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Egypt Genome Project low coverage whole genome sequencing

ABSTRACT: All humans outside Africa are descendants of the same single exit, usually dated at 50-70 thousand years ago. However, the route taken out of Africa is still debated. The two main candidates are a northern route via Egypt and the Levant, or a southern route via Ethiopia and the Arabian Peninsula. We are generating genetic data to evaluate these two possibilities. In this study we propose to generate low-coverage sequencing data for 100 Egyptian samples.

PROVIDER: EGAS00001000480 | EGA |

REPOSITORIES: EGA

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Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians.

Pagani Luca L Schiffels Stephan S Gurdasani Deepti D Danecek Petr P Scally Aylwyn A Chen Yuan Y Xue Yali Y Haber Marc M Ekong Rosemary R Oljira Tamiru T Mekonnen Ephrem E Luiselli Donata D Bradman Neil N Bekele Endashaw E Zalloua Pierre P Durbin Richard R Kivisild Toomas T Tyler-Smith Chris C

American journal of human genetics 20150528 6

The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were incre ...[more]

PMID: 26027499

Similar Datasets

Egypt Genome Project high coverage whole genome sequencing

Project description:All humans outside Africa are descendants of the same single exit, usually dated at 50-70 thousand years ago. However, the route taken out of Africa is still debated. The two main candidates are a northern route via Egypt and the Levant, or a southern route via Ethiopia and the Arabian Peninsula. We are generating genetic data to evaluate these two possibilities. In this study we propose to generate high-coverage sequencing data for 3 Egyptian samples.

| EGAS00001000482 | EGA

EGAS00001000480-sc-20150521 - samples

Project description:All humans outside Africa are descendants of the same single exit, usually dated at 50-70 thousand years ago. However, the route taken out of Africa is still debated. The two main candidates are a northern route via Egypt and the Levant, or a southern route via Ethiopia and the Arabian Peninsula. We are generating genetic data to evaluate these two possibilities. In this study we propose to generate low-coverage sequencing data for 100 Egyptian samples.

| EGAD00001001372 | EGA

EGAS00001000482-sc-20150527 - samples

| EGAD00001001380 | EGA

Palaeoproteomics confirm earliest domesticated sheep in southern Africa ca. 2000 BP

Project description:We use ZooMS to obtain secure species identifications of key specimens of early domesticated fauna from South Africa, dating to ca. 2000 BP. Because it can be difficult to distinguish between fragmentary remains of early domesticates (sheep) and similar-sized local wild bovids (grey duiker, grey rhebok, springbok) based on morphology alone, we explore the use of biomolecular methods to make these distinctions. As well as the traditional method of analysing bone fragments, we show the utility of minimally destructive sampling methods such as PVC eraser and polishing films for successful ZooMS identification. We also show that collagen extracted more than 25 years ago for the purpose of radiocarbon dating can yield successful ZooMS identification. Our study demonstrates the importance of developing appropriate regional frameworks of comparison for future research using ZooMS as a method of biomolecular species identification on archaeological faunal assemblages. We confirm that the specimen from the site of Spoegrivier dated to 2105±65 BP is indeed a sheep. This is the earliest directly dated evidence of domesticated animals in southern Africa.

2021-03-23 | PXD021949 | Pride

Genotyping of 75 individuals from the Afrikaner population of South Africa

Project description:The Afrikaner population of South Africa are the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the “Coloured" populations of South Africa. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct characteristic admixture patterns in the Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records previously estimated the contribution of non-Europeans into the Afrikaners to be between 5.5%-7.2%. NB two individuals withdrew consent so this data contains only 75 individuals as compared to the 77 cited in the article.

2020-01-28 | E-MTAB-8757 | biostudies-arrayexpress

Project description:Zaprionus indianus and tuberculatus from Egypt and Africa

| PRJNA1164717 | ENA

Enamel proteins reveal biological sex and intrataxon variability within Paranthropus robustus

Project description:The evolutionary relationships among extinct African hominin species are highly debated and largely unresolved, due in part to a lack of molecular data. Even within taxa, it is not always clear, based on morphology alone, whether ranges of variation are due to sexual dimorphism versus potentially undescribed taxonomic diversity. For Paranthropus robustus, a Pleistocene hominin found only in South Africa, both phylogenetic relationships to other taxa, and the nature of intraspecific variation are still debated. Here we report the first successful mass spectrometric sequencing of enamel proteomes from four ca. 2 million years old dental specimens morphologically identified as P. robustus from the site of Swartkrans.

2025-06-09 | PXD040221 | Pride

Genotyping by array of genomic variation in seven Khoe-San groups to reveal adaptation and complex African history

Project description:The history of click-speaking Khoe-San, and African populations in general, remains poorly understood. We genotyped ~2.3 million SNPs in 220 southern Africans and found that the Khoe-San diverged from other populations at least 100,000 years ago, but structure within the Khoe-San dated back to about 35,000 years ago. Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa, instead, it indicated a history of admixture and stratification. We found evidence of adaptation targeting muscle function and immune response, potential adaptive introgression of UV-light protection, and selection predating modern human diversification involving skeletal and neurological development. These new findings illustrate the importance of African genomic diversity in understanding human evolutionary history .220 samples were analysed with the Illumina HumanOmni2.5-Quad BeadChip and are described herein.

2012-09-22 | E-MTAB-1259 | biostudies-arrayexpress

RNA-seq of Arabian horses

Project description:Report transcritpome analysis of Arabian horses before and after exercise

2019-01-23 | GSE104388 | GEO

Chromosome-level reference genome for the medically important Arabian horned viper (Cerastes gasperettii)

Project description:Venomous animals have traditionally been studied from a proteomic (but also transcriptomic) perspective, often overlooking the study of venom from a genomic point of view until recently. The rise of genomics has led to an increase in the number of reference genomes for non-model organisms, including venomous taxa, enabling new questions on venom evolution from a genomic context. Although venomous snakes are the fundamental model system in venom research, the number of high-quality reference genomes in the group remains limited. In this study, we present a high-quality chromosome-level reference genome for the Arabian horned viper (Cerastes gasperettii), a highly venomous snake native to the Arabian Peninsula. Our highly-contiguous genome allowed us to explore macrochromosomal rearrangements within the Viperidae family, as well as across squamate reptile evolution. Furthermore, we identified a total of ten different toxins conforming the venom’s core, in line with our proteomic results. We also compared microsyntenic changes in the main toxin gene clusters with those of other venomous snake species, highlighting the pivotal role of gene duplication and loss in the emergence and diversification of the two main toxin families for Cerastes gasperettii. Using Illumina data, we reconstructed the demographic history and genome-wide diversity of the species, revealing how historical aridity likely drove population expansions. Finally, this study highlights the importance of using long-read sequencing as well as chromosome-level reference genomes to disentangle the origin and diversification of toxin families in venomous species.

2025-02-18 | PXD060777 | Pride

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