Residence rule flexibility and descent groups dynamics shape uniparental genetic diversities in South East Asia

Measuring the Efficiency of Purging by non-random Mating in Human Populations

Human populations harbor a high concentration of deleterious genetic variants. Here, we tested the hypothesis that non-random mating practices affect the distribution of these variants, through exposure in the homozygous state, leading to their purging from the population gene pool. To do so, we produced whole-genome sequencing data for two pairs of Asian populations exhibiting different alliance rules and rates of inbreeding, but with similar effective population sizes. The results show that populations with higher rates of inbred matings do not purge deleterious variants more efficiently. Purging therefore has a low efficiency in human populations, and different mating practices lead to a similar mutational load.

Patrilineal segmentary systems provide a peaceful explanation for the post-Neolithic Y-chromosome bottleneck

Studies have found a pronounced decline in male effective population sizes worldwide around 3000-5000 years ago. This bottleneck was not observed for female effective population sizes, which continued to increase over time. Until now, this remarkable genetic pattern was interpreted as the result of an ancient structuring of human populations into patrilineal groups (gathering closely related males) violently competing with each other. In this scenario, violence is responsible for the repeated extinctions of patrilineal groups, leading to a significant reduction in male effective population size. Here, we propose an alternative hypothesis by modelling a segmentary patrilineal system based on anthropological literature. We show that variance in reproductive success between patrilineal groups, combined with lineal fission (i.e., the splitting of a group into two new groups of patrilineally related individuals), can lead to a substantial reduction in the male effective population size without resorting to the violence hypothesis. Thus, a peaceful explanation involving ancient changes in social structures, linked to global changes in subsistence systems, may be sufficient to explain the reported decline in Y-chromosome diversity.

Sex-biased patterns shaped the genetic history of Roma

The Roma population is a European ethnic minority characterized by recent and multiple dispersals and founder effects. After their origin in South Asia around 1,500 years ago, they migrated West. In Europe, they diverged into ethnolinguistically distinct migrant groups that spread across the continent. Previous genetic studies based on genome-wide data and uniparental markers detected Roma founder events and West-Eurasian gene flow. However, to the best of our knowledge, it has not been assessed whether these demographic processes have equally affected both sexes in the population. The present study uses the largest and most comprehensive dataset of complete mitochondrial and Y chromosome Roma sequences to unravel the sex-biased patterns that have shaped their genetic history. The results show that the Roma maternal genetic pool carries a higher lineage diversity from South Asia, as opposed to a single paternal South Asian lineage. Nonetheless, the European gene flow events mainly occurred through the maternal lineages; however, a signal of this gene flow is also traceable in the paternal lineages. We also detect a higher female migration rate among European Roma groups. Altogether, these results suggest that sociocultural factors influenced the emergence of sex-biased genetic patterns at global and local scales in the Roma population through time.

Identifying post-marital residence patterns in prehistory: A phylogenetic comparative analysis of dwelling size

Post-marital residence patterns are an important aspect of human social organization. However, identifying such patterns in prehistoric societies is challenging since they leave almost no direct traces in archaeological records. Cross-cultural researchers have attempted to identify correlates of post-marital residence through the statistical analysis of ethnographic data. Several studies have demonstrated that, in agricultural societies, large dwellings (over ca. 65 m²) are associated with matrilocality (spouse resides with or near the wife’s family), whereas smaller dwellings are associated with patrilocality (spouse resides with or near the husband’s family). In the present study, we tested the association between post-marital residence and dwelling size (average house floor area) using phylogenetic comparative methods and a global sample of 86 pre-industrial societies, 22 of which were matrilocal. Our analysis included the presence of agriculture, sedentism, and durability of house construction material as additional explanatory variables. The results confirm a strong association between matrilocality and dwelling size, although very large dwellings (over ca. 200 m²) were found to be associated with all types of post-marital residence. The best model combined dwelling size, post-marital residence pattern, and sedentism, the latter being the single best predictor of house size. The effect of agriculture on dwelling size becomes insignificant once the fixity of settlement is taken into account. Our results indicate that post-marital residence and house size evolve in a correlated fashion, namely that matrilocality is a predictable response to an increase in dwelling size. As such, we suggest that reliable inferences about the social organization of prehistoric societies can be made from archaeological records.

The paternal and maternal genetic history of Vietnamese populations

Vietnam exhibits great cultural and linguistic diversity, yet the genetic history of Vietnamese populations remains poorly understood. Previous studies focused mostly on the majority Kinh group, and thus the genetic diversity of the many other groups has not yet been investigated. Here we analyze complete mtDNA genome sequences and ~2.3 Mb sequences of the male-specific portion of the Y chromosome from the Kinh and 16 minority populations, encompassing all five language families present in Vietnam. We find highly variable levels of diversity within and between groups that do not correlate with either geography or language family. In particular, the Mang and Sila have undergone recent, independent bottlenecks, while the majority group, Kinh, exhibits low levels of differentiation with other groups. The two Austronesian-speaking groups, Giarai and Ede, show a potential impact of matrilocality on their patterns of variation. Overall, we find that isolation, coupled with limited contact involving some groups, has been the major factor influencing the genetic structure of Vietnamese populations, and that there is substantial genetic diversity that is not represented by the Kinh.

Current ecology, not ancestral dispersal patterns, influences menopause symptom severity

All human females who reach midlife experience menopause, however, it is currently unclear why women experience this period of infertility, and why it is accompanied by many unpleasant symptoms. Using primary data from four ethnic groups in China, we test an existing theory that age of menopause and its symptoms are the result of intragenomic conflict between maternally and paternally inherited genes, with the outcome of such conflict predicted to be contingent on the ancestral postmarital residence pattern of the female (Úbeda, Ohtsuki, & Gardner, Ecology Letters, 17, 2014, 165). The model predicts that being ancestrally patrilocal results in less intragenomic conflict, causing a shorter, less symptomatic perimenopause that terminates in a later menopause. Our findings show no support for this hypothesis and suggest current, rather than ancestral, residence patterns better predict aspects of the menopausal transition. Furthermore, current patrilocality when compared to duolocality is associated with more severe menopause symptoms, which may be due to sexual, rather than intragenomic, conflict.

OPEN RESEARCH BADGES

This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.27s8k0p.

From matrimonial practices to genetic diversity in Southeast Asian populations: the signature of the matrilineal puzzle

In matrilineal populations, the descent group affiliation is transmitted by women whereas the socio-political power frequently remains in the hands of men. This situation, named the 'matrilineal puzzle', is expected to promote local endogamy as a coping mechanism allowing men to maintain their decision-making power over their natal descent group. In this paper, we revisit this 'matrilineal puzzle' from a population genetics' point of view. Indeed, such tendency for local endogamy in matrilineal populations is expected to increase their genetic inbreeding and generate isolation-by-distance patterns between villages. To test this hypothesis, we collected ethno-demographic data for 3261 couples and high-density genetic data for 675 individuals from 11 Southeast Asian populations with a wide range of social organizations: matrilineal and matrilocal populations (M), patrilineal and patrilocal populations (P) or cognatic populations with predominant matrilocal residence (C). We observed that M and C populations have higher levels of village endogamy than P populations, and that such higher village endogamy leads to higher genetic inbreeding. M populations also exhibit isolation-by-distance patterns between villages. We interpret such genetic patterns as the signature of the 'matrilineal puzzle'. Notably, our results suggest that any form of matrilocal marriage (whatever the descent rule is) increases village endogamy. These findings suggest that male dominance, when combined with matrilocality, constrains inter-village migrations, and constitutes an underexplored cultural process shaping genetic patterns in human populations. This article is part of the theme issue 'The evolution of female-biased kinship in humans and other mammals'.

Sex-linked genetic diversity originates from persistent sociocultural processes at microgeographic scales

Population genetics has been successful at identifying the relationships between human groups and their interconnected histories. However, the link between genetic demography inferred at large scales and the individual human behaviours that ultimately generate that demography is not always clear. While anthropological and historical context are routinely presented as adjuncts in population genetic studies to help describe the past, determining how underlying patterns of human sociocultural behaviour impact genetics still remains challenging. Here, we analyse patterns of genetic variation in village-scale samples from two islands in eastern Indonesia, patrilocal Sumba and a matrilocal region of Timor. Adopting a 'process modelling' approach, we iteratively explore combinations of structurally different models as a thinking tool. We find interconnected socio-genetic interactions involving sex-biased migration, lineage-focused founder effects, and on Sumba, heritable social dominance. Strikingly, founder ideology, a cultural model derived from anthropological and archaeological studies at larger regional scales, has both its origins and impact at the scale of villages. Process modelling lets us explore these complex interactions, first by circumventing the complexity of formal inference when studying large datasets with many interacting parts, and then by explicitly testing complex anthropological hypotheses about sociocultural behaviour from a more familiar population genetic standpoint.

Differences between sons and daughters in the intergenerational transmission of wealth

Persistent interest lies in gender inequality, especially with regard to the favouring of sons over daughters. Economists are concerned with how privilege is transmitted across generations, and anthropologists have long studied sex-biased inheritance norms. There has, however, been no focused cross-cultural investigation of how parent-offspring correlations in wealth vary by offspring sex. We estimate these correlations for 38 wealth measures, including somatic and relational wealth, from 15 populations ranging from hunter-gatherers to small-scale farmers. Although small sample sizes limit our statistical power, we find no evidence of ubiquitous male bias, at least as inferred from comparing parent-son and parent-daughter correlations. Rather we find wide variation in signatures of sex bias, with evidence of both son and daughter-biased transmission. Further, we introduce a model that helps pinpoint the conditions under which simple mid-point parent-offspring wealth correlations can reveal information about sex-biased parental investment. Our findings are relevant to the study of female-biased kinship by revealing just how little normative descriptors of kinship systems, such as patrilineal inheritance, capture intergenerational correlations in wealth, and how variable parent-son and parent-daughter correlations can be. This article is part of the theme issue 'The evolution of female-biased kinship in humans and other mammals'.

Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia

Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the nonrecombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic exogamy, a marital practice in which men are required to marry women speaking a different language. We identified 2,969 SNPs in the NRY sequences, only 925 of which were previously described. The NRY and mtDNA data showed different sex-specific demographic histories: female effective population size has been larger than that of males through time, which might reflect larger variance in male reproductive success. Both markers show an increase in lineage diversification beginning ∼5,000 years ago, which may reflect the intensification of agriculture, technological innovations, and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, we find similar excesses of NRY versus mtDNA between-population divergence at both the local and continental scale, suggesting long-term stability of female versus male migration. We also find evidence of the impact of sociocultural practices on diversity patterns. Finally, our study highlights the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between sexes.

Neutral Theory: From Complex Population History to Natural Selection and Sociocultural Phenomena in Human Populations

Here, we present a synthetic view on how Kimura's Neutral theory has helped us gaining insight on the different evolutionary forces that shape human evolution. We put this perspective in the frame of recent emerging challenges: the use of whole genome data for reconstructing population histories, natural selection on complex polygenic traits, and integrating cultural processes in human evolution.