Ancestry-specific recent effective population size in the Americas

Browning, Sharon R.; Browning, Brian L.; Daviglus, Martha L.; Durazo‐Arvizu, Ramón; Schneiderman, Neil; Kaplan, Robert C.; Laurie, Cathy C.

doi:10.1371/journal.pgen.1007385

Cited by 121 publications

(211 citation statements)

References 28 publications

(48 reference statements)

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“…Interestingly, the recovery of the African population component postdates those of the European one, possibly reflecting the different conditions experienced by African slaves and European settlers. On the other hand, the effective population size of the Native American component in Mexicans and Peruvians does not show evidence of decrease, in contrast with historical records reporting a general dramatic decline of the Native American population after European colonization.This observation is in line with Browning et al34 in which a smaller reduction in the effective population size of Mexicans for Native American ancestry compared to other populations was observed. This result is also in line with our GLOBETROTTER results, where we found evidence for admixture between two Native American related sources around 15 generations ago.…”

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confidence: 92%

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The genomic impact of European colonization of the Americas

Ongaro

Scliar

Flores

et al. 2019

Preprint

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The human genetic diversity of the Americas has been shaped by several events of gene flow that have continued since the Colonial Era and the Atlantic slave trade. Moreover, multiple waves of migration followed by local admixture occurred in the last two centuries, the impact of which has been largely unexplored.Here we compiled a genome-wide dataset of ~12,000 individuals from twelve American countries and ~6,000 individuals from worldwide populations and applied haplotype-based methods to investigate how historical movements from outside the New World affected i) the genetic structure, ii) the admixture profile, iii) the demographic history and iv) sex-biased geneflow dynamics, of the Americas.We revealed a high degree of complexity underlying the genetic contribution of European and African populations in North and South America, from both geographic and temporal perspectives, identifying previously unreported sources related to Italy, the Middle East and to specific regions of Africa.

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confidence: 92%

“…al. 34 . Subsequently, we ran the merge-ibd-segments.12Jul18.a0b.jar script to remove breaks and short gaps in the inferred IBD segments (gaps shorter than 0.6cM).…”

Section: Methodsmentioning

confidence: 99%

The genomic impact of European colonization of the Americas

Ongaro

Scliar

Flores

et al. 2019

Preprint

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“…However, we believe this reduction the effective population size, to 64 individuals, is rather unlikely because such a low effective population size is not predicted by our estimates of N e C D B A during the recent bottleneck (N e > 1,000; see Figure 3), nor by the recent genetic estimates of N e in the Americas predicted by Browning and colleagues. 65 Further, historical data suggest that the lowest census population size for just Native Americans was 300 individuals in CO 18 and 1,400 in CR 71 , which is considerably more than 64 individuals, and does not include the unknown number of European and African American individuals. Since we observe considerable amounts of ROHs even in the larger CR population, we conclude that recent consanguineous nonrandom mating was paramount for generating the long ROH that we observed in the Latin American isolates.…”

Section: Determining the Mechanisms That Generate Runs Of Homozygositymentioning

confidence: 99%

Understanding the Hidden Complexity of Latin American Population Isolates

Mooney

Huber

Marsden

et al. 2018

The American Journal of Human Genetics

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Most population isolates examined to date were founded from a single ancestral population. Consequently, there is limited knowledge about the demographic history of admixed population isolates. Here we investigate genomic diversity of recently admixed population isolates from Costa Rica and Colombia and compare their diversity to a benchmark population isolate, the Finnish. These Latin American isolates originated during the 16 th century from admixture between a few hundred European males and Amerindian females, with a limited contribution from African founders. We examine whole-genome sequence data from 449 individuals, ascertained as families to build mutigenerational pedigrees, with a mean sequencing depth of coverage of approximately 363. We find that Latin American isolates have increased genetic diversity relative to the Finnish. However, there is an increase in the amount of identity by descent (IBD) segments in the Latin American isolates relative to the Finnish. The increase in IBD segments is likely a consequence of a very recent and severe population bottleneck during the founding of the admixed population isolates. Furthermore, the proportion of the genome that falls within a long run of homozygosity (ROH) in Costa Rican and Colombian individuals is significantly greater than that in the Finnish, suggesting more recent consanguinity in the Latin American isolates relative to that seen in the Finnish. Lastly, we find that recent consanguinity increased the number of deleterious variants found in the homozygous state, which is relevant if deleterious variants are recessive. Our study suggests that there is no single genetic signature of a population isolate.

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“…Future work using MetHis will allow specifically investigating how effective size changes may influence genetic patterns in the admixed population, a question of major interest as numerous admixed populations are expected to have experienced founding events and/or bottlenecks during their history (e.g. BROWNING et al . 2018).…”

Section: Discussionmentioning

confidence: 99%

Complex genetic admixture histories reconstructed with Approximate Bayesian Computations

Fortes-Lima

Laurent

Thouzeau

et al. 2019

Preprint

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Admixture is a fundamental evolutionary process that has influenced genetic patterns in numerous species. Maximum-likelihood approaches based on allele frequencies and linkage-disequilibrium have been extensively used to infer admixture processes from dense genome-wide datasets mostly in human populations. Nevertheless, complex admixture histories, beyond one or two pulses of admixture, remain methodologically challenging to reconstruct, especially when large datasets are unavailable. We develop an Approximate Bayesian Computations (ABC) framework to reconstruct complex admixture histories from independent genetic markers. We built the software package MetHis to simulate independent SNPs in a two-way admixed population for scenarios with multiple admixture pulses, or monotonically decreasing or increasing admixture at each generation; drawing model-parameter values from prior distributions set by the user. For each simulated dataset, we calculate 24 summary statistics describing genetic diversity and moments of individual admixture fraction. We coupled MetHis with existing ABC algorithms and investigate the admixture history of an African American and a Barbadian population. Results show that Random-Forest ABC scenario-choice, followed by Neural-Network ABC posterior parameter estimation, can distinguish most complex admixture scenarios and provide accurate model-parameter estimations. For both admixed populations, we find that monotonically decreasing contributions over time, from the European and African sources, explain the observed data more accurately than multiple admixture pulses. Furthermore, we find contrasted trajectories of introgression decay from the European and African sources between the two admixed populations. This approach will allow for reconstructing detailed admixture histories in numerous populations and species, particularly when maximum-likelihood methods are intractable.

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Ancestry-specific recent effective population size in the Americas

Cited by 121 publications

References 28 publications

The genomic impact of European colonization of the Americas

The genomic impact of European colonization of the Americas

Understanding the Hidden Complexity of Latin American Population Isolates

Complex genetic admixture histories reconstructed with Approximate Bayesian Computations

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