll, in the Marshall Islands, assessing spatial changes of mangrove cover 1945-2018/19, sea-level trends 1968-2019, and reviewing available information. Inland mangrove depressions occur on Jaluit, as well as coastal lagoon margin mangroves, and both were assessed using the same methods. Spatial analysis results showed both inland and coastal mangroves have increased in area. Inland mangroves on eight of Jaluit's islands mostly expanded after 1976 from 40 to 50 hectares, with progradation and tidal creek infill closing lagoon connections. Shoreline mangroves showed 88-100% of transects prograding 0.1-0.51 m year-1 and 0-11.5% of transects eroding 0-0.18 m year-1. Assessment of a combination of aerial/satellite images, literature and on-the-ground photos indicated that the mangroves are in healthy condition. Vulnerability assessment results showed both inland and coastal mangroves to have similar strengths and weaknesses in resilience, with intrinsic areas of vulnerability persisting during increased future sea level rise, limited sediment supply and extremely low elevations.Supplementary informationThe online version contains supplementary material available at 10.1007/s11273-022-09878-0.
| S-EPMC9091136 | biostudies-literature
Project description:The action of natural selection across heterogeneous natural landscapes drives local adaptation and the formation of plant ecotypes, the precursors to new species. Plant ecotypes typically differ greatly in morphology, physiology, and development, yet we have a poor understanding of the underlying genetic basis of this divergence. Despite their importance, studies of the molecular underpinnings of ecotypic divergence through developmental stages are rare. In this study, we compared gene expression at different developmental time points between two locally adapted populations derived from the coastal perennial and inland annual ecotypes of the yellow monkeyflower, Mimulus guttatus. We conducted gene co-expression network analyses to identify putative genetic and molecular mechanisms driving ecotypic divergence and evaluated gene ontology enrichment. Overall, we found significant global expression differences between the ecotypes and among developmental stages. We also found evidence to support the hypothesis that interacting hormone pathways, especially the gibberellin and jasmonic acid pathways, may play a key role in annual versus perennial ecotype divergence. Further, genes within known chromosomal inversions were more likely to be differentially expressed than genes in colinear regions, but only in leaves and not for floral buds. Collectively, our results reinforce our existing hypotheses about how ecotype formation has occurred in this system through shifts in hormone biosynthesis/signaling and help advance our understanding of the evolution of annuality versus perenniality in plants.
2024-11-10 | GSE280929 | GEO
Project description:The Malay people are an important ethnic composition in Southeast Asia, but their genetic make-up and population structure remain poorly studied. Here we conducted a genome-wide study of four geographical Malay populations: Peninsular Malaysian Malay (PMM), Singaporean Malay (SGM), Indonesian Malay (IDM) and Sri Lankan Malay (SLM). All the four Malay populations showed substantial admixture with multiple ancestries. We identified four major ancestral components in Malay populations: Austronesian (17%-62%), Proto-Malay (15%-31%), East Asian (4%-16%) and South Asian (3%-34%). Approximately 34% of the genetic makeup of SLM is of South Asian ancestry, resulting in its distinct genetic pattern compared with the other three Malay populations. Besides, substantial differentiation was observed between the Malay populations from the north and the south, and between those from the west and the east. In summary, this study revealed that the genetic identity of the Malays comprises a mixed entity of multiple ancestries represented by Austronesian, Proto-Malay, East Asian and South Asian, with most of the admixture events estimated to have occurred 175 to 1,500 years ago, which in turn suggests that geographical isolation and independent admixture have significantly shaped the genetic architectures and the diversity of the Malay populations.
| S-EPMC4585825 | biostudies-other
Project description:The karst underground river ecosystem of Yucatan peninsula is composed of cave systems and sinkholes. The microbial diversity of water from this underground river has been studied, but, structure of the microbial community in its cave sediments remained largely unknown. Here we describe how the microbial community structure of these sediments changes due to different environmental conditions found in sediment zones along the caves of a coastal and an inland sinkhole. We found that dominant microbial groups varied according to the type of sinkhole (Coastal: Chloroflexi and Crenarchaeota; inland: Methylomirabilota and Acidobacteriota) and that the community structures differed both among sinkhole types, and within the sediment zones that were studied. These microorganisms are associated with different types of metabolism, and differed from a microbial community dominated by sulfate reducers at the coastal sinkhole, to one dominated by methylotrophs at the inland sinkhole, suggesting there are biogeochemical processes in the coastal and inland sinkholes that lead to changes in the microbial composition of the underground river ecosystem's sediments. Our results suggest sediments from unexplored sinkhole caves are unique environmental niches with distinct microbial assemblages that putatively play an important role in the biogeochemical cycles of these ecosystems.
| S-EPMC8782880 | biostudies-literature
Project description:Varied environmental conditions in coastal-inland zones tend to influence soil faunal communities. However, few studies have focused on the responses of soil fauna to environmental variations along the coastal-inland gradient. In order to better understand the aforementioned responses, a total of 80 soil macro-faunal samples were collected at the five different distances from the coastline of China's Bohai Bay. The results revealed that the compositions, structural characteristics and diversity of the soil macro-fauna varied among the different habitats. With the increases in the distance from the sea, the individual density, richness and diversity levels of the soil macro-fauna all first increased and then decreased. The individual density, richness and diversity values were all at their maximum at 30 km from the sea. The Edge effect promoted unique and rare soil macro-faunal taxa. Formicidae, Curculionidae and Aphodiidae were found to be the edge taxa. Agelenidae, Liocranidae and Nematocera were considered to be indicator taxa of severe sea effects. Paradoxosomatidae was an indicator taxon of slight effects. Overall, the environmental variations along the coastal-inland gradient were found to have the potential to affect the soil macro-faunal communities, and the different taxa of the soil macro-fauna responded to those variations in different ways. This study further revealed the processes and mechanisms of the sea influencing the soil macro-faunal communities, which had been caused by the coastal-inland gradient. The results of this study also provided a theoretical basis for developing future biodiversity guidelines for coastal ecosystems.
| S-EPMC7367051 | biostudies-literature
Project description:Intensive agriculture and densely populated areas represent major sources of nutrient pollution for European inland and coastal waters, altering the aquatic ecosystems and affecting their capacity to provide ecosystem services and support economic activities. Ambitious water policies are in place in the European Union (EU) for protecting and restoring aquatic ecosystems under the Water Framework Directive and the Marine Strategy Framework Directive. This research quantified the current pressures of point and diffuse nitrogen and phosphorus emissions to European fresh and coastal waters (2005-2012), and analysed the effects of three policy scenarios of nutrient reduction: 1) the application of measures currently planned in the Rural Development Programmes and under the Urban Waste Water Treatment Directive (UWWTD); 2) the full implementation of the UWWTD and the absence of derogations in the Nitrates Directive; 3) high reduction of nutrient, using best technologies in wastewaters treatment and optimal fertilisation in agriculture. The results of the study show that for the period 2005-2012, the nitrogen load to European seas was 3.3-4.1 TgN/y and the phosphorus load was 0.26-0.30 TgP/y. Policy measures supporting technological improvements (third scenario) could decrease the nutrient export to the seas up to 14% for nitrogen and 20% for phosphorus, improving the ecological status of rivers and lakes, but widening the nutrient imbalance in coastal ecosystems (i.e. increasing nitrogen availability with respect to phosphorus), affecting eutrophication. Further nutrient reductions could be possible by a combination of measures especially in the agricultural sector. However, without tackling current agricultural production and consumption system, the reduction might not be sufficient for achieving the goals of EU water policy in some regions. The study analysed the expected changes and the source contribution in different European regional seas, and highlights the advantages of addressing the land-sea dynamics, checking the coherence of measures taken under different policies.
| S-EPMC8386246 | biostudies-literature
Project description:BackgroundHistorical and ecological processes shape patterns of genetic diversity in plant species. Colonization to new environments and geographical landscape features determine, amongst other factors, genetic diversity within- and differentiation between-populations. We analyse the genetic diversity and population structure of Calibrachoa heterophylla to infer the influence of abiotic landscape features on the level of gene flow in this coastal species of the South Atlantic Coastal Plain.ResultsThe C. heterophylla populations located on early-deposited coastal plain regions show higher genetic diversity than those closer to the sea. The genetic differentiation follows a pattern of isolation-by-distance. Landscape features, such as water bodies and wind corridors, and geographical distances equally explain the observed genetic differentiation, whereas the precipitation seasonality exhibits a strong signal for isolation-by-environment in marginal populations. The estimated levels of gene flow suggest that marginal populations had restricted immigration rates enhancing differentiation.ConclusionsTopographical features related to coastal plain deposition history influence population differentiation in C. heterophylla. Gene flow is mainly restricted to nearby populations and facilitated by wind fields, albeit without any apparent influence of large water bodies. Furthermore, differential rainfall regimes in marginal populations seem to promote genetic differentiation.
| S-EPMC8547116 | biostudies-literature
Project description:Previous studies indicated existing, albeit limited, genetic-geographic population substructure in the Dutch population based on genome-wide data and a lack of this for mitochondrial SNP based data. Despite the aforementioned studies, Y-chromosomal SNP data from the Netherlands remain scarce and do not cover the territory of the Netherlands well enough to allow a reliable investigation of genetic-geographic population substructure. Here we provide the first substantial dataset of detailed spatial Y-chromosomal haplogroup information in 2085 males collected across the Netherlands and supplemented with previously published data from northern Belgium. We found Y-chromosomal evidence for genetic-geographic population substructure, and several Y-haplogroups demonstrating significant clinal frequency distributions in different directions. By means of prediction surface maps we could visualize (complex) distribution patterns of individual Y-haplogroups in detail. These results highlight the value of a micro-geographic approach and are of great use for forensic and epidemiological investigations and our understanding of the Dutch population history. Moreover, the previously noted absence of genetic-geographic population substructure in the Netherlands based on mitochondrial DNA in contrast to our Y-chromosome results, hints at different population histories for women and men in the Netherlands.
| S-EPMC7029002 | biostudies-literature
Project description:Organic carbon accumulation in the sediments of inland aquatic and coastal ecosystems is an important process in the global carbon budget that is subject to intense human modification. To date, research has focused on quantifying accumulation rates in individual or groups of aquatic ecosystems to quantify the aquatic carbon sinks. However, there hasn't been a synthesis of rates across aquatic ecosystem to address the variability in rates within and among ecosystems types. Doing so would identify gaps in our understanding of accumulation rates and potentially reveal carbon sinks vulnerable to change. We synthesized accumulation rates from the literature, compiling 464 rate measurements from 103 studies of carbon accumulated in the modern period (ca. 200 years). Accumulation rates from the literature spanned four orders of magnitude varying substantially within and among ecosystem categories, with mean estimates for ecosystem categories ranging from 15.6 to 73.2?g?C m-2 y-1 within ecosystem categories. With the exception of lakes, mean accumulation rates were poorly constrained due to high variability and paucity of data. Despite the high uncertainty, the estimates of modern accumulation rate compiled here are an important step for constructing carbon budgets and predicting future change.
| S-EPMC6200792 | biostudies-literature
Project description:Genetic diversity provides insight into heterogeneous demographic and adaptive history across organisms' distribution ranges. For this reason, decomposing single species into genetic units may represent a powerful tool to better understand biogeographical patterns as well as improve predictions of the effects of GCC (global climate change) on biodiversity loss. Using 279 georeferenced Iberian accessions, we used classes of three intraspecific genetic units of the annual plant Arabidopsis thaliana obtained from the genetic analyses of nuclear SNPs (single nucleotide polymorphisms), chloroplast SNPs, and the vernalization requirement for flowering. We used SDM (species distribution models), including climate, vegetation, and soil data, at the whole-species and genetic-unit levels. We compared model outputs for present environmental conditions and with a particularly severe GCC scenario. SDM accuracy was high for genetic units with smaller distribution ranges. Kernel density plots identified the environmental variables underpinning potential distribution ranges of genetic units. Combinations of environmental variables accounted for potential distribution ranges of genetic units, which shrank dramatically with GCC at almost all levels. Only two genetic clusters increased their potential distribution ranges with GCC. The application of SDM to intraspecific genetic units provides a detailed picture on the biogeographical patterns of distinct genetic groups based on different genetic criteria. Our approach also allowed us to pinpoint the genetic changes, in terms of genetic background and physiological requirements for flowering, that Iberian A. thaliana may experience with a GCC scenario applying SDM to intraspecific genetic units.
| S-EPMC4768750 | biostudies-literature