The historical spread of A rabian P astoralists to the eastern A frican S ahel evidenced by the lactase persistence −13,915*G allele and mitochondrial DNA

Lactase persistence in the Jordanian population: Potential effects of the Arabian Peninsula and Sahara's aridification

The single nucleotide polymorphism (SNP) -13910 C > T has proved a good predictor of the incidence of lactase persistence in Europe and South Asia. Yet, this is not the case in the Near East, although this region is a passageway between the two continents. Lactase persistence is associated with cattle breeding, which originated in the Fertile Crescent of the Near East and spread later during the Middle Neolithic throughout Europe. Here we analyzed five SNPs (-13915 T > G (rs41380347), -13910 C > T (rs4988235), -13907 C > G (rs41525747), -14009 T > G (rs869051967), and -14010 G > C (rs145946881)) in three Jordanian human groups, namely the Bedouins, Jordan valley farmers, and Jordanian urban people. The SNPs -14009 T > G and -14010 G > C were not detected in the sample, -13907 C > G was virtually non-existent, -13910 C > T showed low frequencies, and -13915 T > G exhibited salient frequencies. The estimated incidence of lactase persistence was lower in the urban population (16 %), intermediate in the Jordan Valley's farmer population (30 %), and higher among the Bedouins (62 %). In explaining our findings, we postulated climatic change brought about by the aridification episode of the Arabian Peninsula and the Sahara 4200 years ago. This climatic milestone caused the collapse of the Akkadian Empire and the Old Kingdom in Egypt. Also, it could have led to a drastic decline of cattle in the region, being replaced by the domestication of camels. Loss of traditional crops and increasing dependence on camel milk might have triggered local selective pressures, mainly associated with -13915 T > G and differentiated from the ones in Europe, associated with -13910 C > T.

Sexually dimorphic traits are associated with subsistence strategy in African faces from the Sahel/Savannah belt

OBJECTIVES

Previous research revealed that in some African populations, food-production strategies are associated with facial shape. Nomadic pastoralists living in the African Sahel/Savannah belt have a different facial morphology than their sedentary neighbors. We investigated whether the lifestyle associated with a subsistence pattern has an impact on sexual dimorphism in the facial structure.

METHODS

We employed several methods from geometric morphometrics and demonstrated such effect in four ethnically distinct populations that share the same geographic space.

RESULTS

We show that the facial traits which correlate with a subsistence strategy are systematically associated with levels of facial sex-typicality. In particular, we found that faces with more pronounced pastoralist features have on average more masculine facial traits and that this effect is more pronounced in men than in women.

CONCLUSIONS

In general, though, the magnitude of overall facial dimorphism does not differ between pastoralists and farmers. Pastoralists (in contrast to farmers) tend to have a more masculine facial morphology but facial differences between the sexes are in both groups the same.

Evolutionary Genetics and Admixture in African Populations

As the ancestral homeland of our species, Africa contains elevated levels of genetic diversity and substantial population structure. Importantly, African genomes are heterogeneous: They contain mixtures of multiple ancestries, each of which have experienced different evolutionary histories. In this review, we view population genetics through the lens of admixture, highlighting how multiple demographic events have shaped African genomes. Each of these historical vignettes paints a recurring picture of population divergence followed by secondary contact. First, we give a brief overview of genetic variation in Africa and examine deep population structure within Africa, including the evidence of ancient introgression from archaic "ghost" populations. Second, we describe the genetic legacies of admixture events that have occurred during the past 10,000 years. This includes gene flow between different click-speaking Khoe-San populations, the stepwise spread of pastoralism from eastern to southern Africa, multiple migrations of Bantu speakers across the continent, as well as admixture from the Middle East and Europe into the Sahel region and North Africa. Furthermore, the genomic signatures of more recent admixture can be found in the Cape Peninsula and throughout the African diaspora. Third, we highlight how natural selection has shaped patterns of genetic variation across the continent, noting that gene flow provides a potent source of adaptive variation and that selective pressures vary across Africa. Finally, we explore the biomedical implications of population structure in Africa on health and disease and call for more ethically conducted studies of genetic variation in Africa.

Demographic and Selection Histories of Populations Across the Sahel/Savannah Belt

The Sahel/Savannah belt harbors diverse populations with different demographic histories and different subsistence patterns. However, populations from this large African region are notably under-represented in genomic research. To investigate the population structure and adaptation history of populations from the Sahel/Savannah space, we generated dense genome-wide genotype data of 327 individuals-comprising 14 ethnolinguistic groups, including 10 previously unsampled populations. Our results highlight fine-scale population structure and complex patterns of admixture, particularly in Fulani groups and Arabic-speaking populations. Among all studied Sahelian populations, only the Rashaayda Arabic-speaking population from eastern Sudan shows a lack of gene flow from African groups, which is consistent with the short history of this population in the African continent. They are recent migrants from Saudi Arabia with evidence of strong genetic isolation during the last few generations and a strong demographic bottleneck. This population also presents a strong selection signal in a genomic region around the CNR1 gene associated with substance dependence and chronic stress. In Western Sahelian populations, signatures of selection were detected in several other genetic regions, including pathways associated with lactase persistence, immune response, and malaria resistance. Taken together, these findings refine our current knowledge of genetic diversity, population structure, migration, admixture and adaptation of human populations in the Sahel/Savannah belt and contribute to our understanding of human history and health.

Circum-Saharan Prehistory through the Lens of mtDNA Diversity

African history has been significantly influenced by the Sahara, which has represented a barrier for migrations of all living beings, including humans. Major exceptions were the gene flow events that took place between North African and sub-Saharan populations during the so-called African Humid Periods, especially in the Early Holocene (11.5 to 5.5 thousand years ago), and more recently in connection with trans-Saharan commercial routes. In this study, we describe mitochondrial DNA (mtDNA) diversity of human populations from both sides of the Sahara Desert, i.e., both from North Africa and the Sahel/Savannah belt. The final dataset of 7213 mtDNA sequences from 134 African populations encompasses 470 newly collected and 6743 previously published samples, which were analyzed using descriptive methods and Bayesian statistics. We completely sequenced 26 mtDNAs from sub-Saharan samples belonging to the Eurasian haplogroup N1. Analyses of these N1 mitogenomes revealed their possible routes to the Sahel, mostly via Bab el-Mandab. Our results indicate that maternal gene flow must have been important in this circum-Saharan space, not only within North Africa and the Sahel/Savannah belt but also between these two regions.

Human adaptation, demography and cattle domestication: an overview of the complexity of lactase persistence in Africa

Lactase persistence (LP) is a genetically-determined trait that is prevalent in African, European and Arab populations with a tradition of animal herding and milk consumption. To date, genetic analyses have identified several common variants that are associated with LP. Furthermore, data have indicated that these functional alleles likely have been maintained in pastoralist populations due to the action of recent selection, exemplifying the ongoing evolution of anatomically modern humans. Additionally, demographic history has also played a role in the geographic distribution of LP and associated alleles in Africa. In particular, the migration of ancestral herders and their subsequent admixture with local populations were integral to the spread of LP alleles and the culture of pastoralism across the continent. The timing of these demographic events was often correlated with known major environmental changes and/or the ability of domesticated cattle to resist/avoid infectious diseases. This review summarizes recent advances in our understanding of the genetic basis and evolutionary history of LP, as well as the factors that influenced the origin and spread of pastoralism in Africa.

The genetic variation of lactase persistence alleles in Sudan and South Sudan

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.

Demographic history and admixture dynamics in African Sahelian populations

The Sahel/Savannah belt of Africa is a contact zone between two subsistence systems (nomadic pastoralism and sedentary farming) and of two groups of populations, namely Eurasians penetrating from northern Africa southwards and sub-Saharan Africans migrating northwards. Because pastoralism is characterized by a high degree of mobility, it leaves few significant archaeological traces. Demographic history seen through the lens of population genetic studies complements our historical and archaeological knowledge in this African region. In this review, we highlight recent advances in our understanding of demographic history in the Sahel/Savannah belt as revealed by genetic studies. We show the impact of food-producing subsistence strategies on population structure and the somewhat different migration patterns in the western and eastern part of the region. Genomic studies show that the gene pool of various groups of Sahelians consists in a complex mosaic of several ancestries. We also touch upon various signals of genetic adaptations such as lactase persistence, taste sensitivity and malaria resistance, all of which have different distribution patterns among Sahelian populations. Overall, genetic studies contribute to gain a deeper understanding about the demographic and adaptive history of human populations in this specific African region and beyond.

Genetics of Lactose Intolerance: An Updated Review and Online Interactive World Maps of Phenotype and Genotype Frequencies

In humans the ability to digest milk lactose is conferred by a β-galactosidase enzyme called lactase-phlorizin hydrolase (LPH). While in some humans (approximately two-thirds of humankind) the levels of this enzyme decline drastically after the weaning phase (a trait known as lactase non-persistence (LNP)), some other individuals are capable of maintaining high levels of LPH lifelong (lactase persistence (LP)), thus being able to digest milk during adulthood. Both lactase phenotypes in humans present a complex genetic basis and have been widely investigated during the last decades. The distribution of lactase phenotypes and their associated single nucleotide polymorphisms (SNPs) across human populations has also been extensively studied, though not recently reviewed. All available information has always been presented in the form of static world maps or large dimension tables, so that it would benefit from the newly available visualization tools, such as interactive world maps. Taking all this into consideration, the aims of the present review were: (1) to gather and summarize all available information on LNP and LP genetic mechanisms and evolutionary adaptation theories, and (2) to create online interactive world maps, including all LP phenotype and genotype frequency data reported to date. As a result, we have created two online interactive resources, which constitute an upgrade over previously published static world maps, and allow users a personalized data exploration, while at the same time accessing complete reports by population or ethnicity.

Sahelian pastoralism from the perspective of variants associated with lactase persistence

OBJECTIVES

Archeological evidence shows that first nomadic pastoralists came to the African Sahel from northeastern Sahara, where milking is reported by ~7.5 ka. A second wave of pastoralists arrived with the expansion of Arabic tribes in 7th-14th century CE. All Sahelian pastoralists depend on milk production but genetic diversity underlying their lactase persistence (LP) is poorly understood.

MATERIALS AND METHODS

We investigated SNP variants associated with LP in 1,241 individuals from 29 mostly pastoralist populations in the Sahel. Then, we analyzed six SNPs in the neighboring fragment (419 kb) in the Fulani and Tuareg with the -13910*T mutation, reconstructed haplotypes, and calculated expansion age and growth rate of this variant.

RESULTS

Our results reveal a geographic localization of two different LP variants in the Sahel: -13910*T west of Lake Chad (Fulani and Tuareg pastoralists) and -13915*G east of there (mostly Arabic-speaking pastoralists). We show that -13910*T has a more diversified haplotype background among the Fulani than among the Tuareg and that the age estimate for expansion of this variant among the Fulani (~8.5 ka) corresponds to introduction of cattle to the area.

CONCLUSIONS

This is the first study showing that the "Eurasian" LP allele -13910*T is widespread both in northern Europe and in the Sahel; however, it is limited to pastoralists in the Sahel. Since the Fulani haplotype with -13910*T is shared with contemporary Eurasians, its origin could be in a region encompassing the Near East and northeastern Africa in a population ancestral to both Saharan pastoralists and European farmers.

Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait

Background

Human population history in the Holocene was profoundly impacted by changes in lifestyle following the invention and adoption of food-production practices. These changes triggered significant increases in population sizes and expansions over large distances. Here we investigate the population history of the Fulani, a pastoral population extending throughout the African Sahel/Savannah belt.

Results

Based on genome-wide analyses we propose that ancestors of the Fulani population experienced admixture between a West African group and a group carrying both European and North African ancestries. This admixture was likely coupled with newly adopted herding practices, as it resulted in signatures of genetic adaptation in contemporary Fulani genomes, including the control element of the LCT gene enabling carriers to digest lactose throughout their lives. The lactase persistence (LP) trait in the Fulani is conferred by the presence of the allele T-13910, which is also present at high frequencies in Europe. We establish that the T-13910 LP allele in Fulani individuals analysed in this study lies on a European haplotype background thus excluding parallel convergent evolution. We furthermore directly link the T-13910 haplotype with the Lactase Persistence phenotype through a Genome Wide Association study (GWAS) and identify another genomic region in the vicinity of the SPRY2 gene associated with glycaemic measurements after lactose intake.

Conclusions

Our findings suggest that Eurasian admixture and the European LP allele was introduced into the Fulani through contact with a North African population/s. We furthermore confirm the link between the lactose digestion phenotype in the Fulani to the MCM6/LCT locus by reporting the first GWAS of the lactase persistence trait. We also explored other signals of recent adaptation in the Fulani and identified additional candidates for selection to adapt to herding life-styles.

Tales of Human Migration, Admixture, and Selection in Africa

In the last three decades, genetic studies have played an increasingly important role in exploring human history. They have helped to conclusively establish that anatomically modern humans first appeared in Africa roughly 250,000–350,000 years before present and subsequently migrated to other parts of the world. The history of humans in Africa is complex and includes demographic events that influenced patterns of genetic variation across the continent. Through genetic studies, it has become evident that deep African population history is captured by relationships among African hunter–gatherers, as the world's deepest population divergences occur among these groups, and that the deepest population divergence dates to 300,000 years before present. However, the spread of pastoralism and agriculture in the last few thousand years has shaped the geographic distribution of present-day Africans and their genetic diversity. With today's sequencing technologies, we can obtain full genome sequences from diverse sets of extant and prehistoric Africans. The coming years will contribute exciting new insights toward deciphering human evolutionary history in Africa.

World-wide distributions of lactase persistence alleles and the complex effects of recombination and selection

The genetic trait of lactase persistence (LP) is associated with at least five independent functional single nucleotide variants in a regulatory region about 14 kb upstream of the lactase gene [−13910*T (rs4988235), −13907*G (rs41525747), −13915*G (rs41380347), −14009*G (rs869051967) and −14010*C (rs145946881)]. These alleles have been inferred to have spread recently and present-day frequencies have been attributed to positive selection for the ability of adult humans to digest lactose without risk of symptoms of lactose intolerance. One of the inferential approaches used to estimate the level of past selection has been to determine the extent of haplotype homozygosity (EHH) of the sequence surrounding the SNP of interest. We report here new data on the frequencies of the known LP alleles in the ‘Old World’ and their haplotype lineages. We examine and confirm EHH of each of the LP alleles in relation to their distinct lineages, but also show marked EHH for one of the older haplotypes that does not carry any of the five LP alleles. The region of EHH of this (B) haplotype exactly coincides with a region of suppressed recombination that is detectable in families as well as in population data, and the results show how such suppression may have exaggerated haplotype-based measures of past selection.