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Post marital residence behaviours shape genetic variation in hunter-gatherer and agricultural populations from Central Africa
Abstract
The evolution of the sociocultural behaviours determining lineage transmission and post marital residence rules in human societies has been the subject of intense debates in cultural anthropology and ethnology. Population genetics paradigms and methods can provide new insights into the past mobility behaviour of spouse and their influence on the genetic diversity patterns observed today among communities and populations. Here, we review, for a non-specialized scientific audience, two population genetics papers that we previously published (Verdu et al 2009; 2013). These papers mainly focused on the reconstruction of the demographic history of Central African hunter-gatherer and agricultural populations using genetic data, and on how complex post marital residence behaviours shaped the genetic diversity patterns currently observed within and among these populations. In particular, we found that Central African hunter-gatherer populations show genetic patterns that would be expected for matrilocal populations, while they often report practicing patrilocality similarly as their neighbouring agricultural populations. In fact, we showed that complex and variable gender-specific post marital residence behaviours in the context of patrilocality and socioeconomic discrimination of hunter-gatherer populations could satisfactorily explain the observed genetic patterns. Nevertheless, as an alternative explanation, we propose here that these patterns may result also from past post marital residence rules that are not currently observed in these Central African hunter-gatherer and agricultural populations.
... Among farming populations, genetic studies have evidenced high levels of genetic similarity in autosomal markers, and this genetic homogeneity is likely due to the recent demic expansion of Bantuspeaking populations concomitant with the expansion of agricultural techniques and Bantu languages starting about 4-5 kya [68][69][70][71][72]. However, if we focus on sex-specific genetic diversity patterns in these populations, genetic studies show more genetic differentiation among populations for genetic markers in the Y-chromosome than in the mtDNA [16,[68][69][70][71]. ...
... These studies provide strong evidence for a higher female than male migration rate among farming populations from sub-Saharan Africa. This is consistent with the self-reported patrilocal practices in farming populations, where females move after marriage across communities and populations much more often than males [69,72]. Sex-specific genetic patterns in farming populations may also be linked to the practice of polygyny, which reduces the genetic diversity of male lineages compared to female lineages [65]. ...
Africa is the continent of our species’ origin and the deep history of humans is represented by African genetic variation. Through genetic studies, it has become evident that deep African population history is captured by relationships among African hunter-gatherers and that the world’s deepest population divergences occur among these groups. In this review, we look back at a study published by Cavalli-Sforza and colleagues in 1969 entitled “Studies on African Pygmies. I. A pilot investigation of Babinga Pygmies in the Central African Republic (with an analysis of genetic distances)”. The study analyzed 19 classical polymorphisms and found that the deepest divergences in African populations were represented by hunter-gatherer groups such as the southern African San and the central African rainforest hunter-gatherers. We repeated the original analyses from Cavalli-Sforza et al. [1] with about 22 thousand times more genome-wide genetic markers in populations similar to those included in the original study. Our high-resolution analyses gave similar results regarding the relationships of early-diverging African populations compared to the classical polymorphism analyses. This finding, however, does not imply that research has stagnated and that developments in technology and genetic methods over the last fifty years delivered no additional information regarding African history and adaptation. We review how technology and population genetic methods have advanced to give more detailed inferences about population structure, migrations, admixture patterns, timing of admixture, sex-biased admixture, and inferences of selection and adaptive introgression in rainforest hunter-gatherers and other African populations. We also comment on how sequencing of ancient DNA has influenced findings and deliberate on the progress and development of more complex models of African history, including alternatives to tree-models and the inference of possible archaic admixture in African populations. We review the growing complexity of our picture of population history in central Africa and Africa as a whole, emerging from genomic studies and other disciplines investigating human population history and adaptation. While data and knowledge are accumulating, certain populations and areas remain underrepresented in genomic research. Their inclusion, possibly also through ancient DNA studies, together with new methods of analysis and the testing of representative models of deep population history in Africa, will help to build a more complete picture of past population history in Africa. Based on “Cavalli-Sforza LL, Zonta LA, Nuzzo F, Bernini L, de Jong WW, Meera Khan P, Ray AK, Went LN, Siniscalco M, Nijenhuis LE, van Loghem E, Modiano G. Studies on African Pygmies. I. A pilot investigation of Babinga Pygmies in the Central African Republic (with an analysis of genetic distances). Am J Hum Genet. 1969 May;21(3):252-274”.
... Population genetics studies reveal a distinct matrilocal bias, evident in the localization of mother-todaughter mtDNA lineages compared to father-to-son Y-lineages. This is opposite to the pattern in neighboring farming and pastoralist populations (Schlebusch, 2010, for Khoesan;Verdu & Austerlitz, 2015, for Central African Pygmies). A similar tendency for female relatives to stay together is found in Hadza longitudinal residence data (Blurton Jones, Hawkes, & O'Connell, 2005;Wood & Marlowe, 2011;Woodburn, 1968). ...
Are there constraints on the social conditions that could have given rise to language
and symbolic cognition? Language has emerged in no other species than humans,
suggesting a profound obstacle to its evolution. If language is seen as an aspect of
cognition, limitations can be expected in terms of computational capacity. But if it
is seen it as fundamentally for communication, then the problems will be found in
terms of social relationships. Below a certain threshold of cooperation and trust, no
language or symbolic communication could evolve (Knight & Lewis, 2017a); this
has been termed a “platform of trust” (Wacewicz, 2017)....
In this chapter, I argue that quite specific social conditions were prerequisite for the evolution of language- and symbol-ready hominins. One of the requirements differentiating our ancestors from other African apes was a switch to mainly female philopatry – females living with their relatives, rather than dispersing at sexual maturity – coevolving with an increasing tendency to egalitarianism....How did increasing egalitarianism affect males and potentially “feminize” male behavior for cooperative offspring care? How were male and female relations affected in the evolution of genus Homo and Homo sapiens?
A rift runs through anthropology. Year on year we explain to our students that anthropology is the overarching study of what it means to be human; and yet our discipline is fragmented. We can, we explain, study humans as biological beings, understanding the anatomical, physiological and life-history differences between ourselves and the other great apes, or the Neanderthals. Or we can study humans within their own communities as cultural beings, analysing the rituals they perform and the stories they tell. What defines us as Homo sapiens compared with other hominins appears a tractable scientific area of enquiry. Interpretations of cultural voices, values and meanings feel by contrast negotiable and contested, throwing into question the prospect of scientific objectivity. On each side of this divide data takes different forms and is collected quite differently; theory and hypothesis are applied with hypothetico-deductive method, inductively or not at all; and epistemologies are radically opposed. As detailed in Metaphors We Live By (Lakoff and Johnson 1980), the human body forms a basis of universal shared experiences, structures of cognition and mutual understandings. Yet the body and its reproduction generate a multiplicity of folk models, with highly variable ideas about sex, kinship and shared substance each able to operate with perfect, or at least practical logic in its own cultural setting. Social and cultural anthropologists glory in the contrariness of these folk models to the scientifically accumulated 'facts' of how human bodies work and reproduce. Fundamentally it is 'fictions' which are the business of social anthropologists – fictions about kinship, about gods and spirits, in our rules and games, fictions on our tongues as we speak and in taxonomies as we carve up the world. Given that we are fiction-sharing and game-playing apes, do shared fictions and games matter for the understanding of our origins? 2 Camilla Power, Morna Finnegan and Hilary Callan Darwinism, the coherent and unifying theory that powers all investigation of living beings, has itself been named a fiction, the origins myth that fitted the newly emergent world of high Victorian capitalism. As we enter 'a period in which evolutionary theory is being applied to every conceivable domain of enquiry' (Aunger 2000: 1), including economics, moral philosophy, psychology, linguistics, law, medicine and beyond, social anthropology could be respected for holding out, swimming against this powerful tide, maintaining its critical faculties in solidarity with the humanities. Or it could be viewed as insular and idealist, obfuscating and jealously guarding its domain of ideology from unwelcome intrusion (cf Bloch 2000: 202). In Engaging Anthropology, Thomas Eriksen (2006: 23) certainly sees social anthropology as having withdrawn from general intellectual discourse, pondering why contemporary anthropologists are so reluctant to present their work to large audiences, lay and academic. It would seem that social anthropology has lost its voice in debates about human origins. The broad comparative framework inherited from Morgan and Tylor in the nineteenth century has given way to perspectives emphasizing reflexivity and cultural particularism. Yet the opportunities for intervention have never been greater. Evolutionary and physical anthropology, archaeology and palaeogenetics have made major advances in an emerging picture of human origins. A range of new evidence is revealing the place of the human species in the natural world and the material record of our past. Given these developments, it must be time to rethink social anthropology's absenteeism. This book seeks to take up that challenge by bringing together a group of anthropologists to examine key areas of human origins research that could and should be informed by social anthropology. As we show, the social anthropology that can be brought into play for this purpose naturally includes writings specifically addressed to human origins, but it is not confined to these. As will be seen, questions about origins bring key figures from social anthropology's own history into new focus, while ethnography, originally conducted for entirely different purposes, gains new significance in this context. The book's chapters cover areas including the sexual division of labour and gender egalitarianism (Finnegan); sexual insult and female militancy as a mode of resistance (Shirley Ardener); metaphor as the basic principle of the symbolic (Smith and Hoefler; Knight and Lewis); shared structures of cosmology, ritual and myth (Power, Skaanes, Watts); body techniques in healing and cognition (Low); the evolution of kinship (Joseph); and ethnobiological classification (Ellen). Spanning several decades of debates around disciplinary boundaries
Le terme « Pygmée » est offensant quand il renvoie à la petitesse de la taille et/ ou de l'intelli-gence ou à un archétype historique de sauvage primitif. Il est valorisant quand il s'agit de désigner des peuples minoritaires, dits « autochtones », portant des noms différents, parlant des langues différentes, menacés de disparition ainsi que leurs écosystèmes forestiers, dans différentes nations d'Afrique centrale, célèbres pour les compétences de leurs musiciens, chasseurs, cueilleurs et devins-guérisseurs. La discrimination négative dont ils sont l'objet est un trait constant, avec des variantes allant du paternalisme au racisme, en passant par l'infantilisation, l'asservissement et parfois le viol et le meurtre. Elle est toujours sous-tendue par des archétypes racistes, conscients et inconscients, relatifs à la sauvagerie, la pusillanimité, la médiocrité de l'intelligence, la nudité, la saleté, la consom-mation d'alcool et de cannabis, le vol. L'emploi du terme « Pygmée », dans une perspective valorisante, renouvelé par le concept de « pygmitude » et structuré par une « fierté pygmée », après une phase d'abandon légitime, est à présent revendiqué par un grand nombre d'interlocuteurs aka, kola, koya, bongo… notamment les plus rebelles aux humiliations quotidiennes. Abstract : The term " pygmy " is derogative when it refers to their small height and/or limited intelligence, or to the archetype of the primitive savage. it is complimentary when it indicates minority peoples, so called " natives " known by different names, who speak different languages, and who are endangered as well as their forest ecosystems, who live in various nations of Central Africa and who are celebrated for their skills as musicians, hunters, gatherers and soothsayers-quacks. They suffer constant discrimination, with variants spreading from paternalism to racism, by way of infantilisation, subjection, sometimes rape and murder. This discrimination relies on aware or unaware racist archetypes, pointing to their wildness, cowardness, limited intelligence, nudity, dirt, their consumption of alcohol and cannabis, thievery. When used in a positive perspective, the use of the term « Pygmy » is enhanced by the concept of " pygmitude " and structured through " pygmy pride ". After a period of understandable neglect, this word is now claimed by a large number of Aka, Kola, Koya, Bongo... especially those who resent daily humiliations most.
The emergence of agriculture in West-Central Africa approximately 5,000 years ago, profoundly modified the cultural landscape and mode of subsistence of most sub-Saharan populations. How this major innovation has had an impact on the genetic history of rainforest hunter-gatherers-historically referred to as 'pygmies'-and agriculturalists, however, remains poorly understood. Here we report genome-wide SNP data from these populations located west-to-east of the equatorial rainforest. We find that hunter-gathering populations present up to 50% of farmer genomic ancestry, and that substantial admixture began only within the last 1,000 years. Furthermore, we show that the historical population sizes characterizing these communities already differed before the introduction of agriculture. Our results suggest that the first socio-economic interactions between rainforest hunter-gatherers and farmers introduced by the spread of farming were not accompanied by immediate, extensive genetic exchanges and occurred on a backdrop of two groups already differentiated by their specialization in two ecotopes with differing carrying capacities.
Resume. — Si on comprend de facon intuitive la signification du terme Pygmee, on ne dispose pas pour autant d'une definition claire de cette categorie (ou de toute autre) dans l'espece humaine. Les Pygmees sont des marginaux, tant a cause de leurs caracteres physiques que de leur mode de vie de chasseurs et collecteurs, suppose herite de la prehistoire. Celui- ci connaissant a present des bouleversements, on a opte ici pour une definition exclusivement biologique, qui est proprement etymologique. Pour decrire leur variation anatomique, des analyses morphologiques multivariees detaillees sont entreprises afin d'evaluer leur distance aux autres populations. Leurs relations avec d'autres chasseurs, tels les San, sont discutees. Les reactions face aux pressions selectives du milieu sont examinees. Tant par leur anatomie que leurs groupes sanguins, qui donnent des resultats comparables, les Pygmees accentuent les caracteristiques negro-africaines, et se rattachent sans hiatus a l'ensemble des groupes humains du sous-continent. Il est des lors impossible de les en separer par des criteres biologiques absolus ; cependant, leur position peripherique et leur isolement sexuel les enferment dans une categorisation qu'ils pourront difficilement surmonter sans renoncer a leur culture.
Sociocultural phenomena, such as exogamy or phylopatry, can largely determine human sex-specific demography. In Central Africa, diverging patterns of sex-specific genetic variation have been observed between mobile hunter-gatherer Pygmies and sedentary agricultural non-Pygmies. However, their sex-specific demography remains largely unknown. Using population genetics and approximate Bayesian computation approaches, we inferred male and female effective population sizes, sex-specific migration, and admixture rates in 23 Central African Pygmy and non-Pygmy populations, genotyped for autosomal, X-linked, Y-linked, and mitochondrial markers. We found much larger effective population sizes and migration rates among non-Pygmy populations than among Pygmies, in agreement with the recent expansions and migrations of non-Pygmies and, conversely, the isolation and stationary demography of Pygmy groups. We found larger effective sizes and migration rates for males than for females for Pygmies, and vice versa for non-Pygmies. Thus, although most Pygmy populations have patrilocal customs, their sex-specific genetic patterns resemble those of matrilocal populations. In fact, our results are consistent with a lower prevalence of polygyny and patrilocality in Pygmies compared with non-Pygmies and a potential female transmission of reproductive success in Pygmies. Finally, Pygmy populations showed variable admixture levels with the non-Pygmies, with often much larger introgression from male than from female lineages. Social discrimination against Pygmies triggering complex movements of spouses in intermarriages can explain these male-biased admixture patterns in a patrilocal context. We show how gender-related sociocultural phenomena can determine highly variable sex-specific demography among populations, and how population genetic approaches contrasting chromosomal types allow inferring detailed human sex-specific demographic history.
The study of Y chromosome variation has helped reconstruct demographic events associated with the spread of languages, agriculture, and pastoralism in sub-Saharan Africa, but little attention has been given to the early history of the continent. In order to overcome this lack of knowledge, we carried out a phylogeographic analysis of haplogroups A and B in a broad data set of sub-Saharan populations. These two lineages are particularly suitable for this objective because they are the two most deeply rooted branches of the Y chromosome genealogy. Their distribution is almost exclusively restricted to sub-Saharan Africa where their frequency peaks at 65% in groups of foragers. The combined high-resolution single nucleotide polymorphism analysis with short tandem repeats variation of their subclades reveals strong geographic and population structure for both haplogroups. This has allowed us to identify specific lineages related to regional preagricultural dynamics in different areas of sub-Saharan Africa. In addition, we observed signatures of relatively recent contact, both among Pygmies and between them and Khoisan speaker groups from southern Africa, thus contributing to the understanding of the complex evolutionary relationships among African hunter-gatherers. Finally, by revising the phylogeography of the very early human Y chromosome lineages, we have obtained support for the role of southern Africa as a sink, rather than a source, of the first migrations of modern humans from eastern and central parts of the continent. These results open new perspectives on the early history of Homo sapiens in Africa, with particular attention to areas of the continent where human fossil remains and archaeological data are scant.
Technological and cultural innovations as well as climate changes are thought to have influenced the diffusion of major language phyla in sub-Saharan Africa. The most widespread and the richest in diversity is the Niger-Congo phylum, thought to have originated in West Africa ∼ 10,000 years ago (ya). The expansion of Bantu languages (a family within the Niger-Congo phylum) ∼ 5,000 ya represents a major event in the past demography of the continent. Many previous studies on Y chromosomal variation in Africa associated the Bantu expansion with haplogroup E1b1a (and sometimes its sublineage E1b1a7). However, the distribution of these two lineages extends far beyond the area occupied nowadays by Bantu-speaking people, raising questions on the actual genetic structure behind this expansion. To address these issues, we directly genotyped 31 biallelic markers and 12 microsatellites on the Y chromosome in 1,195 individuals of African ancestry focusing on areas that were previously poorly characterized (Botswana, Burkina Faso, Democratic Republic of Congo, and Zambia). With the inclusion of published data, we analyzed 2,736 individuals from 26 groups representing all linguistic phyla and covering a large portion of sub-Saharan Africa. Within the Niger-Congo phylum, we ascertain for the first time differences in haplogroup composition between Bantu and non-Bantu groups via two markers (U174 and U175) on the background of haplogroup E1b1a (and E1b1a7), which were directly genotyped in our samples and for which genotypes were inferred from published data using linear discriminant analysis on short tandem repeat (STR) haplotypes. No reduction in STR diversity levels was found across the Bantu groups, suggesting the absence of serial founder effects. In addition, the homogeneity of haplogroup composition and pattern of haplotype sharing between Western and Eastern Bantu groups suggests that their expansion throughout sub-Saharan Africa reflects a rapid spread followed by backward and forward migrations. Overall, we found that linguistic affiliations played a notable role in shaping sub-Saharan African Y chromosomal diversity, although the impact of geography is clearly discernible.
Interrelations entre les chasseurs-collecteurs du bassin congolais et les agriculteurs.
S. Bahuchet — Inventing Pygmies.
A verse by Homer is used to show how the word "pygmy"—handed down and validated since Aristotle—was used till the 19th century. During all epochs, efforts were made to explain who Aristotle's Pygmies were: monsters, monkeys or men —until, after big apes in the 18th century, the small men of Equatorial Africa would become our Pygmies.
Hunter-gatherer Pygmies from Central Africa are described as being extremely mobile. Using neutral genetic markers and population genetics theory, we explored the dispersal behaviour of the Baka Pygmies from Cameroon, one of the largest Pygmy populations in Central Africa. We found a strong correlation between genetic and geographical distances: a pattern of isolation by distance arising from limited parent-offspring dispersal. Our study suggests that mobile hunter-gatherers do not necessarily disperse over wide geographical areas.
Little is known about the Pygmy groups living in Gabon. The Bakoya, along with the Babongo and the Baka Pygmy groups live in this central African country. They settled about seventy years ago and now share the same village space with Bantu ethnic groups. After a summary of the historical background and the social organization of the Bakoya Pygmies, I will give a brief description of their subsistence activities to highlight the social changes and economic transformations that the Bakoya underwent, by comparing two groups of Bakoya Pygmies, one living in Imbong and the other in Ekata. This fi rst anthropological study has found how agriculture is important for subsistence and for earning money, a shift from collective to individualistic activities, and less dependence on non-Pygmy neighbors, with some noted differences between the two Bakoya villages.
Africa is the source of all modern humans, but characterization of genetic variation and of relationships among populations
across the continent has been enigmatic. We studied 121 African populations, four African American populations, and 60 non-African
populations for patterns of variation at 1327 nuclear microsatellite and insertion/deletion markers. We identified 14 ancestral
population clusters in Africa that correlate with self-described ethnicity and shared cultural and/or linguistic properties.
We observed high levels of mixed ancestry in most populations, reflecting historical migration events across the continent.
Our data also provide evidence for shared ancestry among geographically diverse hunter-gatherer populations (Khoesan speakers
and Pygmies). The ancestry of African Americans is predominantly from Niger-Kordofanian (~71%), European (~13%), and other
African (~8%) populations, although admixture levels varied considerably among individuals. This study helps tease apart the
complex evolutionary history of Africans and African Americans, aiding both anthropological and genetic epidemiologic studies.
The expansion of Bantu languages, which started around 5,000 years before present in west/central Africa and spread all throughout sub-Saharan Africa, may represent one of the major and most rapid demographic movements in the history of the human species. Although the genetic footprints of this expansion have been unmasked through the analyses of the maternally inherited mitochondrial DNA lineages, information on the genetic impact of this massive movement and on the genetic composition of pre-Bantu populations is still scarce.
Here, we analyze an extensive collection of Y-chromosome markers—41 single nucleotide polymorphisms and 18 short tandem repeats—in 883 individuals from 22 Bantu-speaking agriculturalist populations and 3 Pygmy hunter-gatherer populations from Gabon and Cameroon. Our data reveal a recent origin for most paternal lineages in west Central African populations most likely resulting from the expansion of Bantu-speaking farmers that erased the more ancient Y-chromosome diversity found in this area. However, some traces of ancient paternal lineages are observed in these populations, mainly among hunter-gatherers. These results are at odds with those obtained from mtDNA analyses, where high frequencies of ancient maternal lineages are observed, and substantial maternal gene flow from hunter-gatherers to Bantu farmers has been suggested. These differences are most likely explained by sociocultural factors such as patrilocality. We also find the intriguing presence of paternal lineages belonging to Eurasian haplogroup R1b1*, which might represent footprints of demographic expansions in central Africa not directly related to the Bantu expansion.
The transition from hunting and gathering to farming involved a major cultural innovation that has spread rapidly over most of the globe in the last ten millennia. In sub-Saharan Africa, hunter-gatherers have begun to shift toward an agriculture-based lifestyle over the last 5,000 years. Only a few populations still base their mode of subsistence on hunting and gathering. The Pygmies are considered to be the largest group of mobile hunter-gatherers of Africa. They dwell in equatorial rainforests and are characterized by their short mean stature. However, little is known about the chronology of the demographic events-size changes, population splits, and gene flow--ultimately giving rise to contemporary Pygmy (Western and Eastern) groups and neighboring agricultural populations. We studied the branching history of Pygmy hunter-gatherers and agricultural populations from Africa and estimated separation times and gene flow between these populations. We resequenced 24 independent noncoding regions across the genome, corresponding to a total of approximately 33 kb per individual, in 236 samples from seven Pygmy and five agricultural populations dispersed over the African continent. We used simulation-based inference to identify the historical model best fitting our data. The model identified included the early divergence of the ancestors of Pygmy hunter-gatherers and farming populations approximately 60,000 years ago, followed by a split of the Pygmies' ancestors into the Western and Eastern Pygmy groups approximately 20,000 years ago. Our findings increase knowledge of the history of the peopling of the African continent in a region lacking archaeological data. An appreciation of the demographic and adaptive history of African populations with different modes of subsistence should improve our understanding of the influence of human lifestyles on genome diversity.
Central Africa is currently peopled by numerous sedentary agriculturalist populations neighboring the largest group of mobile hunter-gatherers, the Pygmies [1-3]. Although archeological remains attest to Homo sapiens' presence in the Congo Basin for at least 30,000 years, the demographic history of these groups, including divergence and admixture, remains widely unknown [4-6]. Moreover, it is still debated whether common history or convergent adaptation to a forest environment resulted in the short stature characterizing the pygmies [2, 7]. We genotyped 604 individuals at 28 autosomal tetranucleotide microsatellite loci in 12 nonpygmy and 9 neighboring pygmy populations. We found a high level of genetic heterogeneity among Western Central African pygmies, as well as evidence of heterogeneous levels of asymmetrical gene flow from nonpygmies to pygmies, consistent with the variable sociocultural barriers against intermarriages. Using approximate Bayesian computation (ABC) methods [8], we compared several historical scenarios. The most likely points toward a unique ancestral pygmy population that diversified approximately 2800 years ago, contemporarily with the Neolithic expansion of nonpygmy agriculturalists [9, 10]. Our results show that recent isolation, genetic drift, and heterogeneous admixture enabled a rapid and substantial genetic differentiation among Western Central African pygmies. Such an admixture pattern is consistent with the various sociocultural behaviors related to intermariages between pygmies and nonpygmies.
The hypervariable 1 region of human mtDNA shows markedly reduced variability in Polynesians, and this variability decreases from western to eastern Polynesia. Fifty-four sequences from New Zealand Maori show that the mitochondrial variability with just four haplotypes is the lowest of any sizeable human group studied and that the frequency of haplotypes is markedly skewed. The Maori sequences, combined with 268 published sequences from the Pacific, are consistent with a series of founder effects from small populations settling new island groups. The distributions of haplotypes were used to estimate the number of females in founding population of New Zealand Maori. The three-step simulation used a randomly selected founding population from eastern Polynesia, an expansionary phase in New Zealand, and finally the random selection of 54 haplotypes. The results are consistent with a founding population that includes approximately 70 women (between 50 and 100), and sensitivity analysis shows that this conclusion is robust to small changes in haplotype frequencies. This size is too large for models postulating a very small founding population of "castaways," but it is consistent with a general understanding of Maori oral history as well as the results of recent canoe voyages recreating early trans-oceanic voyages.
Mitochondrial DNA and the Y chromosome have been used extensively in the study of modern human origins and other phylogenetic questions, but not in the context of their sex-specific modes of transmission. mtDNA is transmitted exclusively by females, whereas the Y chromosome is passed only among males. As a result, differences in the reproductive output or migration rate of males and females will influence the geographic patterns and relative level of genetic diversity on the Y chromosome, autosomes and mtDNA (ref. 1). We have found that Y chromosome variants tend to be more localized geographically than those of mtDNA and the autosomes. The fraction of variation within human populations for Y chromosome single nucleotide polymorphisms (SNPs) is 35.5%, versus 80-85% for the autosomes and mtDNA (refs 6-8). A higher female than male migration rate (via patrilocality, the tendency for a wife to move into her husband's natal household) explains most of this discrepancy, because diverse Y chromosomes would enter a population at a lower rate than mtDNA or the autosomes. Polygyny may also contribute, but the reduction of variation within populations that we measure for the Y chromosome, relative to the autosomes and mitochondrial DNA, is of such magnitude that differences in the effective population sizes of the sexes alone are insufficient to produce the observation.
The observation of high frequencies of certain inherited disorders in the population of Saguenay-Lac Saint Jean can be explained in terms of the variance and the correlation of effective family size (EFS) from one generation to the next. We have shown this effect by using the branching process approach with real demographic data. When variance of EFS is included in the model, despite its profound effect on mutant allele frequency, any mutant introduced in the population never reaches the known carrier frequencies (between 0.035 and 0.05). It is only when the EFS correlation between generations is introduced into the model that we can explain the rise of the mutant alleles. This correlation is described by a c parameter that reflects the dependency of children's EFS on their parents' EFS. The c parameter can be considered to reflect social transmission of demographic behavior. We show that such social transmission dramatically reduces the effective population size. This could explain particular distributions in allele frequencies and unusually high frequency of certain inherited disorders in some human populations.
The out-of-Africa scenario has hitherto provided little evidence for the precise route by which modern humans left Africa. Two major routes of dispersal have been hypothesized: one through North Africa into the Levant, documented by fossil remains, and one through Ethiopia along South Asia, for which little, if any, evidence exists. Mitochondrial DNA (mtDNA) can be used to trace maternal ancestry. The geographic distribution and variation of mtDNAs can be highly informative in defining potential range expansions and migration routes in the distant past. The mitochondrial haplogroup M, first regarded as an ancient marker of East-Asian origin, has been found at high frequency in India and Ethiopia, raising the question of its origin. (A haplogroup is a group of haplotypes that share some sequence variations.) Its variation and geographical distribution suggest that Asian haplogroup M separated from eastern-African haplogroup M more than 50,000 years ago. Two other variants (489C and 10873C) also support a single origin of haplogroup M in Africa. These findings, together with the virtual absence of haplogroup M in the Levant and its high frequency in the South-Arabian peninsula, render M the first genetic indicator for the hypothesized exit route from Africa through eastern Africa/western India. This was possibly the only successful early dispersal event of modern humans out of Africa.
We examined 43 biallelic polymorphisms on the nonrecombining portion of the Y chromosome (NRY) in 50 human populations encompassing a total of 2,858 males to study the geographic structure of Y-chromosome variation. Patterns of NRY diversity varied according to geographic region and method/level of comparison. For example, populations from Central Asia had the highest levels of heterozygosity, while African populations exhibited a higher level of mean pairwise differences among haplotypes. At the global level, 36% of the total variance of NRY haplotypes was attributable to differences among populations (i.e., Phi(ST) = 0.36). When a series of AMOVA analyses was performed on different groupings of the 50 populations, high levels of among-groups variance (Phi(CT)) were found between Africans, Native Americans, and a single group containing all 36 remaining populations. The same three population groupings formed distinct clusters in multidimensional scaling plots. A nested cladistic analysis (NCA) demonstrated that both population structure processes (recurrent gene flow restricted by isolation by distance and long-distance dispersals) and population history events (contiguous range expansions and long-distance colonizations) were instrumental in explaining this tripartite division of global NRY diversity. As in our previous analyses of smaller NRY data sets, the NCA detected a global contiguous range expansion out of Africa at the level of the total cladogram. Our new results support a general scenario in which, after an early out-of-Africa range expansion, global-scale patterns of NRY variation were mainly influenced by migrations out of Asia. Two other notable findings of the NCA were (1) Europe as a "receiver" of intercontinental signals primarily from Asia, and (2) the large number of intracontinental signals within Africa. Our AMOVA analyses also supported the hypothesis that patrilocality effects are evident at local and regional scales, rather than at intercontinental and global levels. Finally, our results underscore the importance of subdivision of the human paternal gene pool and imply that caution should be exercised when using models and experimental strategies based on the assumption of panmixia.
Genetic differences among human populations are usually larger for the Y chromosome than for mtDNA. One possible explanation is the higher rate of female versus male migration due to the widespread phenomenon of patrilocality, in which the woman moves to her mate's residence after marriage. To test this hypothesis, we compare mtDNA and Y-chromosome variation in three matrilocal (in which the man moves to his mate's residence after marriage) and three patrilocal groups among the hill tribes of northern Thailand. Genetic diversity in these groups shows a striking correlation with residence pattern, supporting the role of sex-specific migration in influencing human genetic variation.
A resource of 1064 cultured lymphoblastoid cell lines (LCLs) (1) from individuals in different world populations and corresponding milligram quantities of DNA is deposited at the Foundation Jean Dausset (CEPH) (2) in Paris. LCLs were collected from various laboratories by the Human Genome Diversity Project (HGDP) (3) and CEPH to provide unlimited supplies of DNA for studies of sequence diversity and history of modern human populations. Information for each LCL is limited to sex, population, and geographic origin of the individual. Each LCL is registered in a project-‐‑specific database and provided with a CEPH-‐‑generated, numeric identifier that labels the LCL, its corresponding DNA, and subject information. Every product derived from an LCL is labeled with a unique alpha-‐‑numeric bar-‐‑code. LCLs were tested for mycoplasma infestation by a polymerase chain reaction-‐‑based test (4). All lines showing infestation were discarded. LCLs were expanded for storage at −196°C and for production of milligram quantities of DNA.
We studied human population structure using genotypes at 377 autosomal microsatellite loci in 1056 individuals from 52 populations.
Within-population differences among individuals account for 93 to 95% of genetic variation; differences among major groups
constitute only 3 to 5%. Nevertheless, without using prior information about the origins of individuals, we identified six
main genetic clusters, five of which correspond to major geographic regions, and subclusters that often correspond to individual
populations. General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments
of epidemiological risks but does not obviate the need to use genetic information in genetic association studies.
A recent dispersal of modern humans out of Africa is now widely accepted, but the routes taken across Eurasia are still disputed. We show that mitochondrial DNA variation in isolated "relict" populations in southeast Asia supports the view that there was only a single dispersal from Africa, most likely via a southern coastal route, through India and onward into southeast Asia and Australasia. There was an early offshoot, leading ultimately to the settlement of the Near East and Europe, but the main dispersal from India to Australia approximately 65,000 years ago was rapid, most likely taking only a few thousand years.
Human social organization can deeply affect levels of genetic diversity. This fact implies that genetic information can be used to study social structures, which is the basis of ethnogenetics. Recently, methods have been developed to extract this information from genetic data gathered from subdivided populations that have gone through recent spatial expansions, which is typical of most human populations. Here, we perform a Bayesian analysis of mitochondrial and Y chromosome diversity in three matrilocal and three patrilocal groups from northern Thailand to infer the number of males and females arriving in these populations each generation and to estimate the age of their range expansion. We find that the number of male immigrants is 8 times smaller in patrilocal populations than in matrilocal populations, whereas women move 2.5 times more in patrilocal populations than in matrilocal populations. In addition to providing genetic quantification of sex-specific dispersal rates in human populations, we show that although men and women are exchanged at a similar rate between matrilocal populations, there are far fewer men than women moving into patrilocal populations. This finding is compatible with the hypothesis that men are strictly controlling male immigration and promoting female immigration in patrilocal populations and that immigration is much less regulated in matrilocal populations.
• ethnogenetics
• human evolution
• sex-bias dispersal
Fertility inheritance, a phenomenon in which an individual's number of offspring is positively correlated with his or her number of siblings, is a cultural process that can have a strong impact on genetic diversity. Until now, fertility inheritance has been detected primarily using genealogical databases. In this study, we develop a new method to infer fertility inheritance from genetic data in human populations. The method is based on the reconstruction of the gene genealogy of a sample of sequences from a given population and on the computation of the degree of imbalance in this genealogy. We show indeed that this level of imbalance increases with the level of fertility inheritance, and that other phenomena such as hidden population structure are unlikely to generate a signal of imbalance in the genealogy that would be confounded with fertility inheritance. By applying our method to mtDNA samples from 37 human populations, we show that matrilineal fertility inheritance is more frequent in hunter-gatherer populations than in food-producer populations. One possible explanation for this result is that in hunter-gatherer populations, individuals belonging to large kin networks may benefit from stronger social support and may be more likely to have a large number of offspring.
Human genetic diversity is shaped by both demographic and biological factors and has fundamental implications for understanding
the genetic basis of diseases. We studied 938 unrelated individuals from 51 populations of the Human Genome Diversity Panel
at 650,000 common single-nucleotide polymorphism loci. Individual ancestry and population substructure were detectable with
very high resolution. The relationship between haplotype heterozygosity and geography was consistent with the hypothesis of
a serial founder effect with a single origin in sub-Saharan Africa. In addition, we observed a pattern of ancestral allele
frequency distributions that reflects variation in population dynamics among geographic regions. This data set allows the
most comprehensive characterization to date of human genetic variation.
This article presents a synthesis of available information about the framework of re- lations between Pygmy peoples and neighbouring local communities called "villagers" or "farmers." From an epistemological point of view, the literature is more detailed about the origin of that rela- tionship than about the analysis of its framework. From an ethnographic viewpoint, a comparison of the two most researched case studies in different cultural settings provides evidence of the existence of a similar relational interethnic model in the Congo River basin. This model involves both aspects of the "ideology of solidarity," sustained by links of pseudo-kinship, and of the "ideology of domi- nation," political-economic dominance over the Pygmy peoples by the "villagers." The relationship also appears fluid in that it allows a multiplicity of partnerships. The interethnic relational model suits an environment of mobility and of acephalous political organization. The author argues that the model is not specific to hunter-gatherer societies, nor to Pygmy communities in general, but rather to Pygmy groups in regular contact with villager communities characterised by mobility and non-hierarchical political organization.
Opening Paragraph
Un énorme travail a été réalisé sur les populations Pygmées du Zaïre. Dans ce domaine, l'ethnologie, l'anthropologie, la théologie africaine doivent beaucoup à J.-P. Hallet, à P. Schebesta, à C. M. Turnbull et á bien d'autres. Bon nombre de ces études ont diffusé et privilgié l'image prédominante du Pygmée nomadisant á travers la forêt, son milieu naturel. Cependant, elles ont occulté la connaissance et empêché l'investigation sur de nombreux autres groupes de Pygmées vivant loin de la forêt. En effet, pour Schebesta, qui fait de l'anthropométrie un critère privilégié, les seuls vrais Pygmées sont les Bambuti de la forêt de l'Ituri (1933: 63). Tous les autres ne seraient que des ‘Pygmoformes’ ou des ‘Pygmoïdes’, des ‘peuples métissés dont un croisement aura abâtardi les caractères de race et de culture’ (1940: 20). De nos jours, les critéres ont changé. Certains chercheurs se fondent sur le caractère polyphonique de la musique comme élément primordial dans la définition du Pygmée.
Guided by life-history theory, we examine the contexts in which reproductive interests (e.g., attracting and keeping a spouse) shape forager mobility. Using quantitative intercultural and intracultural mating distance data, we report significant correlations between mating distance and population density not only among foragers but also among farmers. Further, in all of the cultures for which we could find data males on average traveled considerably farther than females in a lifetime, and among Aka foragers of Central Africa age and sex significantly impacted distances traveled. We propose a descriptive model of forager mobility that supplements existing subsistence-focused models by incorporating reproductive interests at all levels. © 1999 by The Wenner-Gren Foundation for Anthropological Research. All rights reserved.
New linguistic evidence about the classification of the Bantu languages does not support the current view that these languages spread as the result of a massive migration or ‘expansion’ by its speakers. Rather the present geographic distribution of Bantu languages is the outcome of many complex historical dynamics involving successive dispersals of individual languages over a time span of millennia and involving reversals as well as successes. This is as true for eastern and southern Africa, where a close correlation between the archaeological evidence documenting the diffusion of basic food-related technologies, including metallurgy and the spreading of Bantu languages has become an axiom, as it is elsewhere. The linguistic evidence concerning the dispersal of Bantu languages in these regions of Africa is completely incongruent with the archaeological record. The existing Bantu expansion hypothesis must be totally abandoned. The scrapping of the hypothesis will make room for more realistic and quite different interpretations and research hypotheses. For example, it follows that the local or regional contribution of speakers of other languages, autochthons and others, to the development of later cultures and societies was probably considerably greater than has hitherto been acknowledged and that the continuities in historical dynamics of all sorts between the Bantu-speaking parts of Africa and areas further north and west are greater than has been hitherto realized.
In this article I am illustrating the linguistic diversity of African Pygmy populations in order to better address their anthropological diversity and history. I am also introducing a new method, based on the analysis of specialized vocabulary, to reconstruct the substratum of some languages they speak. I show that Pygmy identity is not based on their languages, which have often been borrowed from neighboring non-Pygmy farmer communities with whom each Pygmy group is linked. Understanding the nature of this partnership, quite variable in history, is essential to addressing Pygmy languages, identity, and history. Finally, I show that only a multidisciplinary approach is likely to push forward the understanding of African Pygmy societies as genetic, archeological, anthropological, and ethnological evidence suggest.
In the human species, the two uniparental genetic systems (mitochondrial DNA and Y chromosome) exhibit contrasting diversity patterns. It has been proposed that sex-specific behaviours, and in particular differences in migration rate between men and women, may explain these differences. The availability of high-density genomic data and the comparison of genetic patterns on autosomal and sex chromosomes at global and local scales allow a reassessment of the extent to which sex-specific behaviours shape our genome. In this article, we first review studies comparing the genetic patterns at uniparental and biparental genetic systems and assess the extent to which sex-specific migration processes explain the differences between these genetic systems. We show that differences between male and female migration rates matter, but that they are certainly not the only contributing factor. In particular, differences in effective population size between men and women are also likely to account for these differences. Then, we present and discuss three anthropological processes that may explain sex-specific differences in effective population size and thus human genomic variation: (i) variance in reproductive success arising from, for example, polygyny; (ii) descent rules; and (iii) transmission of reproductive success.
The current distribution of Bantu languages is commonly considered to be a consequence of a relatively recent population expansion (3-5kya) in Central Western Africa. While there is a substantial consensus regarding the centre of origin of Bantu languages (the Benue River Valley, between South East Nigeria and Western Cameroon), the identification of the area from where the population expansion actually started, the relation between the processes leading to the spread of languages and peoples and the relevance of local migratory events remain controversial. In order to shed new light on these aspects, we studied Y chromosome variation in a broad dataset of populations encompassing Nigeria, Cameroon, Gabon and Congo. Our results evidence an evolutionary scenario which is more complex than had been previously thought, pointing to a marked differentiation of Cameroonian populations from the rest of the dataset. In fact, in contrast with the current view of Bantu speakers as a homogeneous group of populations, we observed an unexpectedly high level of interpopulation genetic heterogeneity and highlighted previously undetected diversity for lineages associated with the diffusion of Bantu languages (E1b1a (M2) sub-branches). We also detected substantial differences in local demographic histories, which concord with the hypotheses regarding an early diffusion of Bantu languages into the forest area and a subsequent demographic expansion and migration towards eastern and western Africa.
The past decade of advances in molecular genetic technology has heralded a new era for all evolutionary studies, but especially the science of human evolution. Data on various kinds of DNA variation in human populations have rapidly accumulated. There is increasing recognition of the importance of this variation for medicine and developmental biology and for understanding the history of our species. Haploid markers from mitochondrial DNA and the Y chromosome have proven invaluable for generating a standard model for evolution of modern humans. Conclusions from earlier research on protein polymorphisms have been generally supported by more sophisticated DNA analysis. Co-evolution of genes with language and some slowly evolving cultural traits, together with the genetic evolution of commensals and parasites that have accompanied modern humans in their expansion from Africa to the other continents, supports and supplements the standard model of genetic evolution. The advances in our understanding of the evolutionary history of humans attests to the advantages of multidisciplinary research.
In this paper, we present a study of genetic variation in sub-Saharan Africa, which is based on published and unpublished data on fast-evolving (hypervariable region 1 of mitochondrial DNA and six microsatellites of Y chromosome) and slow-evolving (haplogroup frequencies) polymorphisms of mtDNA and Y chromosome. Our study reveals a striking difference in the genetic structure of food-producer (Bantu and Sudanic speakers) and hunter-gatherer populations (Pygmies, Kung, and Hadza). In fact, the ratio of mtDNA to Y-chromosome Nupsilon is substantially higher in food producers than in hunter-gatherers as determined by fast-evolving polymorphisms (1.76 versus 0.11). This finding indicates that the two population groups differ substantially in female and male migration rate and/or effective size. The difference also persists when linguistically homogeneous populations are used and outlier populations are eliminated (1.78 vs 0.19) or when the jacknife procedure is applied to a paired population data set (1.32 to 7.84 versus 0.14 to 0.66). The higher ratio of mtDNA to Y-chromosome Nnu in food producers than in hunter-gatherers is further confirmed by the use of slow-evolving polymorphisms (1.59 to 7.91 versus 0.12 to 0.35). To explain these results, we propose a model that integrates demographic and genetic aspects and incorporates ethnographic knowledge. In such a model, the asymmetric gene flow, polyginy, and patrilocality play an important role in differentiating the genetic structure of sub-Saharan populations. The existence of an asymmetric gene flow is supported by the phylogeographic features of mtDNA and Y-chromosome haplogroups found in the two population groups. The role of polyginy and patrilocality is sustained by the evidence of a differential pressure of genetic drift and gene flow on maternal and paternal lineages of food producers and hunter-gatherers that is revealed through the analysis of mitochondrial and Y-chromosomal intrapopulational variation.
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