scholarly journals Assortative mating and the dynamical decoupling of genetic admixture levels from phenotypes that differ between source populations

2019 ◽  
Author(s):  
Jaehee Kim ◽  
Michael D. Edge ◽  
Amy Goldberg ◽  
Noah A. Rosenberg
Keyword(s):  
Assortative Mating ◽  
Genetic Architecture ◽  
Genetic Ancestry ◽  
Genetic Admixture ◽  
Human Populations ◽  
Source Population ◽  
Specific Source ◽  
Admixed Population ◽  
Source Populations ◽  
Over Time

AbstractSource populations for an admixed population can possess distinct patterns of genotype and pheno-type at the beginning of the admixture process. Such differences are sometimes taken to serve as markers of ancestry—that is, phenotypes that are initially associated with the ancestral background in one source population are taken to reflect ancestry in that population. Examples exist, however, in which genotypes or phenotypes initially associated with ancestry in one source population have decoupled from overall admixture levels, so that they no longer serve as proxies for genetic ancestry. We develop a mechanistic model for describing the joint dynamics of admixture levels and phenotype distributions in an admixed population. The approach includes a quantitative-genetic model that relates a phenotype to underlying loci that affect its trait value. We consider three forms of mating. First, individuals might assort in a manner that is independent of the overall genetic admixture level. Second, individuals might assort by a quantitative phenotype that is initially correlated with the genetic admixture level. Third, individuals might assort by the genetic admixture level itself. Under the model, we explore the relationship between genetic admixture level and phenotype over time, studying the effect on this relationship of the genetic architecture of the phenotype. We find that the decoupling of genetic ancestry and phenotype can occur surprisingly quickly, especially if the phenotype is driven by a small number of loci. We also find that positive assortative mating attenuates the process of dissociation in relation to a scenario in which mating is random with respect to genetic admixture and with respect to phenotype. The mechanistic framework suggests that in an admixed population, a trait that initially differed between source populations might be a reliable proxy for ancestry for only a short time, especially if the trait is determined by relatively few loci. The results are potentially relevant in admixed human populations, in which phenotypes that have a perceived correlation with ancestry might have social significance as ancestry markers, despite declining correlations with ancestry over time.Author SummaryAdmixed populations are populations that descend from two or more populations that had been separated for a long time at the beginning of the admixture process. The source populations typically possess distinct patterns of genotype and phenotype. Hence, early in the admixture process, phenotypes of admixed individuals can provide information about the extent to which these individuals possess ancestry in a specific source population. To study correlations between admixture levels and phenotypes that differ between source populations, we construct a genetic and phenotypic model of the dynamical process of admixture. Under the model, we show that correlations between admixture levels and these phenotypes dissipate over time—especially if the genetic architecture of the phenotypes involves only a small number of loci, or if mating in the admixed population is random with respect to both the admixture levels and the phenotypes. The result has the implication that a trait that once reflected ancestry in a specific source population might lose this ancestry correlation. As a consequence, in human populations, after a sufficient length of time, salient phenotypes that can have social meaning as ancestry markers might no longer bear any relationship to genome-wide genetic ancestry.

scholarly journals Autosomal admixture levels are informative about sex bias in admixed populations

2014 ◽  
Author(s):  
Amy Goldberg ◽  
Paul Verdu ◽  
Noah A Rosenberg
Keyword(s):  
Sex Chromosomes ◽  
Sex Bias ◽  
Source Population ◽  
Effective Population ◽  
History Of ◽  
Specific Source ◽  
Unequal Number ◽  
Admixed Population ◽  
Source Populations

AbstractSex-biased admixture has been observed in a wide variety of admixed populations. Genetic variation in sex chromosomes and ratios of quantities computed from sex chromosomes and autosomes have often been examined in order to infer patterns of sex-biased admixture, typically using statistical approaches that do not mechanistically model the complexity of a sex-specific history of admixture. Here, expanding on a model of Verdu & Rosenberg (2011) that did not include sex specificity, we develop a model that mechanistically examines sex-specific admixture histories. Under the model, multiple source populations contribute to an admixed population, potentially with their male and female contributions varying over time. In an admixed population descended from two source groups, we derive the moments of the distribution of the autosomal admixture fraction from a specific source population as a function of sex-specific introgression parameters and time. Considering admixture processes that are constant in time, we demonstrate that surprisingly, although the mean autosomal admixture fraction from a specific source population does not reveal a sex bias in the admixture history, the variance of autosomal admixture is informative about sex bias. Specifically, the long-term variance decreases as the sex bias from a contributing source population increases. This result can be viewed as analogous to the reduction in effective population size for populations with an unequal number of breeding males and females. Our approach can contribute to methods for inference of the history of complex sex-biased admixture processes by enabling consideration of the effect of sex-biased admixture on autosomal DNA.

scholarly journals The genomic signatures of natural selection in admixed human populations

2021 ◽  
Author(s):  
Sebastian Cuadros-Espinoza ◽  
Guillaume Laval ◽  
Lluís Quintana-Murci ◽  
Etienne Patin
Keyword(s):  
Natural Selection ◽  
Human Populations ◽  
Genomic Signatures ◽  
Local Environments ◽  
Admixed Population ◽  
Resistance To Infection ◽  
Source Populations ◽  
Neutral Mutations ◽  
New Evidence

Admixture has been a pervasive phenomenon in human history, shaping extensively the patterns of population genetic diversity. There is increasing evidence to suggest that admixture can also facilitate genetic adaptation to local environments, i.e., admixed populations acquire beneficial mutations from source populations, a process that we refer to as adaptive admixture. However, the role of adaptive admixture in human evolution and the power to detect it are poorly characterized. Here, we use extensive computer simulations to evaluate the power of several neutrality statistics to detect natural selection in the admixed population, accounting for background selection and assuming different admixture scenarios. We show that two statistics based on admixture proportions, F_adm and LAD, show high power to detect mutations that are beneficial in the admixed population, whereas iHS and F_ST falsely detect neutral mutations that have been selected in the source populations only. By combining F_adm and LAD into a single statistic, we scanned the genomes of 15 worldwide, admixed populations for signatures of adaptive admixture. We confirm that lactase persistence and resistance to malaria have been under adaptive admixture in West Africa and in Madagascar, North Africa and South Asia, respectively. Our approach also uncovers new cases of adaptive admixture, including the APOL1 / MYH9 locus in the Fulani nomads and PKN2 in East Indonesians, involved in resistance to infection and metabolism, respectively. Collectively, our study provides new evidence that adaptive admixture has occurred in multiple human populations, whose genetic history is characterized by periods of isolation and spatial expansions resulting in increased gene flow.

scholarly journals Genetic and phenotypic changes in an Atlantic salmon population supplemented with non-local individuals: a longitudinal study over 21 years

2015 ◽  
Vol 282 (1802) ◽  
pp. 20142765 ◽  
Author(s):  
Sabrina Le Cam ◽  
Charles Perrier ◽  
Anne-Laure Besnard ◽  
Louis Bernatchez ◽  
Guillaume Evanno
Keyword(s):  
Genetic Diversity ◽  
Life History ◽  
Atlantic Salmon ◽  
Life History Traits ◽  
Genetic Admixture ◽  
Phenotypic Traits ◽  
Source Population ◽  
Wild Populations ◽  
Non Local ◽  
Source Populations

While introductions and supplementations using non-native and potentially domesticated individuals may have dramatic evolutionary effects on wild populations, few studies documented the evolution of genetic diversity and life-history traits in supplemented populations. Here, we investigated year-to-year changes from 1989 to 2009 in genetic admixture at 15 microsatellite loci and in phenotypic traits in an Atlantic salmon ( Salmo salar ) population stocked during the first decade of this period with two genetically and phenotypically distinct source populations. We detected a pattern of temporally increasing introgressive hybridization between the stocked population and both source populations. The proportion of fish returning to the river after a single winter at sea ( versus several ones) was higher in fish assigned to the main source population than in local individuals. Moreover, during the first decade of the study, both single-sea-winter and multi-sea-winter (MSW) fish assigned to the main source population were smaller than local fish. During the second decade of the study, MSW fish defined as hybrids were lighter and smaller than fish from parental populations, suggesting outbreeding depression. Overall, this study suggests that supplementation with non-local individuals may alter not only the genetic diversity of wild populations but also life-history traits of adaptive significance.

scholarly journals On the heterozygosity of an admixed population

2019 ◽  
Author(s):  
Simina M. Boca ◽  
Lucy Huang ◽  
Noah A. Rosenberg
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Genetic Variants ◽  
Simulated Data ◽  
Source Population ◽  
Admixed Population ◽  
Source Populations ◽  
Special Case

A population is termed admixed if its members possess recent ancestry from two or more separate sources. As a result of the fusion of source populations with different genetic variants, admixed populations can exhibit high levels of genetic variation, reflecting contributions of their multiple ancestral groups. For a model of an admixed population derived from K source groups, we obtain a relationship between its level of genetic variation, as measured by heterozygosity, and its proportions of admixture from the various source populations. We show that the heterozygosity of the admixed population is at least as great as that of the least heterozygous source population, and that it potentially exceeds the heterozygosities of all of the source populations. The admixture proportions that maximize the heterozygosity possible for an admixed population formed from a specified set of source populations are also obtained under specific conditions. We examine the special case of K = 2 source populations in detail, characterizing the maximal admixture in terms of the heterozygosities of the two source populations and the value of FST between them. In this case, the heterozygosity of the admixed population exceeds the maximal heterozygosity of the source groups if the divergence between them, measured by FST, is large enough, namely above a certain bound that is a function of the heterozygosities of the source groups. We present applications to simulated data as well as to data from human admixture scenarios, providing results useful for interpreting the properties of genetic variability in admixed populations.

scholarly journals Assortative mating by population of origin in a mechanistic model of admixture

2019 ◽  
Author(s):  
Amy Goldberg ◽  
Ananya Rastogi ◽  
Noah A Rosenberg
Keyword(s):  
Assortative Mating ◽  
Mechanistic Model ◽  
Random Mating ◽  
Population History ◽  
Source Population ◽  
Mating Preferences ◽  
Positive Assortative Mating ◽  
Special Cases ◽  
Mating Population ◽  
Over Time

AbstractPopulations whose mating pairs have levels of similarity in phenotypes or genotypes that differ systematically from the level expected under random mating are described as experiencing assortative mating. Excess similarity in mating pairs is termed positive assortative mating, and excess dissimilarity is negative assortative mating. In humans, empirical studies suggest that mating pairs from various admixed populations—whose ancestry derives from two or more source populations—possess correlated ancestry components that indicate the occurrence of positive assortative mating on the basis of ancestry. Generalizing a two-sex mechanistic admixture model, we devise a model of one form of ancestry-assortative mating that occurs through preferential mating based on source population. Under the model, we study the moments of the admixture fraction distribution for different assumptions about mating preferences, including both positive and negative assortative mating by population. We consider the special cases of assortative mating by population that involve a single admixture event and that consider a model of constant contributions to the admixed population over time. We demonstrate that whereas the mean admixture under assortative mating is equivalent to that of a corresponding randomly mating population, the variance of admixture depends on the level and direction of assortative mating. In contrast to standard settings in which positive assortment increases variation within a population, certain assortative mating scenarios allow the variance of admixture to decrease relative to a corresponding randomly mating population: with the three populations we consider, the variance-increasing effect of positive assortative mating within a population might be overwhelmed by a variance-decreasing effect emerging from mating preferences involving other pairs of populations. The effect of assortative mating is smaller on the X chromosome than the autosomes because inheritance of the X in males depends only on the mother’s ancestry, not on the mating pair. Because the variance of admixture is informative about the timing of admixture and possibly about sex-biased admixture contributions, the effects of assortative mating are important to consider in inferring features of population history from distributions of admixture values. Our model provides a framework to quantitatively study assortative mating under flexible scenarios of admixture over time.

scholarly journals The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium

2016 ◽  
Author(s):  
Noah Zaitlen ◽  
Scott Huntsman ◽  
Donglei Hu ◽  
Melissa Spear ◽  
Celeste Eng ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
African Americans ◽  
Assortative Mating ◽  
Random Mating ◽  
Historical Narrative ◽  
Model Complexity ◽  
Human Populations ◽  
Local Ancestry ◽  
Admixed Population ◽  
Demographic Inference

1AbstractStatistical models in medical and population genetics typically assume that individuals assort randomly in a population. While this simplifies model complexity, it contradicts an increasing body of evidence of non-random mating in human populations. Specifically, it has been shown that assortative mating is significantly affected by genomic ancestry. In this work we examine the effects of ancestry-assortative mating on the linkage disequilibrium between local ancestry tracks of individuals in an admixed population. To accomplish this, we develop an extension to the Wright-Fisher model that allows for ancestry based assortative mating. We show that ancestry-assortment perturbs the distribution of local ancestry linkage disequilibrium (LAD) and the variance of ancestry in a population as a function of the number of generations since admixture. This assortment effect can induce errors in demographic inference of admixed populations when methods assume random mating. We derive closed form formulae for LAD under an assortative-mating model with and without migration. We observe that LAD depends on the correlation of global ancestry of couples in each generation, the migration rate of each of the ancestral populations, the initial proportions of ancestral populations, and the number of generations since admixture. We also present the first evidence of ancestry-assortment in African Americans and examine LAD in simulated and real admixed population data of African Americans. We find that demographic inference under the assumption of random mating significantly underestimates the number of generations since admixture, and that accounting for assortative mating using the patterns of LAD results in estimates that more closely agrees with the historical narrative.

scholarly journals Effect of first-line biologic initiation on glucocorticoid exposure in children hospitalized with new-onset systemic juvenile idiopathic arthritis: emulation of a pragmatic trial using observational data

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Rosemary G. Peterson ◽  
Rui Xiao ◽  
Hannah Katcoff ◽  
Brian T. Fisher ◽  
Pamela F. Weiss
Keyword(s):  
Juvenile Idiopathic Arthritis ◽  
Biologic Therapy ◽  
Tertiary Care ◽  
Pragmatic Trial ◽  
Systemic Juvenile Idiopathic Arthritis ◽  
Source Population ◽  
First Line ◽  
Eligibility Criteria ◽  
Over Time ◽  
New Onset

Abstract Background Glucocorticoid exposure is a significant driver of morbidity in children with systemic juvenile idiopathic arthritis (sJIA). We determined the effect of early initiation of biologic therapy (IL-1 or IL-6 inhibition) on glucocorticoid exposure in hospitalized patients with new-onset sJIA. Methods We emulated a pragmatic sequence of trials (“pseudo-trials”) of biologic initiation in children (≤ 18 years) hospitalized with new-onset sJIA utilizing retrospective data from an administrative database from 52 tertiary care children’s hospitals from 2008 to 2019. Eligibility window, treatment assignment and start of follow-up between biologic and non-biologic study arms were aligned for each pseudo-trial. Patients in the source population could meet eligibility criteria at several timepoints. Mixed-effects logistic regression was used to determine the effect of biologic initiation on in-hospital glucocorticoid exposure. Results Four hundred sixty-eight children met eligibility criteria, of which 19% received biologic therapy without preceding or concomitant initiation of immunomodulatory medications. This proportion significantly increased over time during the study period (p <  0.01). 1451 trial subjects were included across 4 pseudo-trials with 71 assigned to the biologic arm and 1380 assigned to the non-biologic arm. After adjustment, there was a trend toward decreased odds of glucocorticoid initiation in the biologic arm compared to the non-biologic arm (OR 0.39, 95% CI [0.13, 1.15]). Conclusion Biologic initiation in children hospitalized with new-onset sJIA significantly increased over time and may be associated with reduced glucocorticoid exposure. The increasing use of first-line biologic therapy may lead to clinically relevant reductions in treatment-related adverse effects of glucocorticoid-reliant therapeutic approaches.

scholarly journals Association of serum lipid components and obesity with genetic ancestry in an admixed population of elderly women

2012 ◽  
Vol 35 (3) ◽  
pp. 575-582 ◽  
Author(s):  
Tulio C. Lins ◽  
Alause S. Pires ◽  
Roberta S. Paula ◽  
Clayton F. Moraes ◽  
Rodrigo G. Vieira ◽  
...  
Keyword(s):  
Serum Lipid ◽  
Elderly Women ◽  
Genetic Ancestry ◽  
Admixed Population ◽  
Lipid Components

scholarly journals Positive Selection Affects the Expression of Systemic Lupus Erythematosus Associated Loci in Human Populations

2021 ◽  
Author(s):  
Victoria Oberreiter ◽  
Tobias Goellner ◽  
David L. Morris ◽  
Helmut Schaschl
Keyword(s):  
Gene Expression ◽  
Systemic Lupus Erythematosus ◽  
Positive Selection ◽  
Lupus Erythematosus ◽  
Lifestyle Changes ◽  
Genetic Ancestry ◽  
Selection Function ◽  
Human Populations ◽  
Systemic Lupus ◽  
A Genome

Abstract Background: Systemic lupus erythematosus (SLE) shows marked population-specific disparities in disease prevalence, including substantial variation in manifestations and complications according to genetic ancestry. Several recent studies suggest that a substantial proportion of variation of gene expression shows genetic ancestry-associated differences in gene regulation on immune responses. Positive selection may act in a population-specific manner on expression quantitative trait loci (eQTLs) and thereby contributes to the difference in the differences of SLE prevalence and manifestation in human populations. We tested the hypothesises that some of the identified SLE risk polymorphisms display pleiotropic effects or polygenicity driven by positive selection. We performed a genome-wide scan for recent positive selection by using integrated Haplotype Score (iHS) statistics in different human populations. In addition, we estimated the timing of beneficial mutations to understand what possible selective pressures drive positive selection at SLE-associated loci. Results: We identified several SLE risk loci that are population-specifically under positive selection. Almost all SNPs that are under positive selection function as cis-eQTLs in different tissue types. We determined that adaptive eQTLs affect the expression of fewer genes than non-adaptive eQTLs, suggesting a limited range of effect of an eQTL at SLE risk sites that show signatures of positive selection. Furthermore, some positively selected SNPs are located in transcription factor binding sequences. The timing of positive selection for the studied loci suggests that both environmental and recent lifestyle changes during as well as after the Neolithic Transition may have become selectively effective. We propose a novel link between positively selected eQTLs at a certain SLE risk locus in Europeans and a physiological pathway not previously considered in SLE.Conclusions: We conclude that population-specific adaptive eQTLs contribute to the observed variation in specific manifestations and complications of SLE in different ethnicities. Our results suggest also that human populations adapt more rapidly to environmental and lifestyle stimuli via modification of gene expression without having to alter the genetic code.

scholarly journals Putting RFMix and ADMIXTURE to the test in a complex admixed population

2020 ◽  
Author(s):  
Caitlin Uren ◽  
Eileen G. Hoal ◽  
Marlo Möller
Keyword(s):  
World Wide ◽  
Association Studies ◽  
Structured Populations ◽  
Human Populations ◽  
Computational Tools ◽  
Association Analyses ◽  
Local Ancestry ◽  
Diverse World ◽  
Admixed Population ◽  
Global And Local

Abstract Background Global and local ancestry inference in admixed human populations can be performed using computational tools implementing distinct algorithms. The development and resulting accuracy of these tools has been tested largely on populations with relatively straightforward admixture histories but little is known about how well they perform in more complex admixture scenarios. Results Using simulations, we show that RFMix outperforms ADMIXTURE in determining global ancestry proportions even in a complex 5-way admixed population, in addition to assigning local ancestry with an accuracy of 89%. The ability of RFMix to determine global and local ancestry to a high degree of accuracy, particularly in admixed populations provides the opportunity for more accurate association analyses. Conclusion This study highlights the utility of the extension of computational tools to become more compatible to genetically structured populations, as well as the need to expand the sampling of diverse world-wide populations. This is particularly noteworthy as modern-day societies are becoming increasingly genetically complex and some genetic tools and commonly used ancestral populations are less appropriate. Based on these caveats and the results presented here, we suggest that RFMix be used for both global and local ancestry estimation in world-wide complex admixture scenarios particularly when including these estimates in association studies.

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