HLA class I variation in the West African Pygmies and their genetic relationship with other African populations

We have studied the polymorphism of HLA class I in two West African Pygmy populations, namely, the Bakola from Cameroon and the Mbenzele from the Central African Republic. A unique number of HLA alleles and haplotypes showed specific patterns of these populations. In this study, we identify two alleles (B*37, B*41) and three haplotypes (A*30-B*37, A*66-B*41 and A*68-B*58) that appear to be 'private' or typical of Western Pygmies. These data reflect similarities with the AKA Pygmies from the Central African Republic. On the other hand, we failed to identify alleles that are found at high frequencies among other sub-Saharan populations (B*42, B*51). Allelic and haplotypic frequency distributions show differences between the two Pygmy groups, e.g. B*35 was very common in the Mbenzele but has been found to be absent in the Bakola. In contrast, B*53, which is found in the Bakola, has been found to be rare in the Mbenzele Pygmies. In order to analyse the genetic relationships of the Bakola and Mbenzele Pygmies with other sub-Saharan populations, HLA gene frequencies were subjected to the Neighbour-Joining tree analysis. The Mbenzele, Bakola and AKA were found to be relatively close to each other and isolated from other sub-African populations. However, both the genetic distances and the within-group variation suggests that the Bakola are more admixed with Bantu farmers than Mbenzele.     

HPA polymorphism in sub-Saharan African populations: Beninese, Cameroonians, Congolese, and Pygmies

The frequency of human platelet antigen-1 (HPA-1) to HPA-11w (excluding HPA-8w) and HPA-15 systems was studied in four sub-Saharan populations: Beninese, Congolese (Democratic Republic of Congo Kinshasa), Cameroonians, and Aka pygmies (Central African Republic). No report of HPA prevalence has previously been published concerning these populations which are characterized by the highest HPA-2b gene frequencies of any reported to date (Aka 0.393, Benin 0.292, Cameroon 0.237, and Congo 0.224) and at lesser degree HPA-5b (Aka 0.405, Congo 0.268, Cameroon 0.254, and Benin 0.182). This study is of great importance (i) particularly in the context of the diversity caused by the population migrations, we may observe today in our hospitals (ii) to confirm that the Pygmy population with distinctive frequencies (absence of the HPA-1b, HPA-2b, and HPA-5b highest frequencies) is an isolated population.     

HLA class II polymorphism in Aka Pygmies and Bantu Congolese and a reassessment of HLA-DRB1 African diversity

HLA-DRB1, -DQB1 and -DPB1 polymorphisms were investigated in two African populations, the Basse Lobaye Aka Pygmies of the Central African Republic, and a Bantu-speaking group from the Democratic Republic of Congo Kinshasa. Allelic and haplotypic frequency distributions reveal marked differences between the two populations in spite of their geographical proximity: the Aka exhibit high frequencies for several alleles, especially at the DPB1 locus (0.695 for DPB1*0402), probably due to rapid genetic drift, while the Bantu distributions are more even. Genetic distances computed from DRB1 allelic frequencies among 21 populations from North and sub-Saharan Africa were applied to a multidimensional scaling analysis. African populations genetic structure is significantly shaped by linguistic differentiation, as confirmed by an analysis of molecular variance. However, selective neutrality tests indicate that many African populations exhibit an excess of heterozygotes for DRB1, which is likely to explain the genetic similarity observed between some North African and Bantu populations. Overall, this study shows that natural selection must be taken into account when interpreting the patterns of HLA diversity, but that this effect is probably minor in relation to the stochastic events of human population differentiations.     

Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies

Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in Eurasia. Within Africa, fossil evidence suggests that anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr; however, the absence of ancient DNA in Africa has limited our ability to make a direct comparison between archaic and modern human genomes. Here, we use statistical inference based on high coverage whole-genome data (greater than 60×) from contemporary African Pygmy hunter-gatherers as an alternative means to study the evolutionary history of the genus Homo. Using whole-genome simulations that consider demographic histories that include both isolation and gene flow with neighboring farming populations, our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing the first whole genome-level evidence of African archaic admixture. Our inferences also suggest a complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH, likely within the last 30,000 yr.Introgression, the transfer of genetic material between closely related species through hybridization, is an important and ubiquitous evolutionary force in both plants and animals (Mallet 2007). Although hybrids are often nonviable or infertile, hybridization can be an important driving force for the origin of novel traits and new species (Mallet 2007; Zinner et al. 2011). Within our genus, Homo, there is strong evidence for multiple introgression events between our own species, H. sapiens, and now extinct sister taxa outside Africa (Pääbo 2014). Neanderthal whole-genome sequencing (Green et al. 2010; Prüfer et al. 2014) revealed that Neanderthals contributed an average of ∼2% of the genetic variation of present-day humans living outside of sub-Saharan Africa. This gene flow likely took place 37–86 thousand yr ago (kya), after early modern humans emigrated from Africa and before archaic forms went extinct in Eurasia (Sankararaman et al. 2012), and it may have occurred multiple times (Vernot and Akey 2014, 2015; Kim and Lohmueller 2015). Analyses of genome sequences from another extinct archaic human species, known as Denisovan, found in a cave in Siberia suggest that this archaic form or its closely related species contributed ∼5% of genetic variation to present-day Melanesians (Reich et al. 2010; Pääbo 2014). Furthermore, studies also suggest that the Denisovan genome has sequences that came from admixture with an unknown extinct hominin (Reich et al. 2010) and with Neanderthals (Prüfer et al. 2014). An important implication of these findings is that interbreeding among archaic humans may have promoted adaptation through the transfer of advantageous introgressive alleles (Hardy et al. 2005; Evans et al. 2006; Mendez et al. 2012; Huerta-Sánchez et al. 2014; Sankararaman et al. 2014; Vernot and Akey 2014; Racimo et al. 2015).Although it is becoming clear that modern humans interbred with archaic humans outside of Africa, it is not clear to what extent similar interbreeding took place in the history of anatomically modern humans (AMH) in Africa, the continent on which AMH originated ∼200 kya (Cavalli-Sforza et al. 1994). Recent fossil evidence suggests that Homo emerged ∼2.8 million yr ago (Mya) in Eastern Africa (Villmoare et al. 2015). Several morphologically mosaic forms of Homo coexisted until ∼35 kya, well after the first appearance of AMH (Bräuer 2008; Rightmire 2009). The persistent coexistence of a variety of transitional forms of Homo with a mosaic of archaic and modern traits throughout Africa during the Pleistocene (Bräuer 2008; Rightmire 2009; Harvati et al. 2011) suggests ample opportunity for interbreeding among the ancestors of modern and archaic humans (Hammer et al. 2011). Unfortunately, owing to the tropical environment over most of sub-Sahara Africa, to date efforts to obtain DNA from archaic hominin fossil bones and teeth have not been successful (Campana et al. 2013; Veeramah and Hammer 2014). Archaic introgression in Africa can thus not be studied by directly comparing DNA sequences from archaic and modern populations.Using a more indirect approach to infer archaic admixture, Plagnol and Wall (2006) recently analyzed patterns of divergence and linkage disequilibrium (LD) in DNA sequence polymorphism data from extant modern humans. Their summary statistic, S*, exploits the fact that recently introgressed lineages from long-isolated archaic humans show increased divergence and extensive LD (Plagnol and Wall 2006). S* has been widely used to identify ancient admixture in modern humans both inside and outside Africa (Plagnol and Wall 2006; Wall et al. 2009; Hammer et al. 2011; Lachance et al. 2012; Vernot and Akey 2014). Plagnol and Wall (2006) and Wall et al. (2009) inferred a 5% genetic contribution from a now-extinct taxon to the Niger-Kordofanian Yoruba farmers or their ancestors. Hammer et al. (2011) analyzed DNA sequence data from 61 noncoding loci in three contemporary sub-Saharan African populations. They found that hunter-gatherer African populations, including the Biaka Pygmy, Mbuti Pygmy, and San, contain ∼2% genetic material likely introgressed ∼35 kya from an archaic population that split from the ancestors of modern humans ∼700 kya. Recently, Lachance et al. (2012) applied S* to whole-genome data of three African hunter-gatherer populations and showed that their top-ranked S* loci are enriched for long-isolated lineages. These studies provide strong evidence for archaic admixture in Africa, but their inferences are limited because (1) they used genic sequences, in which recent natural selection may complicate inference (Plagnol and Wall 2006; Wall et al. 2009); (2) they surveyed only a small sample of genomic loci (Hammer et al. 2011); or (3) they did not control for confounding effects such as the demographic history of the interrogated populations (Lachance et al. 2012), which can bias S* scores.Here, we search for whole genome–level evidence of archaic admixture by analyzing high coverage whole-genome sequence data from two Western African Pygmy populations, Biaka and Baka. We chose these African Pygmies to study the evolutionary history of modern humans in Africa because of prior evidence of archaic introgression in these two groups (Garrigan et al. 2005; Hayakawa et al. 2006; Hammer et al. 2011; Lachance et al. 2012) and because these populations are one of the basal groups on the extant human phylogeny, implying that they harbor some of the most ancient genetic lineages in humans (Tishkoff et al. 2009; Pickrell et al. 2012). We apply the S* statistic to detect putatively introgressive genomic loci in the Pygmy populations. We assess the statistical significance of candidates through sophisticated whole-genome simulations that incorporate demography and variation in both recombination and mutation rates. We then test the hypothesis of no archaic introgression in Africa at the whole-genome level by comparing these null simulations with the data. To understand the demographic dynamics between the ancestors of archaic and modern humans, for our candidate introgressive loci, we investigate the joint distribution of time to the most recent common ancestor (TMRCA) (Thomson et al. 2000) and genetic length, which represent the divergence between candidate archaic introgressive and modern human lineages as well as the time of introgression, respectively. Lastly, we discuss the number and timing of archaic admixture events in Africa by analyzing the pattern of LD and the distribution of genetic length using our candidate loci. Together, our results provide the first model-based whole-genome perspective on archaic introgression in Africa.     

Linkage disequilibrium between HLA-G*0104 and HLA-E*0103 alleles in Tswa Pygmies

Nonclassical human leukocyte antigen (HLA)-G and -E loci are separated by approximately 660 kb on the short arm of chromosome 6. Interestingly, some functional and expression characteristics are relatively identical or associated for both molecules. For example, expression of HLA-E on the cell surface has been linked to preferential binding of nonameric leader peptides derived from the signal sequence of HLA-G. It has been suggested that these two molecules act synergistically in modulating susceptibility to infectious or chronic inflammatory diseases. A possible explanation for these observations is that HLA-E and HLA-G are evolving under analogous selective pressures and have functions that place them under selective regimes differing from classical HLA genes. The purpose of this study was to investigate the consistency of this hypothesis based on the characterization of the molecular polymorphism of these two genes and their linkage disequilibrium (LD) in three populations, i.e. Southeastern French (n = 57), Teke Congolese (n = 84) and Tswa Pygmies (n = 74). Allelic frequencies observed for HLA-G and HLA-E and for 14-bp ins/del polymorphism in the three populations were similar to those observed in the literature for populations from corresponding geographic areas. Only one of the recently described HLA-G polymorphisms (HLA-G*01:07-01:16) was found, i.e. HLA-G*01:15 in one individual from Congo. We showed that two haplotypes in Tswa Pygmies, i.e. HLA-G*01:04-E*01:03:01 and G*01:04-E*01:01, exhibited highly significant positive and negative D' values respectively. Although these LD could have functional implications, it is more likely because of the genetic drift as the two other populations did not display any significant LD.     

Hemoglobin comparisons between African American and European American males with hemoglobin values in the normal range

There are conflicting reports about the nature and magnitude of hemoglobin (Hb) differences between African Americans (AA) and European Americans (EA). Several reports suggest that AA have lower mean Hb values and that differences between AA and EA are large and are due to “racial” differences. Some have even called for separate Hb standards. In this study, Hb comparisons were made between AA and EA males in the Second National Health and Nutrition Examination Survey, 1976–1980. Comparison of AA and EA males with normal Hb values (i.e., 13.0 g/dl or greater) indicated that observed mean Hb differences exist primarily at the lower end of the Hb distribution (i.e., the distribution is skewed to the left). Several factors are likely contributors to lower hemoglobin values at the lower end of the distribution, including hemoglobinopathies, thalassemias, and/or nutritional deficiencies. If racial differences exist between these groups, controlled prospective studies are necessary to demonstrate this possibility. This study supports a single Hb standard for AA and EA males. © 1992 Wiley-Liss, Inc.     

Becoming sedentary, acculturation and infectious diseases: socio-ecological problems of the Bayaka Pygmies

The falling of tropical rain forests in Equatorial Africa, and the subsequent penetration of Bantu hoe farmers into the former jungle regions are depriving the Pygmies of the basis for their traditional way of life as roaming hunters and gatherers. Most of the former roaming groups now live in permanent settlements near Bantu villages. But becoming sedentary and adapting to the habits of the Bantu have had catastrophic results for the Pygmies: today, this people suffers to a great extent from infectious diseases and animal parasites, which were once almost unknown among them. In particular, Yaws, a skin disease which is widespread in Africa affects whole tribes. With the loss of their cultural identity their social structure also collapses: formerly free Pygmies get employed as cheap labour on coffee plantations.     

Assortative mating in mice. I. Female mating preference

Females of two inbred strains ofMus musculus domesticus, C57BL/Ibg and DBA/Ibg, were allowed to choose between two males, one of each strain, who were restrained within their cages. Females of both strains preferred to spend more time with, and to mate with, the males of the opposite strain rather than with males of their own strain. No major strain difference for the degree of preference was found. Preference was also unchanged between trials. There is a general lack of correlation between trials which is explained in terms of the nature of the variance in inbred strains. Female mating preference may have an evolutionary significance in reducing inbreeding.This work was supported by NIGMS Grant GM-14547.     

Assortative mating in affective disorders

Assortative mating was determined in 170 spouses of patients with major affective illness (bipolar and unipolar). An increase in affective disorders was found in both wives of affected men and husbands of affected women. The data suggest that assortative mating is present in the familial transmission of affective disorder.     

Assortative mating in mice. III. Genetic determination of female mating preference

Females from the inbred strains BALB/Ibg and DBA/Ibg and females from the reciprocal crosses between these strains, which were fostered by BALB/Ibg and DBA/Ibg males, were tested for mating preference between BALB/Ibg and DBA/Ibg males. The tests included the use of both the standard and the tubetechnique methods. In these strains, it was found that the main determinant of female mating preference was the genotype of the foster father. Females reared by DBA/Ibg males had a tendency for negative mating preference, whereas females reared by BALB/Ibg did not. The genotype of the mothers had some effect on the degree of the preference. Females reared by BALB/Ibg mothers had somewhat lower preference for BDA/Ibg males than did daughters' of BDA/Ibg females. The effect of the female's own genotype on mating preference was found to be only minor in a comparison done between these strains and their F ₁ crosses which had been raised by foster parents of the same genotype.This work was supported by NIGMS grant GM- 14547.     

Isolate mixture and random mating

Under some conditions, a heterogeneous mixture of random mating isolates cannot be distinguished from a homogeneous random mating population. This emphasizes that knowledge of the homogeneity of the population is imperative before the assumption of panmixia can be invoked. Such cautions are more important because with usual sample size the natural level of deviations from panmixia is difficult to detect.     

Assortative mating and affective disorders

Seventy-two spouses of subjects with recurrent primary affective disorders (PAD), were investigated for the presence of psychiatric disorders in their lives and in those of their first degree relatives, and compared with 71 spouses of non-psychiatrically ill control subjects. No difference was found in the risk for PAD; on the other hand spouses of affective patients manifested a greater occurrence of psychiatric disorders belonging to the affective spectrum, as did their respective first-degree relatives.     

Aging and frequency-dependent mating inDrosophila

Frequency-dependent mating behavior has been observed inDrosophila pseudoobscura, but most experiments have used only 4-day-old virgin flies. One report has indicated that rare-male behavior may be affected by age. Males and females of the Arrowhead strain along with rare orange-eyed males were used in the present study to confirm that frequency-dependent mating behavior is operating with 4-day-old females but is absent by 11 days. The same situation is also observed when Chiricahua males and females are used along with rare Arrowhead males.This work was supported by NIH Training Grant No. GM 02299, from the National Institute of General Medical Sciences.     

Streptococcus pneumoniae Serotype 1 Burden in the African Meningitis Belt: Exploration of Functionality in Specific Antibodies

Streptococcus pneumoniae serotype 1 (Sp1) constitutes an important cause of seasonal endemic meningitis in all age groups in the African meningitis belt. Despite a higher meningitis incidence, the Burkinabé population has an Sp1-specific antibody seroprevalence similar to that reported in the United Kingdom (UK). We aimed to establish whether the opsonophagocytic activity (OPA) of pneumococcal IgG naturally present in Burkina Faso differs from that seen in individuals in the UK and to compare the OPAs generated by natural and vaccine-induced immunity. Samples collected from pneumococcal vaccine-naive Burkinabé and UK subjects were matched for age (1 to 39 years) and anti-Sp1 IgG level, analyzed for OPA to 3 S. pneumoniae serotypes (1, 5, and 19A), and compared to postvaccine samples. Furthermore, the Burkinabé samples were assessed for IgG avidity and serotype-specific IgM concentrations. One hundred sixty-nine matched serum samples from both populations were selected. A greater proportion of Burkinabé subjects aged 1 to 19 years had functional Sp1 activity (OPA ≥ 8) compared to UK subjects (12% versus 2%, P < 0.001); however, the proportions were similar among adults (9%). The correlation between Sp1 IgG concentration and OPA was good (P < 0.001), but many individuals had nonfunctional IgG, which was not related to avidity. While the Sp1 IgM concentrations correlated with OPA, not all of the function in serum samples with low IgG could be attributed to IgM. Finally, vaccine-induced Sp1-specific IgG was more functional than equivalent amounts of naturally occurring IgG. In conclusion, despite a substantially higher pneumococcal meningitis incidence, no decreased functional immunity to Sp1 could be evidenced in the Burkinabé population compared to that in the population from the UK. Furthermore, the naturally induced antibodies were less functional than vaccine-induced antibodies.     

Molecular genetic analyses of mating pheromones reveal intervariety mating or hybridization in Cryptococcus neoformans

The sexual mating of the pathogenic yeast Cryptococcus neoformans is important for pathogenesis studies because the fungal virulence is linked to the alpha mating type (MAT(alpha)). We characterized C. neoformans mating pheromones (MF(alpha) 1 and MFa1) from 122 strains to understand intervariety hybridization or mating and intervariety virulence. MF(alpha) 1 in three C. neoformans varieties showed (a) specific nucleotide polymorphisms, (b) different copy numbers and chromosomal localizations, and (c) unique deduced amino acids in two geographic populations of C. neoformans var. gattii. MF(alpha) 1 of different varieties cross-hybridized in Southern hybridizations. Their phylogenetic analyses showed purifying selection (neutral evolution). These observations suggested that MAT(alpha) strains from any of the three C. neoformans varieties could mate or hybridize in nature with MATa strains of C. neoformans var. neoformans. A few serotype A/D diploid strains provided evidence for mating or hybridization, while a majority of A/D strains tested positive for haploid MF(alpha) 1 identical to that of C. neoformans var. grubii. MF(alpha) 1 sequence and copy numbers in diploids were identical to those of C. neoformans var. grubii, while their MFa1 sequences were identical to those of C. neoformans var. neoformans; thus, these strains were hybrids. The mice survival curves and histological lesions revealed A/D diploids to be highly pathogenic, with pathogenicity levels similar to that of the C. neoformans var. grubii type strain and unlike the low pathogenicity levels of C. neoformans var. neoformans strains. In contrast to MF(alpha) 1 in three varieties, MFa1 amplicons and hybridization signals could be obtained only from two C. neoformans var. neoformans reference strains and eight A/D diploids. This suggested that a yet undiscovered MFa pheromone(s) in C. neoformans var. gattii and C. neoformans var. grubii is unrelated to, highly divergent from, or rarer than that in C. neoformans var. neoformans. These observations could form the basis for future studies on the role of intervariety mating in C. neoformans biology and virulence.     

Neonatla vestibular stimulation and mating in cerebellar mutants

Two cerebellar mutants, staggerer and reeler, and their congenic nonmutants were used in this experiment. Experimental animals were subjected to intense rotational stimulation on a tilted plane during the first 3 weeks of life, while controls were left nonstimulated. The capacity for mating, as evidenced by vaginal plugs or the occurrence of pregnancy, was assayed during two periods: between 36 and 89 days of age (Experiment A) and between 90 and 120 days of age (Experiment B). During Experiment A the mutants as well as the normals were caged inter se with partners of the opposite sex. During Experiment B the animals were caged with intact, sexually experienced partners. The animals were examined daily for evidence of mating. During Experiment A, only 3 of the 89 couples participating in this study showed evidence of mating. During Experiment B, the number of males of both strains which had mated increased significantly. The staggerer females showed a relatively high level of mating activity, whether stimulated or not. The reeler females, in contrast, rarely mated, although early stimulation significantly increased the level of sexual efficiency. The majority of the normal males and females mated, whether stimulated or not. It was concluded that massive motor-sensory stimulation in infancy, improving gait and body balance in staggerer and reeler mice, may also improve mating efficiency.