scholarly journals On the distribution of tract lengths during adaptive introgression

2019 ◽  
Author(s):  
Vladimir Shchur ◽  
Jesper Svedberg ◽  
Paloma Medina ◽  
Russ Corbett-Detig ◽  
RASMUS Nielsen
Keyword(s):  
Linkage Disequilibrium ◽  
Natural Selection ◽  
Positive Selection ◽  
Allele Frequency ◽  
Genetic Drift ◽  
Evolutionary Genetics ◽  
Logistic Function ◽  
Adaptive Introgression ◽  
Selective Neutrality ◽  
Admixture Linkage Disequilibrium

ABSTRACTAdmixture is increasingly being recognized as an important factor in evolutionary genetics. The distribution of genomic admixture tracts, and the resulting effects on admixture linkage disequilibrium, can be used to date the timing of admixture between species or populations. However, the theory used for such prediction assumes selective neutrality despite the fact that many famous examples of admixture involve natural selection acting for or against admixture. In this paper, we investigate the effects of positive selection on the distribution of tract lengths. We develop a theoretical framework that relies on approximating the trajectory of the selected allele using a logistic function. By numerically calculating the expected allele trajectory, we also show that the approach can be extended to cases where the logistic approximation is poor due to the effects of genetic drift. Using simulations, we show that the model is highly accurate under most scenarios. We use the model to show that positive selection on average will tend to increase the admixture tract length. However, perhaps counter-intuitively, conditional on the allele frequency at the time of sampling, positive selection will actually produce shorter expected tract lengths. We discuss the consequences of our results in interpreting the timing of the introgression of EPAS1 from Denisovans into the ancestors of Tibetans.

scholarly journals On the Distribution of Tract Lengths During Adaptive Introgression

2020 ◽  
Vol 10 (10) ◽  
pp. 3663-3673 ◽  
Author(s):  
Vladimir Shchur ◽  
Jesper Svedberg ◽  
Paloma Medina ◽  
Russell Corbett-Detig ◽  
Rasmus Nielsen
Keyword(s):  
Linkage Disequilibrium ◽  
Natural Selection ◽  
Positive Selection ◽  
Allele Frequency ◽  
Genetic Drift ◽  
Evolutionary Genetics ◽  
Logistic Function ◽  
Adaptive Introgression ◽  
Selective Neutrality ◽  
Admixture Linkage Disequilibrium

Admixture is increasingly being recognized as an important factor in evolutionary genetics. The distribution of genomic admixture tracts, and the resulting effects on admixture linkage disequilibrium, can be used to date the timing of admixture between species or populations. However, the theory used for such prediction assumes selective neutrality despite the fact that many famous examples of admixture involve natural selection acting for or against admixture. In this paper, we investigate the effects of positive selection on the distribution of tract lengths. We develop a theoretical framework that relies on approximating the trajectory of the selected allele using a logistic function. By numerically calculating the expected allele trajectory, we also show that the approach can be extended to cases where the logistic approximation is poor due to the effects of genetic drift. Using simulations, we show that the model is highly accurate under most scenarios. We use the model to show that positive selection on average will tend to increase the admixture tract length. However, perhaps counter-intuitively, conditional on the allele frequency at the time of sampling, positive selection will actually produce shorter expected tract lengths. We discuss the consequences of our results in interpreting the timing of the introgression of EPAS1 from Denisovans into the ancestors of Tibetans.

scholarly journals Evolution of gene regulatory networks by means of selection and random genetic drift

2018 ◽  
Author(s):  
Antonios Kioukis ◽  
Pavlos Pavlidis
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Genetic Drift ◽  
Regulatory Networks ◽  
Fitness Landscape ◽  
Random Genetic Drift ◽  
Maturation Period ◽  
Evolutionary Forces ◽  
Gene Regulatory

The evolution of a population by means of genetic drift and natural selection operating on a gene regulatory network (GRN) of an individual has not been scrutinized in depth. Thus, the relative importance of various evolutionary forces and processes on shaping genetic variability in GRNs is understudied. Furthermore, it is not known if existing tools that identify recent and strong positive selection from genomic sequences, in simple models of evolution, can detect recent positive selection when it operates on GRNs. Here, we propose a simulation framework, called EvoNET, that simulates forward-in-time the evolution of GRNs in a population. Since the population size is finite, random genetic drift is explicitly applied. The fitness of a mutation is not constant, but we evaluate the fitness of each individual by measuring its genetic distance from an optimal genotype. Mutations and recombination may take place from generation to generation, modifying the genotypic composition of the population. Each individual goes through a maturation period, where its GRN reaches equilibrium. At the next step, individuals compete to produce the next generation. As time progresses, the beneficial genotypes push the population higher in the fitness landscape. We examine properties of the GRN evolution such as robustness against the deleterious effect of mutations and the role of genetic drift. We confirm classical results from Andreas Wagner’s work that GRNs show robustness against mutations and we provide new results regarding the interplay between random genetic drift and natural selection.

scholarly journals Signatures of archaic adaptive introgression in present-day human populations

2016 ◽  
Author(s):  
Fernando Racimo ◽  
Davide Marnetto ◽  
Emilia Huerta-Sánchez
Keyword(s):  
Positive Selection ◽  
Candidate Genes ◽  
Allele Frequency ◽  
Human Populations ◽  
Haplotype Structure ◽  
Promising Candidate ◽  
Adaptive Introgression ◽  
1000 Genomes ◽  
Evolutionary Advantage ◽  
Mutation And Selection

AbstractComparisons of DNA from archaic and modern humans show that these groups interbred, and in some cases received an evolutionary advantage from doing so. This process - adaptive introgression - may lead to a faster rate of adaptation than is predicted from models with mutation and selection alone. Within the last couple of years, a series of studies have identified regions of the genome that are likely examples of adaptive introgression. In many cases, once a region was ascertained as being introgressed, commonly used statistics based on both haplotype as well as allele frequency information were employed to test for positive selection. Introgression by itself, however, changes both the haplotype structure and the distribution of allele frequencies, thus confounding traditional tests for detecting positive selection. Therefore, patterns generated by introgression alone may lead to false inferences of positive selection. Here we explore models involving both introgression and positive selection to investigate the behavior of various statistics under adaptive introgression. In particular, we find that the number and allelic frequencies of sites that are uniquely shared between archaic humans and specific present-day populations are particularly useful for detecting adaptive introgression. We then examine the 1000 Genomes dataset to characterize the landscape of uniquely shared archaic alleles in human populations. Finally, we identify regions that were likely subject to adaptive introgression and discuss some of the most promising candidate genes located in these regions.

Regions on Chromosomes 1 and 14 Are Associated with VWF:Ag Levels in African Americans Using Mapping By Admixture Linkage Disequilibrium

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 2840-2840
Author(s):  
Andrew D Paterson ◽  
Nicole M Roslin ◽  
Pamela A. Christopherson ◽  
Daniel B Bellissimo ◽  
Veronica H Flood ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
African Americans ◽  
Allele Frequency ◽  
Ethnic Differences ◽  
Small Sample ◽  
European Ancestry ◽  
Ancestral Population ◽  
Genome Wide ◽  
Linkage And Association Analysis ◽  
Admixture Linkage Disequilibrium

Abstract Background: VWF:Ag is highly heritable, however, despite genome-wide linkage and association analysis, mostly in European derived populations, the genetic basis for VWF levels is only partially understood. African Americans (AfAm) have significantly higher VWF:Ag than European Americans: although variants in VWF and ABO can account for some of this, it is not clear whether they explain all of this ethnic difference. A powerful method to identify chromosomal regions that account for ethnic differences is mapping by admixture linkage disequilibrium (MALD). MALD uses markers that differ markedly in allele frequency between ancestral populations, estimates the global ancestry for each individual, and compares local ancestry between subjects with different trait values to global estimates to identify regions of the genome that account for the ethnic differences of a trait. Hypothesis: Loci that are associated with VWF:Ag levels in AfAm can be mapped using MALD. Methods: From 188 AfAm healthy volunteers from the Zimmerman Program for the Molecular and Clinical Biology of VWD, 96 were selected to have 98≤VWF:Ag≥ 164 IU which represent the <25% and >75% of VWF:Ag distribution. They were genotyped using Illumina HumanCoreExome genome-wide SNP chip. SNPs were selected for MALD if they had allele frequency difference between ancestral population (YRI and CEU from HapMap) of >0.4. Related and non-admixed individuals were excluded. Extreme trait analysis was performed using ADMIXMAP. Results: 16 males and 68 females (mean age 41 years, SD=13) of whom 41 had with Ag≤98and 43 with Ag ≥164 IU were subjected to analysis with 2254 ancestry informative markers across the genome with a mean spacing of 1.8 cM (1.3 Mb). Estimated African ancestry was 79% (SD=13%, range 24-96%), while European ancestry was 20% (SD=12%, range 4-72%). Comparing the subjects at extremes of VWF, regions on chrs 1 (110-147 Mb) and 14 (22-40 Mb) had |Z| scores >3 (p<0.0025) which is the conventional cut-off in MALD studies. At chrs 1 and 14, greater African admixture was associated with higher VWF:Ag, consistent with the expected direction. No significant admixture signal was observed at the VWF (p=0.39) or ABO (p=0.48) loci, which may represent low power due to small sample size. Discussion: These pilot results require replication in a larger number of independent subjects, as well as fine-mapping to identify the underlying variants responsible for differences in VWF between individuals. Disclosures No relevant conflicts of interest to declare.

scholarly journals Positive natural selection in primate genes of the type I interferon response

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Elena N. Judd ◽  
Alison R. Gilchrist ◽  
Nicholas R. Meyerson ◽  
Sara L. Sawyer
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Type I Interferon ◽  
Interferon Response ◽  
Type I ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Interferon Stimulated Genes ◽  
Interferon Induction

Abstract Background The Type I interferon response is an important first-line defense against viruses. In turn, viruses antagonize (i.e., degrade, mis-localize, etc.) many proteins in interferon pathways. Thus, hosts and viruses are locked in an evolutionary arms race for dominance of the Type I interferon pathway. As a result, many genes in interferon pathways have experienced positive natural selection in favor of new allelic forms that can better recognize viruses or escape viral antagonists. Here, we performed a holistic analysis of selective pressures acting on genes in the Type I interferon family. We initially hypothesized that the genes responsible for inducing the production of interferon would be antagonized more heavily by viruses than genes that are turned on as a result of interferon. Our logic was that viruses would have greater effect if they worked upstream of the production of interferon molecules because, once interferon is produced, hundreds of interferon-stimulated proteins would activate and the virus would need to counteract them one-by-one. Results We curated multiple sequence alignments of primate orthologs for 131 genes active in interferon production and signaling (herein, “induction” genes), 100 interferon-stimulated genes, and 100 randomly chosen genes. We analyzed each multiple sequence alignment for the signatures of recurrent positive selection. Counter to our hypothesis, we found the interferon-stimulated genes, and not interferon induction genes, are evolving significantly more rapidly than a random set of genes. Interferon induction genes evolve in a way that is indistinguishable from a matched set of random genes (22% and 18% of genes bear signatures of positive selection, respectively). In contrast, interferon-stimulated genes evolve differently, with 33% of genes evolving under positive selection and containing a significantly higher fraction of codons that have experienced selection for recurrent replacement of the encoded amino acid. Conclusion Viruses may antagonize individual products of the interferon response more often than trying to neutralize the system altogether.

SHOULD INDIVIDUAL FITNESS INCREASE WITH HETEROZYGOSITY?

Genetics ◽  
1983 ◽  
Vol 104 (1) ◽  
pp. 191-209
Author(s):  
Michael Turelli ◽  
Lev R Ginzburg
Keyword(s):  
Linkage Disequilibrium ◽  
Natural Selection ◽  
Empirical Literature ◽  
Correlated Traits ◽  
Individual Fitness ◽  
Stable Product ◽  
Theoretical Results ◽  
Average Fitness

ABSTRACT Natural selection influences not only gamete frequencies in populations but also the multilocus fitness structures associated with segregating gametes. In particular, only certain patterns of multilocus fitnesses are consistent with the maintenance of stable multilocus polymorphisms. This paper offers support for the proposition that, at stable, viability-maintained, multilocus polymorphisms, the fitness of a genotype tends to increase with the number of heterozygous loci it contains. Average fitness always increases with heterozygosity at stable product equilibria (i.e., those without linkage disequilibrium) maintained by either additive or multiplicative fitness schemes. Simulations suggest that it "generally" increases for arbitrary fitness schemes. The empirical literature correlating allozyme heterozygosity with fitness-correlated traits is discussed in the light of these and other theoretical results.

scholarly journals Inferring Linkage Disequilibrium Between a Polymorphic Marker Locus and a Trait Locus in Natural Populations

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 457-467 ◽  
Author(s):  
Z W Luo ◽  
S H Tao ◽  
Z-B Zeng
Keyword(s):  
Linkage Disequilibrium ◽  
Allele Frequency ◽  
Random Mating ◽  
Natural Populations ◽  
Polymorphic Marker ◽  
Marker Locus ◽  
Model Parameters ◽  
Phenotypic Variance ◽  
Wide Range ◽  
Trait Locus

Abstract Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.

scholarly journals X-chromosomal STR based genetic polymorphisms and demographic history of Sri Lankan ethnicities and their relationship with global populations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nandika Perera ◽  
Gayani Galhena ◽  
Gaya Ranawaka
Keyword(s):  
Allele Frequency ◽  
Demographic History ◽  
Evolutionary Genetics ◽  
Haplotype Frequency ◽  
Allele Frequency Distribution ◽  
Sri Lankan ◽  
Frequency Distributions ◽  
Autosomal Str ◽  
History Of ◽  
Multiplex System

AbstractA new 16 X-short tandem repeat (STR) multiplex PCR system has recently been developed for Sr Lankans, though its applicability in evolutionary genetics and forensic investigations has not been thoroughly assessed. In this study, 838 unrelated individuals covering all four major ethnic groups (Sinhalese, Sri Lankan Tamils, Indian Tamils and Moors) in Sri Lanka were successfully genotyped using this new multiplex system. The results indicated a high forensic efficiency for the tested loci in all four ethnicities confirming its suitability for forensic applications of Sri Lankans. Allele frequency distribution of Indian Tamils showed subtle but statistically significant differences from those of Sinhalese and Moors, in contrast to frequency distributions previously reported for autosomal STR alleles. This suggest a sex biased demographic history among Sri Lankans requiring a separate X-STR allele frequency database for Indian Tamils. Substantial differences observed in the patterns of LD among the four groups demand the use of a separate haplotype frequency databases for each individual ethnicity. When analysed together with other 14 world populations, all Sri Lankan ethnicities except Indian Tamils clustered closely with populations from Indian Bhil tribe, Bangladesh and Europe reflecting their shared Indo-Aryan ancestry.

scholarly journals The genetics of Dacus oleae: III. Amount of variation at two esterase loci in a Greek population

1969 ◽  
Vol 14 (3) ◽  
pp. 249-258 ◽  
Author(s):  
E. Zouros ◽  
C. B. Krimbas
Keyword(s):  
Allele Frequency ◽  
Fruit Fly ◽  
Olive Fruit Fly ◽  
Allele Frequency Distribution ◽  
Natural Conditions ◽  
Dacus Oleae ◽  
Random Drift ◽  
Selective Neutrality ◽  
Esterase Loci ◽  
Silent Allele

Two polymorphic esterase loci, EstA and EstB, of the olive-fruit fly Dacus oleae were studied in a natural population. The analysis of about 500 individuals revealed the presence of 15 alleles for EstA and 12 alleles for EstB. A ‘silent’ allele was found segregating at both loci. Segregation data for most of the alleles are presented. The allele frequency distribution follows the same pattern at both loci: one allele of each gene has a frequency of nearly 0·50, a few have frequencies between 0·05 and 0·15 and many are below 0·05. Two main hypotheses, those of overdominance and selective neutrality, were examined in order to explain these polymorphisms. We deduced that under both hypotheses a relatively high mutation rate is necessary to balance the result of random drift. This rate was estimated to be higher than 4 × 10−5 for the EstA locus. Since homozygotes for the ‘silent’ allele at the first or at the second locus were found in the population in expected frequencies, it was concluded that these alleles are not inferior to active ones under natural conditions.

Exploring Genetic Drift & Natural Selection through a Simulation Activity

1998 ◽  
Vol 60 (9) ◽  
pp. 681-683 ◽  
Author(s):  
Timothy J. Maret ◽  
Steven W. Rissing
Keyword(s):  
Natural Selection ◽  
Genetic Drift
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