Search

Consuming the milk of other species is a unique adaptation of Homo sapiens, with implications for health, birth spacing and evolution. Key questions nonetheless remain regarding the origins of dairying and its relationship to the genetically-determined ability to drink milk into adulthood through lactase persistence (LP). As a major centre of LP diversity, Africa is of significant interest to the evolution of dairying. Here we report proteomic evidence for milk consumption in ancient Africa. Using liquid chromatography tandem mass spectrometry (LC-MS/MS) we identify dairy proteins in human dental calculus from northeastern Africa, directly demonstrating milk consumption at least six millennia ago. Our findings indicate that pastoralist groups were drinking milk as soon as herding spread into eastern Africa, at a time when the genetic adaptation for milk digestion was absent or rare. Our study links LP status in specific ancient individuals with direct evidence for their consumption of dairy products., Nature Communications, 12 (1), ISSN:2041-1723

We are a group of archaeologists, anthropologists, curators and geneticists representing diverse global communities and 31 countries. All of us met in a virtual workshop dedicated to ethics in ancient DNA research held in November 2020. There was widespread agreement that globally applicable ethical guidelines are needed, but that recent recommendations grounded in discussion about research on human remains from North America are not always generalizable worldwide. Here we propose the following globally applicable guidelines, taking into consideration diverse contexts. These hold that: (1) researchers must ensure that all regulations were followed in the places where they work and from which the human remains derived; (2) researchers must prepare a detailed plan prior to beginning any study; (3) researchers must minimize damage to human remains; (4) researchers must ensure that data are made available following publication to allow critical re-examination of scientific findings; and (5) researchers must engage with other stakeholders from the beginning of a study and ensure respect and sensitivity to stakeholder perspectives. We commit to adhering to these guidelines and expect they will promote a high ethical standard in DNA research on human remains going forward., C.J.F. acknowledges support from the Australian Research Council Discovery Project DP160100811. V.G. acknowledges support from the National Research Foundation (NRF) South Africa; opinions expressed and conclusions arrived at are those of the authors and are not necessarily attributed to the NRF. M.O. acknowledges support from Conselho Nacional de Desenvolvimento Científico e Tecnológico grant 302163/2017-4 and from Fundação de Amparo à Pesquisa do Estado de São Paulo grant 2018/23282-5. P.S. acknowledges Francis Crick Institute core funding (FC001595) from Cancer Research UK, the UK Medical Research Council and the Wellcome Trust. V.S. acknowledges funding from the Alon Fellowship. M. Soressi acknowledges support from Dutch Research council grant VI.C.191.070. A.S.-N. acknowledges the János Bolyai Research Scholarship of the Hungarian Academy of Sciences. K.T. was supported by a J. C. Bose Fellowship (JCB/2019/000027), SERB and CSIR, Ministry of Science and Technology, Government of India. C.W. acknowledges support from the European Research Council (ERC-2017-StG 804844- DAIRYCULTURES) and the Werner Siemens Stiftung.

Lactase persistence (LP) is a well-studied example of a Mendelian trait under selection in some human groups due to gene-culture coevolution. We investigated the frequencies of genetic variants linked to LP in Sudanese and South Sudanese populations. These populations have diverse subsistence patterns, and some are dependent on milk to various extents, not only from cows but also from other livestock such as camels and goats. We sequenced a 316-bp region involved in regulating the expression of the LCT gene on chromosome 2, which encompasses five polymorphisms that have been associated with LP. Pastoralist populations showed a higher frequency of LP-associated alleles compared with nonpastoralist groups, hinting at positive selection also among northeast African pastoralists. Among the LP variants, the -14009:G variant occurs at the highest frequency among the investigated populations, followed by the -13915:G variant, which is likely of Middle Eastern origin, consistent with Middle Eastern gene flow to the Sudanese populations. There was no incidence of the “East African” LP allele (-14010:C) in the Sudanese and South Sudanese groups, and only one heterozygous individual for the “European” LP allele (-13910:T), suggesting limited recent admixture from these geographic regions. The Beja population of the Beni Amer show three different LP variants at substantial and similar levels, resulting in one of the greatest aggregation of LP variants among all populations across the world. Introduction Results and Discussion - Allele frequencies of LP-Associated Alleles - The Beja Populations - The Sudanese Arab Populations - The Nubian Populations - The Nilotic Populations - Additional Observed Polymorphisms - Haplotype Structure and Selection Scan Conclusion Materials and Methods - Phasing and imputation to analyze haplotype structure - Selection Scans

Oral contraceptive pills are problems for women, often have many effects, and may cause several diseases. The purpose of this research was to determine the impact of oral contraceptive pills on factor V sufferers. This case-control study conducted in Khartoum Sudan during the period from April to November 2018. The study included 50 women who used oral contraceptive as a case and 50 women who did not use oral contraceptive pills as a control, all of whom were verbally informed of the study and approved for participation. The PCR do for each sample. The results obtained from cases show that the mean age is 30±5.5 and divided into three groups less than 20 with a lower frequency of 4 % (2/50), (20-35) with a higher incidence of 80 % (40/50) and a higher rate of 16 % (8/50) for more than 35 years. Most cases use the oral contraceptive pill for more than one year at a frequency of 60% (30/50) with a mean of 2±0.8. The most frequent oral contraceptive pill use was levonorgestrel 88% (44/50), followed by desogestrel 12% (6/50). The study concludes that there is no significant difference in gene mutation between case and control. There was also an insignificant association between the mutation and demographic data.

The past decade has witnessed great progress in our understanding of the relationship between languages and genes. However, the linguistic-genetic patterns of language isolates and their speakers are not completely understood. The Bandiagara Escarpment in Central-Eastern Mali is a hub to diverse languages, cultures and life subsistence patterns, and a mysterious language isolate called “Bangime”. Here, we investigate genome-wide data of populations from Central-Eastern Mali to reveal the genetic structure of its diverse linguistic groups and help solve the mystery of language isolate Bangime and its speakers “the Bangande”. We show that the Bangande population is also a genetic isolate, with a mean time of divergence from surrounding populations estimated at 9,900 (CI 8,726-10,838) years ago. These findings support the scenario that the Bangande represent the region’s past linguistic and genetic diversity prior to the Dogon Expansion. Moreover, our study reports limited signals of admixture in the Dogon, Bozo, and Songhai of Kikara, suggesting that the cliff dwellings may have acted as a long-term barrier to gene flow. In contrast, we reveal admixture signals in the nomadic Fulani and the Songhai of Hombori, which we interpret in the context of gene-culture interactions for the Fulani. Finally, with simulation modeling, we show that the previous interpretations of the Dogon population structure are probably an artifact of the model-based genetic clustering.

Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gate-way out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of northeast Africa by genotyping ~3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400–200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa., Author summary Northeast Africa has geographic and historical links to Eurasia via the Middle East and the Arabian Peninsula, but the demographic history of the region itself has been more elusive. We investigate genomic diversity of northeast African populations and found a clear bimodal distribution of variation, correlated with geography, and likely driven by Eurasian admixture in the wake of migrations along the Nile. This admixture process largely coincides with the time of the Arab conquest, spreading in a southbound direction along the Nile and the Blue Nile. Nilotic populations occupying the region around the White Nile show long-term continuity, genetic isolation and genetic links to ancestral East African people. Compared to current times, groups that are ancestral to the current-day Nilotes likely inhabited a larger area of northeast Africa prior to the migration from the Middle East as their ancestry component can still be found in a large area. Our findings reveal the genetic history of Sudanese and South Sudanese people, broaden our knowledge on demographic history of humans, and quantify the impact of large-scale historic migration events in northeast Africa.

WOS: 000390231600001 PubMed ID: 27622383 Wild populations of the house mouse (Mus musculus) represent the raw genetic material for the classical inbred strains in biomedical research and are a major model system for evolutionary biology. We provide whole genome sequencing data of individuals representing natural populations of M. m. domesticus (24 individuals from 3 populations), M. m. helgolandicus (3 individuals), M. m. musculus (22 individuals from 3 populations) and M. spretus (8 individuals from one population). We use a single pipeline to map and call variants for these individuals and also include 10 additional individuals of M. m. castaneus for which genomic data are publically available. In addition, RNAseq data were obtained from 10 tissues of up to eight adult individuals from each of the three M. m. domesticus populations for which genomic data were collected. Data and analyses are presented via tracks viewable in the UCSC or IGV genome browsers. We also provide information on available outbred stocks and instructions on how to keep them in the laboratory. Max-Planck Society; DFG [HA 3139/4-1]; ERC [322564]; contract-research-project for the Bundeswehr Medical Service [M/SABX/005] This work was mostly financed by institutional resources of the Max-Planck Society, a DFG grant to B.H. and M.T. (HA 3139/4-1) and an ERC grant to D.T. (NewGenes, 322564). We thank Sonja Ihle, Susanne Krochter, Ruth Rottscheidt for contributing to collecting animals in the wild and our animal care takers for active involvement of optimizing the scheme for wild mouse keeping. The initial analysis of mice from Afghanistan was funded by contract-research-project for the Bundeswehr Medical Service M/SABX/005. We thank Bastian Pfeifer for help with software package PopGenome, Leslie Turner for discussion and Daniel M. Hooper and Trevor Price for helpful comments on the manuscript. D.T. had full access to all the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis.

Copy number variation represents a major source of genetic divergence, yet the evolutionary dynamics of genic copy number variation in natural populations during differentiation and adaptation remain unclear. We applied a read depth approach to genome resequencing data to detect copy number variants (CNVs) ≥1 kb in wild-caught mice belonging to four populations of Mus musculus domesticus. We complemented the bioinformatics analyses with experimental validation using droplet digital PCR. The specific focus of our analysis is CNVs that include complete genes, as these CNVs could be expected to contribute most directly to evolutionary divergence. In total, 1863 transcription units appear to be completely encompassed within CNVs in at least one individual when compared to the reference assembly. Further, 179 of these CNVs show population-specific copy number differences, and 325 are subject to complete deletion in multiple individuals. Among the most copy-number variable genes are three highly conserved genes that encode the splicing factor CWC22, the spindle protein SFI1, and the Holliday junction recognition protein HJURP. These genes exhibit population-specific expansion patterns that suggest involvement in local adaptations. We found that genes that overlap with large segmental duplications are generally more copy-number variable. These genes encode proteins that are relevant for environmental and behavioral interactions, such as vomeronasal and olfactory receptors, as well as major urinary proteins and several proteins of unknown function. The overall analysis shows that genic CNVs contribute more to population differentiation in mice than in humans and may promote and speed up population divergence.

BackgroundThere is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region.ResultWe report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE) was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia.ConclusionWe show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.