The demographic and adaptive history of central African hunter-gatherers and farmers

The behaviour of adult Anopheles gambiae, sub-Saharan Africa's principal malaria vector, and its relevance to malaria control: a review

BACKGROUND

Mosquitoes of the Anopheles gambiae complex are one of the major vectors of malaria in sub-Saharan Africa. Their ability to transmit this disease of major public health importance is dependent on their abundance, biting behaviour, susceptibility and their ability to survive long enough to transmit malaria parasites. A deeper understanding of this behaviour can be exploited for improving vector surveillance and malaria control.

FINDINGS

Adult mosquitoes emerge from aquatic habitats at dusk. After a 24 h teneral period, in which the cuticle hardens and the adult matures, they may disperse at random and search upwind for a mate or to feed. Mating generally takes place at dusk in swarms that form over species-specific 'markers'. Well-nourished females may mate before blood-feeding, but the reverse is true for poorly-nourished insects. Females are monogamous and only mate once whilst males, that only feed on nectar, swarm nightly and can potentially mate up to four times. Females are able to locate hosts by following their carbon dioxide and odour gradients. When in close proximity to the host, visual cues, temperature and relative humidity are also used. Most blood-feeding occurs at night, indoors, with mosquitoes entering houses mainly through gaps between the roof and the walls. With the exception of the first feed, females are gonotrophically concordant and a blood meal gives rise to a complete egg batch. Egg development takes two or three days depending on temperature. Gravid females leave their resting sites at dusk. They are attracted by water gradients and volatile chemicals that provide a suitable aquatic habitat in which to lay their eggs.

CONCLUSION

Whilst traditional interventions, using insecticides, target mosquitoes indoors, additional protection can be achieved using spatial repellents outdoors, attractant traps or house modifications to prevent mosquito entry. Future research on the variability of species-specific behaviour, movement of mosquitoes across the landscape, the importance of light and vision, reproductive barriers to gene flow, male mosquito behaviour and evolutionary changes in mosquito behaviour could lead to an improvement in malaria surveillance and better methods of control reducing the current over-reliance on the indoor application of insecticides.

Dyadic inter-group cooperation in shotgun hunting activities in a Congo Basin village

Understanding the dynamics of inter-group cooperation in human adaptation has been the subject of recent empirical and theoretical studies in evolutionary anthropology, beginning to fill gaps in our knowledge of how interactions across political, economic and social domains can - and often do - lead to stable, large-scale cooperation. Here we investigate dyadic intergroup cooperation in shotgun hunting in the Republic of the Congo. In the Congo Basin, inter-group cooperation between foragers and farmers is at the centre of an exchange system maintained by traditional norms and institutions such as fictive kinship. Here, we focused on what factors predict cooperative shotgun hunting exchanges between BaYaka and Yambe. We conducted structured interviews with 48 BaYaka hunters and 18 Yambe men who organise hunts in a village along the Motaba River. We used Bayesian multilevel regression models to investigate the influence of Yambe and BaYaka attributes on probability of dyadic cooperation. We found that BaYaka men's reputations as skilled hunters and their family size each predicted cooperation in shotgun hunting, whereas there was no effect of Yambe attributes (status, wealth, family size). We discuss the results in terms of evolutionary models of men as hunters and inter-group cooperation, as well as biodiversity conservation implications.

Ancient genomes and the evolutionary path of modern humans

Growing evidence from archaic and early modern human genomes brings new insights to the emergence of modern humans. We recount recent information collected from ancient DNA studies that inform us about the evolutionary pathway to modern humanity. These findings point to both individual- and population-level advantages underlying modern human expansion.

Social ties in the Congo Basin: insights into tropical forest adaptation from BaYaka and their neighbours

Investigating past and present human adaptation to the Congo Basin tropical forest can shed light on how climate and ecosystem variability have shaped human evolution. Here, we first review and synthesize genetic, palaeoclimatological, linguistic and historical data on the peopling of the Congo Basin. While forest fragmentation led to the increased genetic and geographical divergence of forest foragers, these groups maintained long-distance connectivity. The eventual expansion of Bantu speakers into the Congo Basin provided new opportunities for forging inter-group links, as evidenced by linguistic shifts and historical accounts. Building from our ethnographic work in the northern Republic of the Congo, we show how these inter-group links between forest forager communities as well as trade relationships with neighbouring farmers facilitate adaptation to ecoregions through knowledge exchange. While researchers tend to emphasize forager-farmer interactions that began in the Iron Age, we argue that foragers' cultivation of relational wealth with groups across the region played a major role in the initial occupation of the Congo Basin and, consequently, in cultural evolution among the ancestors of contemporary peoples. This article is part of the theme issue 'Tropical forests in the deep human past'.

Genomic Insights Into the Admixture History of Mongolic- and Tungusic-Speaking Populations From Southwestern East Asia

As a major part of the modern Trans-Eurasian or Altaic language family, most of the Mongolic and Tungusic languages were mainly spoken in northern China, Mongolia, and southern Siberia, but some were also found in southern China. Previous genetic surveys only focused on the dissection of genetic structure of northern Altaic-speaking populations; however, the ancestral origin and genomic diversification of Mongolic and Tungusic-speaking populations from southwestern East Asia remain poorly understood because of the paucity of high-density sampling and genome-wide data. Here, we generated genome-wide data at nearly 700,000 single-nucleotide polymorphisms (SNPs) in 26 Mongolians and 55 Manchus collected from Guizhou province in southwestern China. We applied principal component analysis (PCA), ADMIXTURE, f statistics, qpWave/qpAdm analysis, qpGraph, TreeMix, Fst, and ALDER to infer the fine-scale population genetic structure and admixture history. We found significant genetic differentiation between northern and southern Mongolic and Tungusic speakers, as one specific genetic cline of Manchu and Mongolian was identified in Guizhou province. Further results from ADMIXTURE and f statistics showed that the studied Guizhou Mongolians and Manchus had a strong genetic affinity with southern East Asians, especially for inland southern East Asians. The qpAdm-based estimates of ancestry admixture proportion demonstrated that Guizhou Mongolians and Manchus people could be modeled as the admixtures of one northern ancestry related to northern Tungusic/Mongolic speakers or Yellow River farmers and one southern ancestry associated with Austronesian, Tai-Kadai, and Austroasiatic speakers. The qpGraph-based phylogeny and neighbor-joining tree further confirmed that Guizhou Manchus and Mongolians derived approximately half of the ancestry from their northern ancestors and the other half from southern Indigenous East Asians. The estimated admixture time ranged from 600 to 1,000 years ago, which further confirmed the admixture events were mediated via the Mongolians Empire expansion during the formation of the Yuan dynasty.

Phenotypic diversity and history of the Congo Basin populations: Equatorial Guinea, Bantu Speaking Central Africans and African Pygmies

BACKGROUND

African Pygmy Populations (APP) are believed to be one of the first groups of the Congo Basin rainforest peoples to separate from the rest of modern humanity. The arrival of Bantu speaking agriculturalists from 5,000 BP led to the formation of a large number of ethnic complexes in Central Africa and the Atlantic coastal area, mainly due to a one-way flow of pygmy women. There are now only a few small contingents of African Pygmy population groups who are mixed or who have almost disappeared as a result of migratory flows from Cameroon.

AIMS

We analysed the adult phenotypic diversity of 9 populations (17 groups of both sexes) of the Congo basin and Bioko Island, which were anthropometrically characterised in 1948. The phenotypic clusters that we detected, which we interpret as likely mixing of local Pygmy populations and Bantus, may be useful as references for future studies, particularly genetics.

SUBJECTS AND METHODS

The matrix of inter-distances between populations was generated, using the 21 variables, with the Euclidean distance between the mean vectors relating to the standardised variables. When the UPGMA (Unweighted Pair Group Method with Arithmetic Mean) was used separately in men and women, the phylogenetic trees showed a clear separation between populations.

RESULTS

The body measurements that most effectively distinguished the groups are linear dimensions and the width of the hips and mean thoracic circumference. In this study, the cephalo-facial dimensions were of little value in identifying the groups.

CONCLUSIONS

The samples of Equatorial Guinea show a major inter-group overlap, and considerable intra-group variations. There are also notable differences amongst African Pygmy populations in terms of height, but not in body proportions.

Fine scale human genetic structure in three regions of Cameroon reveals episodic diversifying selection

Inferences from genetic association studies rely largely on the definition and description of the underlying populations that highlight their genetic similarities and differences. The clustering of human populations into subgroups (population structure) can significantly confound disease associations. This study investigated the fine-scale genetic structure within Cameroon that may underlie disparities observed with Cameroonian ethnicities in malaria genome-wide association studies in sub-Saharan Africa. Genotype data of 1073 individuals from three regions and three ethnic groups in Cameroon were analyzed using measures of genetic proximity to ascertain fine-scale genetic structure. Model-based clustering revealed distinct ancestral proportions among the Bantu, Semi-Bantu and Foulbe ethnic groups, while haplotype-based coancestry estimation revealed possible longstanding and ongoing sympatric differentiation among individuals of the Foulbe ethnic group, and their Bantu and Semi-Bantu counterparts. A genome scan found strong selection signatures in the HLA gene region, confirming longstanding knowledge of natural selection on this genomic region in African populations following immense disease pressure. Signatures of selection were also observed in the HBB gene cluster, a genomic region known to be under strong balancing selection in sub-Saharan Africa due to its co-evolution with malaria. This study further supports the role of evolution in shaping genomes of Cameroonian populations and reveals fine-scale hierarchical structure among and within Cameroonian ethnicities that may impact genetic association studies in the country.

VolcanoFinder: Genomic scans for adaptive introgression

Recent research shows that introgression between closely-related species is an important source of adaptive alleles for a wide range of taxa. Typically, detection of adaptive introgression from genomic data relies on comparative analyses that require sequence data from both the recipient and the donor species. However, in many cases, the donor is unknown or the data is not currently available. Here, we introduce a genome-scan method—VolcanoFinder—to detect recent events of adaptive introgression using polymorphism data from the recipient species only. VolcanoFinder detects adaptive introgression sweeps from the pattern of excess intermediate-frequency polymorphism they produce in the flanking region of the genome, a pattern which appears as a volcano-shape in pairwise genetic diversity. Using coalescent theory, we derive analytical predictions for these patterns. Based on these results, we develop a composite-likelihood test to detect signatures of adaptive introgression relative to the genomic background. Simulation results show that VolcanoFinder has high statistical power to detect these signatures, even for older sweeps and for soft sweeps initiated by multiple migrant haplotypes. Finally, we implement VolcanoFinder to detect archaic introgression in European and sub-Saharan African human populations, and uncovered interesting candidates in both populations, such as TSHR in Europeans and TCHH-RPTN in Africans. We discuss their biological implications and provide guidelines for identifying and circumventing artifactual signals during empirical applications of VolcanoFinder.

The process by which beneficial alleles are introduced into a species from a closely-related species is termed adaptive introgression. We present an analytically-tractable model for the effects of adaptive introgression on non-adaptive genetic variation in the genomic region surrounding the beneficial allele. The result we describe is a characteristic volcano-shaped pattern of increased variability that arises around the positively-selected site, and we introduce an open-source method VolcanoFinder to detect this signal in genomic data. Importantly, VolcanoFinder is a population-genetic likelihood-based approach, rather than a comparative-genomic approach, and can therefore probe genomic variation data from a single population for footprints of adaptive introgression, even from a priori unknown and possibly extinct donor species.

Evolutionary and population (epi)genetics of immunity to infection

Immune response is one of the functions that have been more strongly targeted by natural selection during human evolution. The evolutionary genetic dissection of the immune system has greatly helped to distinguish genes and functions that are essential, redundant or advantageous for human survival. It is also becoming increasingly clear that admixture between early Eurasians with now-extinct hominins such as Neanderthals or Denisovans, or admixture between modern human populations, can be beneficial for human adaptation to pathogen pressures. In this review, we discuss how the integration of population genetics with functional genomics in diverse human populations can inform about the changes in immune functions related to major lifestyle transitions (e.g., from hunting and gathering to farming), the action of natural selection to the evolution of the immune system, and the history of past epidemics. We also highlight the need of expanding the characterization of the immune system to a larger array of human populations-particularly neglected human groups historically exposed to different pathogen pressures-to fully capture the relative contribution of genetic, epigenetic, and environmental factors to immune response variation in humans.

Trajectories of cultural innovation from the Middle to Later Stone Age in Eastern Africa: Personal ornaments, bone artifacts, and ocher from Panga ya Saidi, Kenya

African Middle Stone Age (MSA) populations used pigments, manufactured and wore personal ornaments, made abstract engravings, and produced fully shaped bone tools. However, ongoing research across Africa reveals variability in the emergence of cultural innovations in the MSA and their subsequent development through the Later Stone Age (LSA). When present, it appears that cultural innovations manifest regional variability, suggestive of distinct cultural traditions. In eastern Africa, several Late Pleistocene sites have produced evidence for novel activities, but the chronologies of key behavioral innovations remain unclear. The 3 m deep, well-dated, Panga ya Saidi sequence in eastern Kenya, encompassing 19 layers covering a time span of 78 kyr beginning in late Marine Isotope Stage 5, is the only known African site recording the interplay between cultural and ecological diversity in a coastal forested environment. Excavations have yielded worked and incised bones, ostrich eggshell beads (OES), beads made from seashells, worked and engraved ocher pieces, fragments of coral, and a belemnite fossil. Here, we provide, for the first time, a detailed analysis of this material. This includes a taphonomic, archeozoological, technological, and functional study of bone artifacts; a technological and morphometric analysis of personal ornaments; and a technological and geochemical analysis of ocher pieces. The interpretation of the results stemming from the analysis of OES beads is guided by an ethnoarcheological perspective and field observations. We demonstrate that key cultural innovations on the eastern African coast are evident by 67 ka and exhibit remarkable diversity through the LSA and Iron Age. We suggest the cultural trajectories evident at Panga ya Saidi were shaped by both regional traditions and cultural/demic diffusion.

Characterising the genetic basis of immune response variation to identify causal mechanisms underlying disease susceptibility

Over the last 10 years, genome-wide association studies (GWAS) have identified hundreds of susceptibility loci for autoimmune diseases. However, despite increasing power for the detection of both common and rare coding variants affecting disease susceptibility, a large fraction of disease heritability has remained unexplained. In addition, a majority of the identified loci are located in noncoding regions, and translation of disease-associated loci into new biological insights on the etiology of immune disorders has been lagging. This highlights the need for a better understanding of noncoding variation and new strategies to identify causal genes at disease loci. In this review, I will first detail the molecular basis of gene expression and review the various mechanisms that contribute to alter gene activity at the transcriptional and post-transcriptional level. I will then review the findings from 10 years of functional genomics studies regarding the genetics on gene expression, in particular in the context of infection. Finally, I will discuss the extent to which genetic variants that modulate gene expression at transcriptional and post-transcriptional level contribute to disease susceptibility and present strategies to leverage this information for the identification of causal mechanisms at disease loci in the era of whole genome sequencing.

Clarifying distinct models of modern human origins in Africa

Accumulating genomic, fossil and archaeological data from Africa have led to a renewed interest in models of modern human origins. However, such discussions are often discipline-specific, with limited integration of evidence across the different fields. Further, geneticists typically require explicit specification of parameters to test competing demographic models, but these have been poorly outlined for some scenarios. Here, we describe four possible models for the origins of Homo sapiens in Africa based on published literature from paleoanthropology and human genetics. We briefly outline expectations for data patterns under each model, with a special focus on genetic data. Additionally, we present schematics for each model, doing our best to qualitatively describe demographic histories for which genetic parameters can be specifically attached. Finally, it is our hope that this perspective provides context for discussions of human origins in other manuscripts presented in this special issue.