Admixture Model Research Articles

Exploring the African genetic influence in the first settlement founded by African slaves in America

The present study aims to outline the genetic makeup of the current population of the town of Yanga (Veracruz State, Mexico), the first Latin American settlement founded by African slaves in Mexico. For this purpose, we carried out the genetic characterization of 60 individuals from Yanga, analysing 15 autosomal short tandem repeats (STRs) and interpreting the results in the context of the admixed population known as Mexican mestizos. The genetic contribution from the three most important human groups in the current admixed Yanga population was calculated using Structure software. We detected a high percentage of Amerindian (48%) and European inheritance (44.7%), and a much less important African contribution (7.3%). These results were then compared with 10 other Mexican mestizo populations. The results fit the tri-hybrid model for admixture characterized by a high genetic contribution from Europeans and Africans in the north—though the African influence is lower—and a decreasing contribution from these two populations to the south and southeast. Conversely, the Amerindian component presents maximum values in the south and minimum values in the north. The Amerindian and European genetic traces are related to their ancestral settlements, but the African contribution can be explained by other parameters. To understand the current African genetic traces, we have to assume that there was a redistribution of these population groups and an important admixture phenomenon which led to the dilution of the African ancestral genetic pool. Furthermore, admixture was favoured by conditions that allowed individuals who intermarried to ascend in social status. These reasons would explain why despite the fact that Yanga was founded by black slaves, high levels of African ancestry are not found in the current population.

Genetic structure of cultivated flax (Linum usitatissimum L.) based on retrotransposon-based markers

Flax (Linum usitatissimum L.) is one of the most important fiber and oil crop plants cultivated since ancient time. The flax seeds contain high amount of omega- 3-fatty acids and biologically active lignans. In spite of economic importance of cultivated flax, no information is available on its genetic variability and population structure in Iran. Therefore, we used six inter-retrotransposon amplified polymorphism (IRAP) markers and 15 combined IRAP markers to reveal within and among population genetic diversity in this crop plant. We used 30 randomly selected plants in three geographical populations for present investigation. AMOVA test produced significant genetic difference (PhiPT = 0.40, P = 0.010) among the studied populations and also revealed that, 40% of total genetic variability was due to within population diversity while, 60% was due to among population genetic differentiation. Gst (0.78, P = 0.001), Hedrick, standardised fixation index (G'st = 0.83, P = 0.001), revealed that the studied populations are genetically differentiated. STRUCTURE plot based on admixture model revealed that the studied populations differed extensively in their genetic content, but some degree of shared alleles occurred between them. Some adaptive IRAP loci were identified by LFMM analysis. These loci were private alleles restricted to geographical populations. Data obtained may be used in breeding and hybridization program of flax in the country.

European Ancestry Is Associated with Acute Chest Syndrome in Sickle Cell Disease

Background: Acute chest syndrome (ACS) is a major cause of morbidity and mortality in patients with sickle cell disease (SCD). The elucidation of genetic modifiers and mechanisms responsible for the phenotypic variability in ACS and SCD would have important clinical implications such as the identification of individuals at high risk for ACS complications and the potential for use of individualized preventive and therapeutic strategies that could ultimately improve outcomes for patients with SCD.We hypothesize that the development of ACS is significantly influenced by ancestry.Methods: Autosomal SNPs were genotyped with the Affymetrix PanAFR array in a University of Illinois cohort and with the Illumina 6.0 platform in the NIH Walk-PHaSST cohort. We merged the two GWAS datasets and there were 100,079 SNPs available after removing SNPs with > 2 alleles and Hardy-Weinberg Equilibrium (HWE) P<0.001. From HapMap Phase 3 genotype data, we selected 5,000 SNPs that exhibit large frequency differences between YRI and CEU (P < 1.57 x 10-29). Five hundred and fifteen of these SNPs were identified in the 100,079 SNPs genotyped in both GWAS arrays. After removing 152 SNPs with FST < 0.3 and 9 SNPs linked to other SNPs with r2>0.2, the total number of SNPs available for ancestry estimates was 354. Genetic ancestry was estimated using HapMap YRI and CEU genotypes as ancestral population (K=2) using STRUCTUR 2.1. We ran STRUCTURE under the admixture model using prior population information and assuming allele frequencies among populations, with a burn-in length of 30,000 for 70,000 repetitions. Logistic regression was used to examine the association between European ancestry (EA) and Acute Chest Syndrome. Age, gender, hemoglobin genotype (HbSS/HbSβ0 vs. others), and use of hydroxyurea were additionally considered during modeling.Results: Seven hundred and thirty patients (UIC= 233, Walk-PHaSST = 497) were included in the analysis (Table 1). In binary logistic regression analysis adjusting for age, gender, Hb genotypes (severe vs. mild) and hydroxyurea use, EA was associated with and increase in ACS risk in both cohorts and when the cohorts where combined (UIC P=0.02, Walk-PHaSST P=0.001, combined P<0.001).A similar trend was observed when degree of EA was stratified (Table 2).Summary: Population structure and admixture influence the risk of ACS. European ancestry is associated with an increased ACS risk.Abstract 4051. Table 1Characteristics of study subjectsUICWalk-PHaSSTPooledACSno-ACSACSno-ACSACSno-ACSNumber19538299198494236Mean Age (SD)36.1 (12.1)40.4 (12.5)a38 (13.4)36 (12.7)37 (12.9)37 (12.7)No. females (%)113 (58%)23 (61%)163 (54%)109 (55%)276 (56%)132 (56%)aHbSS /HbSβ0 (%)153 (79%)21 (55%)b242 (81.5%)136 (70.8%)b395 (80.4%)157 (68.2%)b% European Ancestry (SD)22 (9.9)20 (7.4)20 (13.5)17 (12.5)a21 (12.3)18 (11.9)% West African Ancestry (SD)78 (9.9)80 (7.4)80 (13.5)83 (12.5)a79 (12.3)82 (11.9)aP<0.05 comparing ACS to non-ACS within sitebP<0.002 comparing ACS to non-ACS within siteTable 2European Ancestry Strata and ACS RiskUICWalk-PHaSSTPooledOR (95% CI)P-valueOR (95% CI)P-valueOR (95% CI)P-valueAncestry StrataLess than 14.3%Ref.Ref.Ref.14.3% to 23.2%0.59 (1.2 - 21)0.3391.05 (0.7 - 1.6)0.8311.28 (0.9 - 1.9)0.206Greater than 23.2%1.21 (0.4 - 3.9)0.7411.65 (1.1 - 2.6)0.0282.03 (1.4 - 3.0)0.005 DisclosuresNo relevant conflicts of interest to declare.

Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches.

To understand the genetic basis of tolerance to drought and heat stresses in chickpea, a comprehensive association mapping approach has been undertaken. Phenotypic data were generated on the reference set (300 accessions, including 211 mini-core collection accessions) for drought tolerance related root traits, heat tolerance, yield and yield component traits from 1–7 seasons and 1–3 locations in India (Patancheru, Kanpur, Bangalore) and three locations in Africa (Nairobi, Egerton in Kenya and Debre Zeit in Ethiopia). Diversity Array Technology (DArT) markers equally distributed across chickpea genome were used to determine population structure and three sub-populations were identified using admixture model in STRUCTURE. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations (r2; when r2<0.20) was found to decay rapidly with the genetic distance of 5 cM. For establishing marker-trait associations (MTAs), both genome-wide and candidate gene-sequencing based association mapping approaches were conducted using 1,872 markers (1,072 DArTs, 651 single nucleotide polymorphisms [SNPs], 113 gene-based SNPs and 36 simple sequence repeats [SSRs]) and phenotyping data mentioned above employing mixed linear model (MLM) analysis with optimum compression with P3D method and kinship matrix. As a result, 312 significant MTAs were identified and a maximum number of MTAs (70) was identified for 100-seed weight. A total of 18 SNPs from 5 genes (ERECTA, 11 SNPs; ASR, 4 SNPs; DREB, 1 SNP; CAP2 promoter, 1 SNP and AMDH, 1SNP) were significantly associated with different traits. This study provides significant MTAs for drought and heat tolerance in chickpea that can be used, after validation, in molecular breeding for developing superior varieties with enhanced drought and heat tolerance.

Influence of drift and admixture on population structure of American black bears (Ursus americanus) in the Central Interior Highlands, USA, 50 years after translocation

Bottlenecks, founder events, and genetic drift often result in decreased genetic diversity and increased population differentiation. These events may follow abundance declines due to natural or anthropogenic perturbations, where translocations may be an effective conservation strategy to increase population size. American black bears (Ursus americanus) were nearly extirpated from the Central Interior Highlands, USA by 1920. In an effort to restore bears, 254 individuals were translocated from Minnesota, USA, and Manitoba, Canada, into the Ouachita and Ozark Mountains from 1958 to 1968. Using 15 microsatellites and mitochondrial haplotypes, we observed contemporary genetic diversity and differentiation between the source and supplemented populations. We inferred four genetic clusters: Source, Ouachitas, Ozarks, and a cluster in Missouri where no individuals were translocated. Coalescent models using approximate Bayesian computation identified an admixture model as having the highest posterior probability (0.942) over models where the translocation was unsuccessful or acted as a founder event. Nuclear genetic diversity was highest in the source (AR = 9.11) and significantly lower in the translocated populations (AR = 7.07-7.34; P = 0.004). The Missouri cluster had the lowest genetic diversity (AR = 5.48) and served as a natural experiment showing the utility of translocations to increase genetic diversity following demographic bottlenecks. Differentiation was greater between the two admixed populations than either compared to the source, suggesting that genetic drift acted strongly over the eight generations since the translocation. The Ouachitas and Missouri were previously hypothesized to be remnant lineages. We observed a pretranslocation remnant signature in Missouri but not in the Ouachitas.

Admixture mapping of growth related traits in F2 mice dataset using ancestry informative markers

Most of the associated single nucleotide polymorphisms (SNPs) for genome wide association studies (GWAS) explain very little proportion of phenotypic variance in outbred populations. One reason is; large number of markers raises the problem of multiple hypothesis testing correction using conservative statistical tests in single marker models. Admixture mapping could be used as alternative model to detect the genes associated with quantitative traits by less number of ancestry informative markers. Ancestral genotypes of founder populations were available for the F₂ mice dataset for growth related traits. The objectives of this study were (1) to detect genomic signals by admixture mapping for growth related traits by ancestry informative markers and ancestral genotypes (2) to detect genomic signals for growth related traits by Bayes C(π) model and compare results with those obtained by use of admixture mapping. Bayes C(π) model detected more SNPs that has high ancestry informative markers. But due to stringent significance tests and small SNPs effects admixture model did not detect the same SNPs in Bayes C(π). As was expected higher ancestral informative markers lead to higher Z values in admixture model with a little variation. Admixture model could incorporate and use ancestral genomic information.

Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes

Although there has been much interest in estimating histories of divergence and admixture from genomic data, it has proved difficult to distinguish recent admixture from long-term structure in the ancestral population. Thus, recent genome-wide analyses based on summary statistics have sparked controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. Here we derive the probability of full mutational configurations in nonrecombining sequence blocks under both admixture and ancestral structure scenarios. Dividing the genome into short blocks gives an efficient way to compute maximum-likelihood estimates of parameters. We apply this likelihood scheme to triplets of human and Neandertal genomes and compare the relative support for a model of admixture from Neandertals into Eurasian populations after their expansion out of Africa against a history of persistent structure in their common ancestral population in Africa. Our analysis allows us to conclusively reject a model of ancestral structure in Africa and instead reveals strong support for Neandertal admixture in Eurasia at a higher rate (3.4-7.3%) than suggested previously. Using analysis and simulations we show that our inference is more powerful than previous summary statistics and robust to realistic levels of recombination.

Characterization of mitochondrial haplogroups in a large population-based sample from the United States

Mitochondrial DNA (mtDNA) haplogroups are valuable for investigations in forensic science, molecular anthropology, and human genetics. In this study, we developed a custom panel of 61 mtDNA markers for high-throughput classification of European, African, and Native American/Asian mitochondrial haplogroup lineages. Using these mtDNA markers, we constructed a mitochondrial haplogroup classification tree and classified 18,832 participants from the National Health and Nutrition Examination Surveys (NHANES). To our knowledge, this is the largest study to date characterizing mitochondrial haplogroups in a population-based sample from the United States, and the first study characterizing mitochondrial haplogroup distributions in self-identified Mexican Americans separately from Hispanic Americans of other descent. We observed clear differences in the distribution of maternal genetic ancestry consistent with proposed admixture models for these subpopulations, underscoring the genetic heterogeneity of the United States Hispanic population. The mitochondrial haplogroup distributions in the other self-identified racial/ethnic groups within NHANES were largely comparable to previous studies. Mitochondrial haplogroup classification was highly concordant with self-identified race/ethnicity (SIRE) in non-Hispanic whites (94.8 %), but was considerably lower in admixed populations including non-Hispanic blacks (88.3 %), Mexican Americans (81.8 %), and other Hispanics (61.6 %), suggesting SIRE does not accurately reflect maternal genetic ancestry, particularly in populations with greater proportions of admixture. Thus, it is important to consider inconsistencies between SIRE and genetic ancestry when performing genetic association studies. The mitochondrial haplogroup data that we have generated, coupled with the epidemiologic variables in NHANES, is a valuable resource for future studies investigating the contribution of mtDNA variation to human health and disease.

Empirical comparison of association and admixture mapping for body weight using F&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; mice data set

Abstract. Recent advances in molecular genetics have provided hundreds of thousands of single nucleotide polymorphisms (SNPs) to detect mutations in genes related with complex traits. Undetected shared ancestry within samples of individuals could lead to the detection of false genomic signals in association mapping. Pedigree-based relationship matrices or genomic relationship matrices could be used in a mixed model to predict and correct for genetic stratifications. Genotypic information of founder populations could also be used to explore patterns of inheritance for complex traits by admixture mapping. An F2 population was created using M16 and ICR mouse lines for studying body weight at 8 weeks of age. Genotypes were collected for 1813 SNPs for each animal, including the founders. Bayesian residuals were used for population stratification in the admixture model. Association and admixture mapping detected similar genomic signals from chromosome 10. Our results provide empirical proof that gene flow from ancestral populations could be traced by admixture mapping with founder genotypes.

Hypothesis Testing in Normal Admixture Models to Detect Heterogeneous Genetic Signals

In this work we consider a three-component normal mixture model in which one component is known to have mean zero and the other two contaminating components have a nonnegative and a no positive mean respectively, while all three components share a common unknown variance parameter. One potential application of this model may be in prioritizing statistical scores obtained in biological experiments, including genetics data. Such a mixture model may be useful in describing the distribution of numerous Z test statistics corresponding to different genes or SNPs, such that a “significant” Z test statistic for a particular gene suggests its connection to a medical condition. More specifically, the inferences drawn from such a mixture model may be useful in a filtration algorithm to remove large subsets of genes or SNPs from consideration, thereby reducing the need for stringent and power-depleting multiplicity adjustments for controlling type I error rates on the remaining genes. We show how to test whether there is contamination in at least one direction (i.e., the mixture model truly requires at least two components) and, if so, how to test whether there is contamination in both directions (i.e., the mixture model truly requires all three components). We assess our testing procedures in simulation studies and illustrate them through application to LOD scores in a genome-wide linkage analysis from an autism study.

A Relaxed Admixture Model of Language Contact

Under conditions of language contact, a language may gain features from its neighbors that it is unlikely to have gained endogenously. We describe a method for evaluating pairs of languages for potential contact by comparing a null hypothesis, in which a target language obtained all its features by inheritance, with an alternative hypothesis in which the target language obtained its features via inheritance and via contact with a proposed donor language. Under the alternative hypothesis, the donor may influence the target to gain features, but not to lose features. When applied to a database of phonological characters in South American languages, this method proves useful for detecting the effects of relatively mild and recent contact, and for highlighting several potential linguistic areas in South America.

Demographic model of admixture predicts symmetric introgression when a species expands into the range of another: A comment on Currat et al. (2008)

A recent model by Currat et al. indicates that when one species colonizes an area already occupied by a closely related species, massive introgression of neutral genes should take place primarily in the direction from the local to the invasive species. Here, I show that this model relies on an assumption that might not capture the true dynamics of how species exchange migrants during admixture. As an alternative, I formulate a new model, based on a different and perhaps more biologically realistic assumption of interbreeding, that demonstrates symmetric introgression as compared to the large and asymmetric introgression predicted by the original model. The new model indicates that asymmetry is not a default property of introgressions, thus necessitating alternative explanations for the common observation of massive asymmetric introgression including sex-biased dispersal.

Likelihood-based inference of population history from low-coveragede novogenome assemblies

Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate between recent, nonequilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida), which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning the Western Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources.

Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers in 236 samples. All estimated loci were very polymorphic indicated by high values of polymorphism information content (from 0.76 in S0225 to 0.92 in Sw2410). Indigenous populations had very high level of genetic diversity (mean He = 0.75); of all indigenous breeds, Lung Pu showed highest mean number of alleles (MNA = 10.1), gene diversity (He = 0.82), allele richness (5.33) and number of private alleles (10). Thirteen percentage of the total genetic variation observed was due to differences among populations. The neighbour-joining dendrogram obtained from Nei's standard genetic distance differentiated eight populations into four groups including Yorkshire, two wild populations, Mong Cai population and a group of four other indigenous populations. The Bayesian clustering with the admixture model implemented in Structure 2.1 indicated seven possible homogenous clusters among eight populations. From 79% (Ha Lang) to 98% (Mong Cai). individuals in indigenous pigs were assigned to their own populations. The results confirmed high level of genetic diversity and shed a new light on genetic structure of Vietnam indigenous pig populations.

Distribution of ancestral chromosomal segments in admixed genomes and its implications for inferring population history and admixture mapping

The ancestral chromosomal segments in admixed genomes are of significant importance for both population history inference and admixture mapping, because they essentially provide the basic information for tracking genetic events. However, the distributions of the lengths of ancestral chromosomal segments (LACS) under some admixture models remain poorly understood. Here we introduced a theoretical framework on the distribution of LACS in two representative admixture models, that is, hybrid isolation (HI) model and gradual admixture (GA) model. Although the distribution of LACS in the GA model differs from that in the HI model, we demonstrated that the mean LACS in the HI model is approximately half of that in the GA model if both admixture proportion and admixture time in the two models are identical. We showed that the theoretical framework greatly facilitated the inference and understanding of population admixture history by analyzing African-American and Mexican empirical data. In addition, we found the peak of association signatures in the HI model was much narrower and sharper than that in the GA model, indicating that the identification of putative causal allele in the HI model is more efficient than that in the GA model. Thus admixture mapping with case-only data would be a reasonable and economical choice in the HI model due to the weak background noise. However, according to our previous studies, many populations are likely to be gradually admixed and have pretty high background linkage disequilibrium. Therefore, we suggest using a case-control approach rather than a case-only approach to conduct admixture mapping to retain the statistics power in recently admixed populations.

ISSR fingerprinting of Coffea arabica throughout Ethiopia reveals high variability in wild populations and distinguishes them from landraces

Forests of SW Ethiopia constitute the native habitat of Coffea arabica and also the place where domestication of Arabica coffee started. Selection from wild populations has led to numerous landraces (farmer’s varieties) and cultivars. Inter-simple sequence repeats (ISSRs) were generated from a representative set of forest coffee populations and landraces across Ethiopia. For the broad diversity assessment, nine di- and tri-nucleotide ISSR primers were applied, as chosen from a total of 102 primers tested initially. Tetranucleotide ISSR primers differed in amplifying fingerprints that could hardly be analysed due to excessive variation. Tree building analysis (NJ, UPGMA) of 84 polymorphic loci amplified for 125 C. arabica individuals provided evidence for several groups of related genotypes occurring in certain geographical areas of Ethiopia and underscored the existence of wild coffee distinct from landraces. Landraces seem to have originated in different geographical areas of Ethiopia in a stepwise domestication process. While the overall geographical signal in the dataset was weak, analysis in a Bayesian framework using the admixture model with geographical priors in STRUCTURE recovered some genetic clustering. Based on Shannon’s diversity index, populations from Yayu (0.47) and Bonga (0.46) showed highest diversity, followed by individuals from Berhane Kontir (0.41). A likely scenario for the differentiation of C. arabica after an allopolyploidization event is that the hierarchical-geographical patterning of wild Coffea genotypes expected from stepwise range extension was obscured by recent or ancient gene flow. The diversity and geographical distribution of autochthonous C. arabica genotypes indicates the need for a multi-site in situ conservation approach.

A model-based ‘varimax’ sampling strategy for a heterogeneous population

Background and aims: Sampling strategies are planned to enhance the homogeneity of a sample, hence to minimize confounding errors. A sampling strategy was developed to minimize the variation within population groups. Karachi, the largest urban agglomeration in Pakistan, was used as a model population.Subjects and methods: Blood groups ABO and Rh factor were determined for 3000 unrelated individuals selected through simple random sampling. Among them five population groups, namely Balochi, Muhajir, Pathan, Punjabi and Sindhi, based on paternal ethnicity were identified. An index was designed to measure the proportion of admixture at parental and grandparental levels. Population models based on index score were proposed. For validation, 175 individuals selected through stratified random sampling were genotyped for the three STR loci CSF1PO, TPOX and TH01.Results: ANOVA showed significant differences across the population groups for blood groups and STR loci distribution. Gene diversity was higher across the sub-population model than in the agglomerated population. At parental level gene diversities are significantly higher across No admixture models than Admixture models. At grandparental level the difference was not significant.Conclusion: A sub-population model with no admixture at parental level was justified for sampling the heterogeneous population of Karachi.

Efficacy of population structure analysis with breeding populations and inbred lines

The objective was to assess by simulation the efficacy of population structure analysis in plant breeding. Twelve populations and 300 inbred lines were simulated and genotyped using 100 microsatellite loci. The experimental material included populations with and without admixture, ancestry relationship and linkage disequilibrium, and with distinct levels of genetic differentiation and effective sizes. The analyses were performed using Structure software and employed all available models. For all the group number (K) tested, for both populations and inbred lines, the admixture model with correlated allelic frequencies provided the highest value for the logarithm of the marginal likelihood. Fitting appropriate model and using adequate sample size for individuals and markers, Structure was effective in identifying the correct population structure, migrants and individuals with genome from distinct populations. The linkage model did not result in an improvement in clustering relative to the admixture model with correlated allelic frequencies. The inclusion of prior information did not change the results; for some K values the analyses showed slight higher values of the marginal likelihood. The reduction in the number of individuals and markers negatively affected the results. There was a high variation in the most probable K value between the evaluated methods.

Reevaluating a model of gender-biased gene flow among Sub-Saharan Hunter-gatherers and farmers.

In a previous study, we proposed a model for genetic admixture between African hunter-gatherers and food producers, in which we integrated demographic and genetic aspects together with ethnographic knowledge (Destro-Bisol et al. 2004b). In that study it was possible to test the model only using genetic information from widely dispersed and genetically heterogeneous populations. Here we reevaluate the congruence between the model and patterns of genetic variation using an anthropologically and geographically more homogeneous data set that includes Pygmies and farmers from Cameroon, Congo, and the Central African Republic. As implied by the model, the ratios of mtDNA to Y chromosome Nm estimates (effective population size, N, times the migration rate, m; 0.154 in Pygmies and 6.759 in farmers), support an asymmetric gene flow, with a higher Bantu-to-Pygmy gene flow for paternal than for maternal lineages, and vice versa for farmers. Analyses of intra- and interpopulation genetic variation further support the above observation, showing a prevailing effect of genetic drift on maternal lineages and gene flow on paternal lineages among Pygmies, and an opposite pattern among farmers. We also detected differences between patterns for classical and molecular measures of Y chromosome intrapopulation variation, which likely represent signatures of the introgression of Bantu lineages into the gene pool of Pygmy populations. On the whole, our results seem to reflect differences in the demographic history and the degree of patrilocality and polygyny between the two population groups, thus providing further support to our microevolutionary model in an anthropologically coherent framework.

Reevaluating a Model of Gender-Biased Gene Flow among Sub-Saharan Hunter-Gatherers and Farmers

In a previous study, we proposed a model for genetic admixture between African hunter-gatherers and food producers, in which we integrated demographic and genetic aspects together with ethnographic knowledge (). In that study it was possible to test the model only using genetic information from widely dispersed and genetically heterogeneous populations. Here we reevaluate the congruence between the model and patterns of genetic variation using an anthropologically and geographically more homogeneous data set that includes Pygmies and farmers from Cameroon, Congo, and the Central African Republic. As implied by the model, the ratios of mtDNA to Y chromosome Nm estimates (effective population size, N, times the migration rate, m; 0.154 in Pygmies and 6.759 in farmers), support an asymmetric gene flow, with a higher Bantu-to-Pygmy gene flow for paternal than for maternal lineages, and vice versa for farmers. Analyses of intra- and interpopulation genetic variation further support the above observation, showing a prevailing effect of genetic drift on maternal lineages and gene flow on paternal lineages among Pygmies, and an opposite pattern among farmers. We also detected differences between patterns for classical and molecular measures of Y chromosome intrapopulation variation, which likely represent signatures of the introgression of Bantu lineages into the gene pool of Pygmy populations. On the whole, our results seem to reflect differences in the demographic history and the degree of patrilocality and polygyny between the two population groups, thus providing further support to our microevolutionary model in an anthropologically coherent framework.