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Unraveling a fine-scale high genetic heterogeneity and recent continental connections of an Arabian Peninsula population.

ABSTRACT: Recent studies have showed the diverse genetic architecture of the highly consanguineous populations inhabiting the Arabian Peninsula. Consanguinity coupled with heterogeneity is complex and makes it difficult to understand the bases of population-specific genetic diseases in the region. Therefore, comprehensive genetic characterization of the populations at the finest scale is warranted. Here, we revisit the genetic structure of the Kuwait population by analyzing genome-wide single nucleotide polymorphisms data from 583 Kuwaiti individuals sorted into three subgroups. We envisage a diverse demographic genetic history among the three subgroups based on drift and allelic sharing with modern and ancient individuals. Furthermore, our comprehensive haplotype-based analyses disclose a high genetic heterogeneity among the Kuwaiti populations. We infer the major sources of ancestry within the newly defined groups; one with an obvious predominance of sub-Saharan/Western Africa mostly comprising Kuwait-B individuals, and other with West Eurasia including Kuwait-P and Kuwait-S individuals. Overall, our results recapitulate the historical population movements and reaffirm the genetic imprints of the legacy of continental trading in the region. Such deciphering of fine-scale population structure and their regional genetic heterogeneity would provide clues to the uncharted areas of disease-gene discovery and related associations in populations inhabiting the Arabian Peninsula.

SUBMITTER: Eaaswarkhanth M

PROVIDER: S-EPMC8904638 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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Unraveling a fine-scale high genetic heterogeneity and recent continental connections of an Arabian Peninsula population.

Eaaswarkhanth Muthukrishnan M Pathak Ajai K AK Ongaro Linda L Montinaro Francesco F Hebbar Prashantha P Alsmadi Osama O Metspalu Mait M Al-Mulla Fahd F Thanaraj Thangavel Alphonse TA

European journal of human genetics : EJHG 20210322 3

Recent studies have showed the diverse genetic architecture of the highly consanguineous populations inhabiting the Arabian Peninsula. Consanguinity coupled with heterogeneity is complex and makes it difficult to understand the bases of population-specific genetic diseases in the region. Therefore, comprehensive genetic characterization of the populations at the finest scale is warranted. Here, we revisit the genetic structure of the Kuwait population by analyzing genome-wide single nucleotide p ...[more]

PMID: 33753911

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Project description:BackgroundTwo potential migratory routes followed by modern humans to colonize Eurasia from Africa have been proposed. These are the two natural passageways that connect both continents: the northern route through the Sinai Peninsula and the southern route across the Bab al Mandab strait. Recent archaeological and genetic evidence have favored a unique southern coastal route. Under this scenario, the study of the population genetic structure of the Arabian Peninsula, the first step out of Africa, to search for primary genetic links between Africa and Eurasia, is crucial. The haploid and maternally inherited mitochondrial DNA (mtDNA) molecule has been the most used genetic marker to identify and to relate lineages with clear geographic origins, as the African Ls and the Eurasian M and N that have a common root with the Africans L3.ResultsTo assess the role of the Arabian Peninsula in the southern route, we genetically analyzed 553 Saudi Arabs using partial (546) and complete mtDNA (7) sequencing, and compared the lineages obtained with those present in Africa, the Near East, central, east and southeast Asia and Australasia. The results showed that the Arabian Peninsula has received substantial gene flow from Africa (20%), detected by the presence of L, M1 and U6 lineages; that an 18% of the Arabian Peninsula lineages have a clear eastern provenance, mainly represented by U lineages; but also by Indian M lineages and rare M links with Central Asia, Indonesia and even Australia. However, the bulk (62%) of the Arabian lineages has a Northern source.ConclusionAlthough there is evidence of Neolithic and more recent expansions in the Arabian Peninsula, mainly detected by (preHV)1 and J1b lineages, the lack of primitive autochthonous M and N sequences, suggests that this area has been more a receptor of human migrations, including historic ones, from Africa, India, Indonesia and even Australia, than a demographic expansion center along the proposed southern coastal route.

Project description:Genetic structure within marine species may be driven by local adaptation to their environment, or alternatively by historical processes, such as geographic isolation. The gulfs and seas bordering the Arabian Peninsula offer an ideal setting to examine connectivity patterns in coral reef fishes with respect to environmental gradients and vicariance. The Red Sea is characterized by a unique marine fauna, historical periods of desiccation and isolation, as well as environmental gradients in salinity, temperature, and primary productivity that vary both by latitude and by season. The adjacent Arabian Sea is characterized by a sharper environmental gradient, ranging from extensive coral cover and warm temperatures in the southwest, to sparse coral cover, cooler temperatures, and seasonal upwelling in the northeast. Reef fish, however, are not confined to these seas, with some Red Sea fishes extending varying distances into the northern Arabian Sea, while their pelagic larvae are presumably capable of much greater dispersal. These species must therefore cope with a diversity of conditions that invoke the possibility of steep clines in natural selection. Here, we test for genetic structure in two widespread reef fish species (a butterflyfish and surgeonfish) and eight range-restricted butterflyfishes across the Red Sea and Arabian Sea using genome-wide single nucleotide polymorphisms. We performed multiple matrix regression with randomization analyses on genetic distances for all species, as well as reconstructed scenarios for population subdivision in the species with signatures of isolation. We found that (a) widespread species displayed more genetic subdivision than regional endemics and (b) this genetic structure was not correlated with contemporary environmental parameters but instead may reflect historical events. We propose that the endemic species may be adapted to a diversity of local conditions, but the widespread species are instead subject to ecological filtering where different combinations of genotypes persist under divergent ecological regimes.

Project description:A key aim of ecology is to understand the drivers of ecological patterns, so that we can accurately predict the effects of global environmental change. However, in many cases, predictors are measured at a finer resolution than the ecological response. We therefore require data aggregation methods that avoid loss of information on fine-grain heterogeneity.We present a data aggregation method that, unlike current approaches, reduces the loss of information on fine-grain spatial structure in environmental heterogeneity for use with coarse-grain ecological datasets. Our method contains three steps: (a) define analysis scales (predictor grain, response grain, scale-of-effect); (b) use a moving window to calculate a measure of variability in environment (predictor grain) at the process-relevant scale (scale-of-effect); and (c) aggregate the moving window calculations to the coarsest resolution (response grain). We show the theoretical basis for our method using simulated landscapes and the practical utility with a case study. Our method is available as the grainchanger r package.The simulations show that information about spatial structure is captured that would have been lost using a direct aggregation approach, and that our method is particularly useful in landscapes with spatial autocorrelation in the environmental predictor variable (e.g. fragmented landscapes) and when the scale-of-effect is small relative to the response grain. We use our data aggregation method to find the appropriate scale-of-effect of land cover diversity on Eurasian jay Garrulus glandarius abundance in the UK. We then model the interactive effect of land cover heterogeneity and temperature on G. glandarius abundance. Our method enables us quantify this interaction despite the different scales at which these factors influence G. glandarius abundance.Our data aggregation method allows us to integrate variables that act at varying scales into one model with limited loss of information, which has wide applicability for spatial analyses beyond the specific ecological context considered here. Key ecological applications include being able to estimate the interactive effect of drivers that vary at different scales (such as climate and land cover), and to systematically examine the scale dependence of the effects of environmental heterogeneity in combination with the effects of climate change on biodiversity.

Project description:The leatherback turtle Dermochelys coriacea is the most widely distributed sea turtle species in the world. It exhibits complex life traits: female homing and migration, migrations of juveniles and males that remain poorly known, and a strong climatic influence on resources, breeding success and sex-ratio. It is consequently challenging to understand population dynamics. Leatherbacks are critically endangered, yet the group from the Northwest Atlantic is currently considered to be under lower risk than other populations while hosting some of the largest rookeries. Here, we investigated the genetic diversity and the demographic history of contrasted rookeries from this group, namely two large nesting populations in French Guiana, and a smaller one in the French West Indies. We used 10 microsatellite loci, of which four are newly isolated, and mitochondrial DNA sequences of the control region and cytochrome b. Both mitochondrial and nuclear markers revealed that the Northwest Atlantic stock of leatherbacks derives from a single ancestral origin, but show current genetic structuration at the scale of nesting sites, with the maintenance of migrants amongst rookeries. Low nuclear genetic diversities are related to founder effects that followed consequent bottlenecks during the late Pleistocene/Holocene. Most probably in response to climatic oscillations, with a possible influence of early human hunting, female effective population sizes collapsed from 2 million to 200. Evidence of founder effects and high numbers of migrants make it possible to reconsider the population dynamics of the species, formerly considered as a metapopulation model: we propose a more relaxed island model, which we expect to be a key element in the currently observed recovering of populations. Although these Northwest Atlantic rookeries should be considered as a single evolutionary unit, we stress that local conservation efforts remain necessary since each nesting site hosts part of the genetic diversity and species history.

Dataset Information

Unraveling a fine-scale high genetic heterogeneity and recent continental connections of an Arabian Peninsula population.

Publications

Unraveling a fine-scale high genetic heterogeneity and recent continental connections of an Arabian Peninsula population.

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