African Gene Flow Reduces Beta-Ionone Anosmia/Hyposmia Prevalence in Admixed Malagasy Populations.

While recent advances in genetics make it possible to follow the genetic exchanges between populations and their phenotypic consequences, the impact of the genetic exchanges on the sensory perception of populations has yet to be explored. From this perspective, the present study investigated the consequences of African gene flow on odor perception in a Malagasy population with a predominantly East Asian genetic background. To this end, we combined psychophysical tests with genotype data of 235 individuals who were asked to smell the odorant molecule beta-ionone (ßI). Results showed that in this population the ancestry of the OR5A1 gene significantly influences the ability to detect ßI. At the individual level, African ancestry significantly protects against specific anosmia/hyposmia due to the higher frequency of the functional gene (OR ratios = 14, CI: 1.8-110, p-value = 0.012). At the population level, African introgression decreased the prevalence of specific anosmia/hyposmia to this odorous compound. Taken together, these findings validate the conjecture that in addition to cultural exchanges, genetic transfer may also influence the sensory perception of the population in contact.

Sucrose Is Not the Whole Story: Risk Factors and Oral Health at the Contact (Yakutia, Siberia-16th/19th).

(1) Background: contact between indigenous and European populations has often resulted in changes in oral health attributed to the introduction of sucrose. Most studies are per tooth over considerable periods and with few ethnological references. (2) Aim: dental epidemiology of 96 autochthonous frozen bodies from Yakutia between the early 17th century and the late 19th century; comparisons with historical texts and ethnographic data. (3) Material and methods: we use descriptive statistics and discriminant factorial analyses to identify dominant variables in the dataset and compare periods and subjects, considering all variables. (4) Results: the peculiarities of the population are the rarity of cavities and the relative frequency of dental pathologies leading to death. Assimilation into the Russian Orthodox culture has led to decreased tooth wear and an increase in tooth loss. Dental health evolves only two centuries after the contact. (5) Conclusions: the confrontation with historical data suggests that changes are not related to the growing importance of sucrose but to a combined action: the substitution of dendrophagy by cereal flour; the decrease in immunity linked to the development of chronic infectious diseases; tobacco addiction and the mandibular torus: a risk factor promoting apical cysts.

Influence of gender and culture on the perception of acidic compounds of human body odor.

There is increasing evidence that human body odor is involved in interpersonal communication. However, among the wide variety of substances excreted by the human body that might act as chemosignals, much attention has been granted to androstenes to the detriment of other categories. Here, we focused on the acidic fraction of human body odor. We investigated men and women's perceptual descriptions and detection thresholds of the sexually dimorphic (male) compound 3-hydroxy-3-methylhexanoic acid (HMHA) in two contrasted cultures, France and Madagascar. Perceptual responses to HMHA in both countries were very similar. HMHA proved to be more typical of body odor than another chemically-related major compound of human body odor 3MHA (3-methylhex-2-enoic acid also known as 3M2H). A significant portion of the samples studied (between 8 and 19%) was likely to be anosmic to HMHA (and to 3MHA: 25%). Although differences would be expected between men and women's perceptual responses to HMHA, based on the assumption that this compound would have a function in human partner choice, no sex differences were found for any of the perceptual variables. However, in Malagasy women, perceived intensity of HMHA was higher in participants who were in the fertile phase of the menstrual cycle. Whether HMHA is relevant in the perception of a potential partner thus requires further explorations, with more implicit approaches for example and/or by investigating the repercussions of HMHA specific anosmia on interpersonal relationships.

Strong selection during the last millennium for African ancestry in the admixed population of Madagascar.

While admixed populations offer a unique opportunity to detect selection, the admixture in most of the studied populations occurred too recently to produce conclusive signals. By contrast, Malagasy populations originate from admixture between Asian and African populations that occurred ~27 generations ago, providing power to detect selection. We analyze local ancestry across the genomes of 700 Malagasy and identify a strong signal of recent positive selection, with an estimated selection coefficient >0.2. The selection is for African ancestry and affects 25% of chromosome 1, including the Duffy blood group gene. The null allele at this gene provides resistance to Plasmodium vivax malaria, and previous studies have suggested positive selection for this allele in the Malagasy population. This selection event also influences numerous other genes implicated in immunity, cardiovascular diseases, and asthma and decreases the Asian ancestry genome-wide by 10%, illustrating the role played by selection in recent human history.

Genomic landscape of human diversity across Madagascar.

Although situated ∼400 km from the east coast of Africa, Madagascar exhibits cultural, linguistic, and genetic traits from both Southeast Asia and Eastern Africa. The settlement history remains contentious; we therefore used a grid-based approach to sample at high resolution the genomic diversity (including maternal lineages, paternal lineages, and genome-wide data) across 257 villages and 2,704 Malagasy individuals. We find a common Bantu and Austronesian descent for all Malagasy individuals with a limited paternal contribution from Europe and the Middle East. Admixture and demographic growth happened recently, suggesting a rapid settlement of Madagascar during the last millennium. However, the distribution of African and Asian ancestry across the island reveals that the admixture was sex biased and happened heterogeneously across Madagascar, suggesting independent colonization of Madagascar from Africa and Asia rather than settlement by an already admixed population. In addition, there are geographic influences on the present genomic diversity, independent of the admixture, showing that a few centuries is sufficient to produce detectable genetic structure in human populations.

Contrasting Linguistic and Genetic Origins of the Asian Source Populations of Malagasy.

The Austronesian expansion, one of the last major human migrations, influenced regions as distant as tropical Asia, Remote Oceania and Madagascar, off the east coast of Africa. The identity of the Asian groups that settled Madagascar is particularly mysterious. While language connects Madagascar to the Ma'anyan of southern Borneo, haploid genetic data are more ambiguous. Here, we screened genome-wide diversity in 211 individuals from the Ma'anyan and surrounding groups in southern Borneo. Surprisingly, the Ma'anyan are characterized by a distinct, high frequency genomic component that is not found in Malagasy. This novel genetic layer occurs at low levels across Island Southeast Asia and hints at a more complex model for the Austronesian expansion in this region. In contrast, Malagasy show genomic links to a range of Island Southeast Asian groups, particularly from southern Borneo, but do not have a clear genetic connection with the Ma'anyan despite the obvious linguistic association.

Genetic Admixture and Flavor Preferences: Androstenone Sensitivity in Malagasy Populations.

The genetic basis of androstenone anosmia has been well studied due to androstenone's putative role as a human sex pheromone and its presence in pork meat. Polymorphisms have been identified on the olfactory receptor gene OR7D4, which significantly affect perception of androstenone pleasantness and intensity in several Western populations. This study aims to investigate androstenone sensitivity and the influence of OR7D4 polymorphisms in non-Western populations. Androstenone perception was tested in 132 individuals from Madagascar using a double three-alternative choice test with two concentrations of androstenone (0.17 and 1.7 µg/ml). We found that Malagasy populations described this molecule in a similar way to European populations, and 21% of the sample was not able to smell androstenone. In contrast to previous studies, there was no significant evidence of the influence of rs61729907: C>T (R88W) and rs5020278: C>T polymorphisms (T133M) on androstenone sensitivity in Malagasy populations. We found, however, a significant effect of the polymorphism rs61732668 (P79L) and a significant difference in androstenone perception between populations in different locations across Madagascar. This study indicates the existence of population-specific factors in androstenone sensitivity, suggesting that population history has a role in shaping an individual's smell and flavor preferences and food preferences in general.

Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations.

BACKGROUND: Linguistic, cultural and genetic characteristics of the Malagasy suggest that both Africans and Island Southeast Asians were involved in the colonization of Madagascar. Populations from the Indonesian archipelago played an especially important role because linguistic evidence suggests that the Malagasy language branches from the Southeast Barito language family of southern Borneo, Indonesia, with the closest language spoken today by the Ma'anyan. To test for a genetic link between Malagasy and these linguistically related Indonesian populations, we studied the Ma'anyan and other Indonesian ethnic groups (including the sea nomad Bajo) that, from their historical and linguistic contexts, may be modern descendants of the populations that helped enact the settlement of Madagascar. RESULT: A combination of phylogeographic analysis of genetic distances, haplotype comparisons and inference of parental populations by linear optimization, using both maternal and paternal DNA lineages, suggests that Malagasy derive from multiple regional sources in Indonesia, with a focus on eastern Borneo, southern Sulawesi and the Lesser Sunda islands. CONCLUSION: Settlement may have been mediated by ancient sea nomad movements because the linguistically closest population, Ma'anyan, has only subtle genetic connections to Malagasy, whereas genetic links with other sea nomads are more strongly supported. Our data hint at a more complex scenario for the Indonesian settlement of Madagascar than has previously been recognized.

A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

Genome-wide evidence of Austronesian-Bantu admixture and cultural reversion in a hunter-gatherer group of Madagascar.

Linguistic and cultural evidence suggest that Madagascar was the final point of two major dispersals of Austronesian- and Bantu-speaking populations. Today, the Mikea are described as the last-known Malagasy population reported to be still practicing a hunter-gatherer lifestyle. It is unclear, however, whether the Mikea descend from a remnant population that existed before the arrival of Austronesian and Bantu agriculturalists or whether it is only their lifestyle that separates them from the other contemporary populations of South Madagascar. To address these questions we have performed a genome-wide analysis of >700,000 SNP markers on 21 Mikea, 24 Vezo, and 24 Temoro individuals, together with 50 individuals from Bajo and Lebbo populations from Indonesia. Our analyses of these data in the context of data available from other Southeast Asian and African populations reveal that all three Malagasy populations are derived from the same admixture event involving Austronesian and Bantu sources. In contrast to the fact that most of the vocabulary of the Malagasy speakers is derived from the Barito group of the Austronesian language family, we observe that only one-third of their genetic ancestry is related to the populations of the Java-Kalimantan-Sulawesi area. Because no additional ancestry components distinctive for the Mikea were found, it is likely that they have adopted their hunter-gatherer way of life through cultural reversion, and selection signals suggest a genetic adaptation to their new lifestyle.

Human testis-specific genes are under relaxed negative selection.

Recent studies have suggested that selective forces and constraints acting on genes varied during human evolution depending on the organ in which they are expressed. To gain insight into the evolution of organ determined negative selection forces, we compared the non-synonymous SNP diversity of genes expressed in different organs. Based on a HAPMAP dataset, we determined for each SNP its frequency in 11 human populations and, in each case, predicted whether or not the change it produces is deleterious. We have shown that, for all organs under study, SNPs predicted to be deleterious are present at a significantly lower frequency than SNPs predicted to be tolerated. However, testis-specific genes contain a higher proportion of deleterious SNPs than other organs. This study shows that negative selection is acting on the whole human genome, but that the action of negative selection is relaxed on testis-specific genes. This result adds to and expands the hypothesis of a recent evolutionary change in the human male reproductive system and its behavior.

Tracing Arab-Islamic inheritance in Madagascar: study of the Y-chromosome and mitochondrial DNA in the Antemoro.

Madagascar is located at the crossroads of the Asian and African worlds and is therefore of particular interest for studies on human population migration. Within the large human diversity of the Great Island, we focused our study on a particular ethnic group, the Antemoro. Their culture presents an important Arab-Islamic influence, but the question of an Arab biological inheritance remains unresolved. We analyzed paternal (n=129) and maternal (n=135) lineages of this ethnic group. Although the majority of Antemoro genetic ancestry comes from sub-Saharan African and Southeast Asian gene pools, we observed in their paternal lineages two specific haplogroups (J1 and T1) linked to Middle Eastern origins. This inheritance was restricted to some Antemoro sub-groups. Statistical analyses tended to confirm significant Middle Eastern genetic contribution. This study gives a new perspective to the large human genetic diversity in Madagascar.

Complete mitochondrial DNA sequences provide new insights into the Polynesian motif and the peopling of Madagascar.

More than a decade of mitochondrial DNA (mtDNA) studies have given the 'Polynesian motif' renowned status as a marker for tracing the late-Holocene expansion of Austronesian speaking populations. Despite considerable research on the Polynesian motif in Oceania, there has been little equivalent work on the western edge of its expansion - leaving major issues unresolved regarding the motif's evolutionary history. This has also led to considerable uncertainty regarding the settlement of Madagascar. In this study, we assess mtDNA variation in 266 individuals from three Malagasy ethnic groups: the Mikea, Vezo, and Merina. Complete mtDNA genome sequencing reveals a new variant of the Polynesian motif in Madagascar; two coding region mutations define a Malagasy-specific sub-branch. This newly defined 'Malagasy motif' occurs at high frequency in all three ethnic groups (13-50%), and its phylogenetic position, geographic distribution, and estimated age all support a recent origin, but without conclusively identifying a specific source region. Nevertheless, the haplotype's limited diversity, similar to those of other mtDNA haplogroups found in our Malagasy groups, best supports a small number of initial settlers arriving to Madagascar through the same migratory process. Finally, the discovery of this lineage provides a set of new polymorphic positions to help localize the Austronesian ancestors of the Malagasy, as well as uncover the origin and evolution of the Polynesian motif itself.

A new deep branch of eurasian mtDNA macrohaplogroup M reveals additional complexity regarding the settlement of Madagascar.

BACKGROUND: Current models propose that mitochondrial DNA macrohaplogroups M and N evolved from haplogroup L3 soon after modern humans left Africa. Increasingly, however, analysis of isolated populations is filling in the details of, and in some cases challenging, aspects of this general model. RESULTS: Here, we present the first comprehensive study of three such isolated populations from Madagascar: the Mikea hunter-gatherers, the neighbouring Vezo fishermen, and the Merina central highlanders (n = 266). Complete mitochondrial DNA genome sequences reveal several unresolved lineages, and a new, deep branch of the out-of-Africa founder clade M has been identified. This new haplogroup, M23, has a limited global distribution, and is restricted to Madagascar and a limited range of African and Southwest Asian groups. CONCLUSIONS: The geographic distribution, phylogenetic placement and molecular age of M23 suggest that the colonization of Madagascar was more complex than previously thought.