Abstract:In model‐based inference of population structure from individual‐level genetic data, individuals are assigned membership coefficients in a series of statistical clusters generated by clustering algorithms. Distinct patterns of variability in membership coefficients can be produced for different groups of individuals, for example, representing different predefined populations, sampling sites or time periods. Such variability can be difficult to capture in a single numerical value; membership coefficient vectors… Show more
“…Membership proportions for this cluster are highly variable across Cabo Verdean islands, with highest average memberships for Santiago-born individuals (71.45%, SD=10.39%) and Maio (70.39%, SD=5.26%), and lowest for Fogo (48.10%, SD=6.89%) and Brava (50.61%, SD=5.80%). Inter-individual membership variation within Cabo Verde islands, captured as FST/FST max values (49), are significantly different across pairs of islands for 32 out of 36 comparisons (Wilcoxon rank-sum test p <3.96×10 −8 ), with variability across islands ranging from a lowest value of 0.010 in individuals from Santo Antão to a highest value of 0.0519 in Santiago ( Figure 3-figure supplement 1 ).…”
Section: Resultsmentioning
confidence: 99%
“…We plotted each modal result comprising two ADMIXTURE runs or more, for each value of K sepa-50 rately, using DISTRUCT (104). We evaluated within-population variance of individual membership proportions as FST/FST max values using FSTruct (105) with 1000 Bootstrap replicates per population, for the ADMIX-TURE mode result at K=2 (Figure 3-figure supplement 1).…”
Section: B Admixture-clumpp-distruct and F3-admixture Analysesmentioning
confidence: 99%
“…f3-admixture tests of admixture for each Cabo Verdean birth-island, the Barbadian-ACB, and the African-American ASW populations related to the TAST. FST/FST max values were computed using FSTruct (49) with 1000 bootstrap replicates per population. All population pairwise distributions of bootstrap FST/FST max values were significantly different from one another after Bonferroni correction (Wilcoxon two-sided rank sum test p<3.96x10 −8 ), except the following pairwise comparisons: ACB-Santiago, Brava-Maio, Fogo-Sal, and Maio-Santo Antão.…”
Section: Cabo Verde and Other Tast-related Admixed Populations In The...mentioning
From the 15th to the 19th century, the Trans-Atlantic Slave-Trade influenced the genetic and cultural diversity of numerous populations. We explore genomic and linguistic data from the nine islands of Cabo Verde, the earliest European colony of the era in Africa, a major Slave-Trade platform between the 16th and 19th centuries, and a previously uninhabited location ideal for investigating early admixture events between Europeans and Africans. We find that genetic admixture in Cabo Verde occurred primarily between Iberian and Senegambian populations, although forced and voluntary migrations to the archipelago involved numerous other populations. Inter-individual genetic and linguistic variation recapitulate geographic distribution of individuals' birth-places across Cabo Verdean islands, suggesting that Kriolu language variants have developed together with genetic divergences. Furthermore, we find that admixture occurred both early in each island, long before the 18th-century massive TAST deportations triggered by the plantation economy, and after this era. Our results illustrate how shifting socio-cultural relationships between enslaved and non-enslaved communities shaped enslaved-African descendants' descent on both sides of the Atlantic.
“…Membership proportions for this cluster are highly variable across Cabo Verdean islands, with highest average memberships for Santiago-born individuals (71.45%, SD=10.39%) and Maio (70.39%, SD=5.26%), and lowest for Fogo (48.10%, SD=6.89%) and Brava (50.61%, SD=5.80%). Inter-individual membership variation within Cabo Verde islands, captured as FST/FST max values (49), are significantly different across pairs of islands for 32 out of 36 comparisons (Wilcoxon rank-sum test p <3.96×10 −8 ), with variability across islands ranging from a lowest value of 0.010 in individuals from Santo Antão to a highest value of 0.0519 in Santiago ( Figure 3-figure supplement 1 ).…”
Section: Resultsmentioning
confidence: 99%
“…We plotted each modal result comprising two ADMIXTURE runs or more, for each value of K sepa-50 rately, using DISTRUCT (104). We evaluated within-population variance of individual membership proportions as FST/FST max values using FSTruct (105) with 1000 Bootstrap replicates per population, for the ADMIX-TURE mode result at K=2 (Figure 3-figure supplement 1).…”
Section: B Admixture-clumpp-distruct and F3-admixture Analysesmentioning
confidence: 99%
“…f3-admixture tests of admixture for each Cabo Verdean birth-island, the Barbadian-ACB, and the African-American ASW populations related to the TAST. FST/FST max values were computed using FSTruct (49) with 1000 bootstrap replicates per population. All population pairwise distributions of bootstrap FST/FST max values were significantly different from one another after Bonferroni correction (Wilcoxon two-sided rank sum test p<3.96x10 −8 ), except the following pairwise comparisons: ACB-Santiago, Brava-Maio, Fogo-Sal, and Maio-Santo Antão.…”
Section: Cabo Verde and Other Tast-related Admixed Populations In The...mentioning
From the 15th to the 19th century, the Trans-Atlantic Slave-Trade influenced the genetic and cultural diversity of numerous populations. We explore genomic and linguistic data from the nine islands of Cabo Verde, the earliest European colony of the era in Africa, a major Slave-Trade platform between the 16th and 19th centuries, and a previously uninhabited location ideal for investigating early admixture events between Europeans and Africans. We find that genetic admixture in Cabo Verde occurred primarily between Iberian and Senegambian populations, although forced and voluntary migrations to the archipelago involved numerous other populations. Inter-individual genetic and linguistic variation recapitulate geographic distribution of individuals' birth-places across Cabo Verdean islands, suggesting that Kriolu language variants have developed together with genetic divergences. Furthermore, we find that admixture occurred both early in each island, long before the 18th-century massive TAST deportations triggered by the plantation economy, and after this era. Our results illustrate how shifting socio-cultural relationships between enslaved and non-enslaved communities shaped enslaved-African descendants' descent on both sides of the Atlantic.
“…To obtain species abundances, we used the MIDAS 43 species module to map sequencing reads against a database of universal, single-copy bacterial genes. We used these sequencing reads to calculate species abundances, which were used to compute Jensen- Shannon divergence and normalized FST 84 , a metric of compositional variability.…”
Section: Methodsmentioning
confidence: 99%
“…In subject pair XLA-XLB, for example, the gut microbiome of subject XLA is shown and colored based on species and strain sharing with subject XLB. Extended Data Figure 3 Community responses to antibiotic perturbation. a , Antibiotic perturbation increased the compositional variability of the microbiome. Points show the compositional variability of each community calculated at days -28, 0, 7, and 35 using normalized FST 84 (Wilcoxon rank-sum two-sided test, n=48, r=0.63, P=3.3 x 10 - 6 ). b , Antibiotic perturbation caused mostly transient declines in community diversity.…”
Humans constantly encounter new microbes, but few become long-term residents of the adult gut microbiome. Classical theories predict that colonization is determined by the availability of open niches, but it remains unclear whether other ecological barriers limit commensal colonization in natural settings. To disentangle these effects, we used a controlled perturbation with the antibiotic ciprofloxacin to investigate the dynamics of gut microbiome transmission in 22 households of healthy, cohabiting adults. Colonization was rare in three-quarters of antibiotic-taking subjects, whose resident strains rapidly recovered in the week after antibiotics ended. In contrast, the remaining subjects exhibited lasting responses to antibiotics, with extensive species losses and transient expansions of potential opportunistic pathogens. These subjects experienced elevated rates of commensal colonization, but only after long delays: many new colonizers underwent sudden, correlated expansions months after the antibiotic perturbation. Furthermore, strains that had previously transmitted between cohabiting partners rarely recolonized after antibiotic disruptions, showing that colonization displays substantial historical contingency. This work demonstrates that there remain substantial ecological barriers to colonization even after major microbiome disruptions, suggesting that dispersal interactions and priority effects limit the pace of community change.
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