Modern African Populations Research Articles

Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations

Helicobacter pylori lives in the human stomach and has a population structure resembling that of its host. However, H. pylori from Europe and the Middle East trace substantially more ancestry from modern African populations than the humans that carry them. Here, we use a collection of Afro-Eurasian H. pylori genomes to show that this African ancestry is due to at least three distinct admixture events. H. pylori from East Asia, which have undergone little admixture, have accumulated many more non-synonymous mutations than African strains. European and Middle Eastern bacteria have elevated African ancestry at the sites of these mutations, implying selection to remove them during admixture. Simulations show that population fitness can be restored after bottlenecks by migration and subsequent admixture of small numbers of bacteria from non-bottlenecked populations. We conclude that recent spread of African DNA has been driven by deleterious mutations accumulated during the original out-of-Africa bottleneck.

Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture.

The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: 1) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; 2) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; 3) how these novel methods can detect archaic introgression in modern African populations; and 4) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.

Mitogenomic diversity in Sacred Ibis Mummies sheds light on early Egyptian practices.

The ancient catacombs of Egypt harbor millions of well-preserved mummified Sacred Ibis (Threskiornis aethiopicus) dating from ~600BC. Although it is known that a very large number of these ‘votive’ mummies were sacrificed to the Egyptian God Thoth, how the ancient Egyptians obtained millions of these birds for mummification remains unresolved. Ancient Egyptian textual evidences suggest they may have been raised in dedicated large-scale farms. To investigate the most likely method used by the priests to secure birds for mummification, we report the first study of complete mitochondrial genomes of 14 Sacred Ibis mummies interred ~2500 years ago. We analysed and compared the mitogenomic diversity among Sacred Ibis mummies to that found in modern Sacred Ibis populations from throughout Africa. The ancient birds show a high level of genetic variation comparable to that identified in modern African populations, contrary to the suggestion in ancient hieroglyphics (or ancient writings) of centralized industrial scale farming of sacrificial birds. This suggests a sustained short-term taming of the wild migratory Sacred Ibis for the ritual yearly demand.

An Odontometric Investigation of the Affinities of the Nazlet Khater Specimen to Prehistoric, Protohistoric and Modern African Populations

This study scrutinizes the affinities of a 33,000-year-old skeleton from Nazler Khater, Egypt, to various prehistoric African populations. The comparative material consists of 231 individuals, ranging in time from the Middle Pleistocene to recent and restricted in space to the African continent and Southern Levant. Possible affinities were first examined with the application of univariate, and bivariate, statistics. Subsequently, principal components analysis and cluster analysis are performed on mean data from 29 populations, utilizing a selected set of tooth dimensions. The results indicate a strong association between some of the sub-Saharan Middle Stone Age (MSA) specimens and he Nazlet Khater skeleton. No clear discrimination was reached between the various African and Levantine populations. The significant differences between male and female mean data factor scores on the first principal component indicate that sexual dimorphism accounts for a large portion of the observed variability in size.

Ancient DNA pushes human emergence back

Human Evolution Anatomically modern humans evolved in Africa, but pinpointing when has been difficult. Schlebusch et al. sequenced three ancient African genomes from the Stone Age, about 2000 years old, and four from the Iron Age, 300 to 500 years old. One of the oldest samples, sequenced to 13× coverage, appears most closely to resemble individuals from the present-day San population. However, this individual seems to have lacked genetic contributions from other modern African populations, including pastoralists and farmers, which were observed in modern San individuals. Thus, the earliest divergence between human populations may have occurred 350,000 to 260,000 years ago. Science , this issue p. [652][1] [1]: /lookup/doi/10.1126/science.aao6266

A Tale of Two Haplotypes: The EDA2R/AR Intergenic Region is the Most Divergent Genomic Segment between Africans and East Asians in the Human Genome

Single nucleotide polymorphisms (SNPs) with large allele frequency differences between human populations are relatively rare. The longest run of SNPs with an allele frequency difference of one between the Yoruba of Nigeria and the Han Chinese is found on the long arm of the X chromosome in the intergenic region separating the EDA2R and AR genes. It has been proposed that the unusual allele frequency distributions of these SNPs are the result of a selective sweep affecting African populations that occurred after the out-of-Africa migration. To investigate the evolutionary history of the EDA2R/AR intergenic region, we characterized the haplotype structure of 52 of its highly differentiated SNPs. Using a publicly available data set of 3,000 X chromosomes from 65 human populations, we found that nearly all human X chromosomes carry one of two modal haplotypes for these 52 SNPs. The predominance of two highly divergent haplotypes at this locus was confirmed by use of a subset of individuals sequenced to high coverage. The first of these haplotypes, the α-haplotype is at high frequencies in most of the African populations surveyed and likely arose before the separation of African populations into distinct genetic entities. The second, the β-haplotype, is frequent or fixed in all non-African populations and likely arose in East Africa before the out-of-Africa migration. We also observed a small group or rare haplotypes with no clear relationship to the α- and β-haplotypes. These haplotypes occur at relatively high frequencies in African hunter-gatherer populations, such as the San and Mbuti Pygmies. Our analysis indicates that these haplotypes are part of a pool of diverse, ancestral haplotypes that have now been almost entirely replaced by the α- and β-haplotypes. We suggest that the rise of the α- and β-haplotypes was the result of the demographic forces that human populations experienced during the formation of modern African populations and the out-of-Africa migration. However, we also present evidence that this region is the target of selection in the form of positive selection on the α- and β-haplotypes and of purifying the selection against α/β recombinants.

A Tale of Two Haplotypes: The EDA2R/AR Intergenic Region Is the Most Divergent Genomic Segment between Africans and East Asians in the Human Genome

1Single nucleotide polymorphisms (SNPs) with large allele frequency differences between human populations are relatively rare. The longest run of SNPs with an allele frequency difference of one between the Yoruba of Nigeria and the Han Chinese is found on the long arm of the X chromosome in the intergenic region separating the EDA2R and AR genes. It has been proposed that the unusual allele frequency distributions of these SNPs are the result of a selective sweep affecting African populations that occurred after the out-of-Africa migration. To investigate the evolutionary history of the EDA2R/AR intergenic region, we characterized the haplotype structure of 52 of its highly differentiated SNPs. Using a publicly available data set of 3,000 X chromosomes from 65 human populations, we found that nearly all human X chromosomes carry one of two modal haplotypes for these 52 SNPs. The predominance of two highly divergent haplotypes at this locus was confirmed by use of a subset of individuals sequenced to high coverage. The first of these haplotypes, the α-haplotype, is at high frequencies in most of the African populations surveyed and likely arose before the separation of African populations into distinct genetic entities. The second, the β-haplotype, is frequent or fixed in all non-African populations and likely arose in East Africa before the out-of-Africa migration. We also observed a small group of rare haplotypes with no clear relationship to the α- and β-haplotypes. These haplotypes occur at relatively high frequencies in African hunter-gatherer populations, such as the San and Mbuti Pygmies. Our analysis indicates that these haplotypes are part of a pool of diverse, ancestral haplotypes that have now been almost entirely replaced by the α- and β-haplotypes. We suggest that the rise of the α- and β-haplotypes was the result of the demographic forces that human populations experienced during the formation of modern African populations and the out-of-Africa migration. However, we also present evidence that this region is the target of selection in the form of positive selection on the α- and β-haplotypes and of purifying selection against α/β recombinants.

An Early Divergence of KhoeSan Ancestors from Those of Other Modern Humans Is Supported by an ABC-Based Analysis of Autosomal Resequencing Data

Sub-Saharan Africa has consistently been shown to be the most genetically diverse region in the world. Despite the fact that a substantial portion of this variation is partitioned between groups practicing a variety of subsistence strategies and speaking diverse languages, there is currently no consensus on the genetic relationships of sub-Saharan African populations. San (a subgroup of KhoeSan) and many Pygmy groups maintain hunter-gatherer lifestyles and cluster together in autosomal-based analysis, whereas non-Pygmy Niger-Kordofanian speakers (non-Pygmy NKs) predominantly practice agriculture and show substantial genetic homogeneity despite their wide geographic range throughout sub-Saharan Africa. However, KhoeSan, who speak a set of relatively unique click-based languages, have long been thought to be an early branch of anatomically modern humans based on phylogenetic analysis. To formally test models of divergence among the ancestors of modern African populations, we resequenced a sample of San, Eastern, and Western Pygmies and non-Pygmy NKs individuals at 40 nongenic (∼2 kb) regions and then analyzed these data within an Approximate Bayesian Computation (ABC) framework. We find substantial support for a model of an early divergence of KhoeSan ancestors from a proto-Pygmy-non-Pygmy NKs group ∼110 thousand years ago over a model incorporating a proto-KhoeSan-Pygmy hunter-gatherer divergence from the ancestors of non-Pygmy NKs. The results of our analyses are consistent with previously identified signals of a strong bottleneck in Mbuti Pygmies and a relatively recent expansion of non-Pygmy NKs. We also develop a number of methodologies that utilize "pseudo-observed" data sets to optimize our ABC-based inference. This approach is likely to prove to be an invaluable tool for demographic inference using genome-wide resequencing data.

Why did modern human populations disperse from Africa ca. 60,000 years ago? A new model.

Recent research has provided increasing support for the origins of anatomically and genetically "modern" human populations in Africa between 150,000 and 200,000 years ago, followed by a major dispersal of these populations to both Asia and Europe sometime after ca. 65,000 before present (B.P.). However, the central question of why it took these populations approximately 100,000 years to disperse from Africa to other regions of the world has never been clearly resolved. It is suggested here that the answer may lie partly in the results of recent DNA studies of present-day African populations, combined with a spate of new archaeological discoveries in Africa. Studies of both the mitochondrial DNA (mtDNA) mismatch patterns in modern African populations and related mtDNA lineage-analysis patterns point to a major demographic expansion centered broadly within the time range from 80,000 to 60,000 B.P., probably deriving from a small geographical region of Africa. Recent archaeological discoveries in southern and eastern Africa suggest that, at approximately the same time, there was a major increase in the complexity of the technological, economic, social, and cognitive behavior of certain African groups, which could have led to a major demographic expansion of these groups in competition with other, adjacent groups. It is suggested that this complex of behavioral changes (possibly triggered by the rapid environmental changes around the transition from oxygen isotope stage 5 to stage 4) could have led not only to the expansion of the L2 and L3 mitochondrial lineages over the whole of Africa but also to the ensuing dispersal of these modern populations over most regions of Asia, Australasia, and Europe, and their replacement (with or without interbreeding) of the preceding "archaic" populations in these regions.

Metrical reconsideration of the Skhul IV and IX and Border Cave 1 crania in the context of modern human origins.

The "out-of-Africa" models for origins of modern Homo sapiens incorporate Skhul as one site documenting that early origination. However, only Skhul V is usually considered in the comparative craniology of the question, neglecting the other substantial crania, Skhul IV and IX. Craniometric comparison demonstrates that IV and IX amplify the picture of continuous gradations of Neandertal-to-modern variations throughout the Levant; much variation is thus represented within this one site, raising serious questions about Neandertals and moderns being discrete and long-separated species. Qafzeh 6 too is craniophenetically closer to Neandertals than to the true anatomically modern people of the European Upper Paleolithic. Proper distance analysis of Border Cave 1 cranium shows it is actually far removed from modern African populations. References to Qafzeh, Skhul, and Border Cave as "fully anatomically modern" require reconsideration.