Balancing selection and genetic drift create unusual patterns of MHCIIβ variation in Galápagos mockingbirds

2016 ◽  
Vol 25 (19) ◽  
pp. 4757-4772 ◽  
Author(s):  
Jakub Vlček ◽  
Paquita E. A. Hoeck ◽  
Lukas F. Keller ◽  
Jessica P. Wayhart ◽  
Iva Dolinová ◽  
...  
Keyword(s):  
Genetic Drift ◽  
Balancing Selection

scholarly journals Balancing selection, genetic drift, and human‐mediated introgression interplay to shape MHC (functional) diversity in Mediterranean brown trout

2021 ◽  
Author(s):  
Lorenzo Talarico ◽  
Silvio Marta ◽  
Anna Rita Rossi ◽  
Simone Crescenzo ◽  
Gerardo Petrosino ◽  
...  
Keyword(s):  
Functional Diversity ◽  
Genetic Drift ◽  
Brown Trout ◽  
Balancing Selection

scholarly journals Can balancing selection on MHC loci counteract genetic drift in small fragmented populations of black grouse?

2012 ◽  
Vol 2 (2) ◽  
pp. 341-353 ◽  
Author(s):  
Tanja M. Strand ◽  
Gernot Segelbacher ◽  
María Quintela ◽  
Lingyun Xiao ◽  
Tomas Axelsson ◽  
...  
Keyword(s):  
Genetic Drift ◽  
Balancing Selection ◽  
Black Grouse ◽  
Fragmented Populations

scholarly journals Establishment of a new sex-determining allele driven by sexually antagonistic selection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Takahiro Sakamoto ◽  
Hideki Innan
Keyword(s):  
Genetic Drift ◽  
Balancing Selection ◽  
Theoretical Description ◽  
Random Genetic Drift ◽  
Antagonistic Selection ◽  
Entire Process ◽  
Turnover Process ◽  
Sexually Antagonistic Selection ◽  
Two Phases ◽  
Theoretical Results

Abstract The turnover of sex-determining loci has repeatedly occurred in a number of species, rather than having a diverged pair of sex chromosomes. We model the turnover process by considering a linked locus under sexually antagonistic selection. The entire process of a turnover may be divided into two phases, which are referred to as the stochastic and deterministic phases. The stochastic phase is when a new sex-determining allele just arises and is still rare and random genetic drift plays an important role. In the deterministic phase, the new allele further increases in frequency by positive selection. The theoretical results currently available are for the deterministic phase, which demonstrated that a turnover of a newly arisen sex-determining locus could benefit from selection at a linked locus under sexually antagonistic selection, by assuming that sexually antagonistic selection works in a form of balancing selection. In this work, we provide a comprehensive theoretical description of the entire process from the stochastic phase to the deterministic phase. In addition to balancing selection, we explore several other modes of selection on the linked locus. Our theory allows us make a quantitative argument on the rate of turnover and the effect of the mode of selection at the linked locus. We also performed simulations to explore the pattern of polymorphism around the new sex-determining locus. We find that the pattern of polymorphism is informative to infer how selection worked through the turnover process.

scholarly journals Genetic drift from the out-of-Africa bottleneck leads to biased estimation of genetic architecture and selection

2021 ◽  
Author(s):  
Bilal Ashraf ◽  
Daniel John Lawson
Keyword(s):  
Sensitivity Analysis ◽  
Genetic Drift ◽  
Effect Size ◽  
Complex Traits ◽  
Joint Distribution ◽  
Genetic Architecture ◽  
Balancing Selection ◽  
1000 Genomes ◽  
Selection Parameter ◽  
Out Of Africa

AbstractMost complex traits evolved in the ancestors of all modern humans and have been under negative or balancing selection to maintain the distribution of phenotypes observed today. Yet all large studies mapping genomes to complex traits occur in populations that have experienced the Out-of-Africa bottleneck. Does this bottleneck affect the way we characterise complex traits? We demonstrate using the 1000 Genomes dataset and hypothetical complex traits that genetic drift can strongly affect the joint distribution of effect size and SNP frequency, and that the bias can be positive or negative depending on subtle details. Characterisations that rely on this distribution therefore conflate genetic drift and selection. We provide a model to identify the underlying selection parameter in the presence of drift, and demonstrate that a simple sensitivity analysis may be enough to validate existing characterisations. We conclude that biobanks characterising more worldwide diversity would benefit studies of complex traits.

scholarly journals A Conservative Test of Genetic Drift in the Endosymbiotic Bacterium Buchnera: Slightly Deleterious Mutations in the Chaperonin groEL

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 1651-1660
Author(s):  
Joshua T Herbeck ◽  
Daniel J Funk ◽  
Patrick H Degnan ◽  
Jennifer J Wernegreen
Keyword(s):  
Genetic Drift ◽  
Balancing Selection ◽  
Purifying Selection ◽  
Nonsynonymous Substitution ◽  
Maximum Likelihood Estimates ◽  
Sequence Evolution ◽  
Endosymbiotic Bacterium ◽  
Deleterious Mutations ◽  
Synonymous Polymorphism ◽  
Slightly Deleterious Mutations

Abstract The obligate endosymbiotic bacterium Buchnera aphidicola shows elevated rates of sequence evolution compared to free-living relatives, particularly at nonsynonymous sites. Because Buchnera experiences population bottlenecks during transmission to the offspring of its aphid host, it is hypothesized that genetic drift and the accumulation of slightly deleterious mutations can explain this rate increase. Recent studies of intraspecific variation in Buchnera reveal patterns consistent with this hypothesis. In this study, we examine inter- and intraspecific nucleotide variation in groEL, a highly conserved chaperonin gene that is constitutively overexpressed in Buchnera. Maximum-likelihood estimates of nonsynonymous substitution rates across Buchnera species are strikingly low at groEL compared to other loci. Despite this evidence for strong purifying selection on groEL, our intraspecific analysis of this gene documents reduced synonymous polymorphism, elevated nonsynonymous polymorphism, and an excess of rare alleles relative to the neutral expectation, as found in recent studies of other Buchnera loci. Comparisons with Escherichia coli generally show patterns predicted by their differences in Ne. The sum of these observations is not expected under relaxed or balancing selection, selective sweeps, or increased mutation rate. Rather, they further support the hypothesis that drift is an important force driving accelerated protein evolution in this obligate mutualist.

scholarly journals Distinct evolutionary strategies of human leucocyte antigen loci in pathogen-rich environments

2012 ◽  
Vol 367 (1590) ◽  
pp. 830-839 ◽  
Author(s):  
Alicia Sanchez-Mazas ◽  
Jean-François Lemaître ◽  
Mathias Currat
Keyword(s):  
Genetic Diversity ◽  
Genetic Drift ◽  
Human Leucocyte Antigen ◽  
Balancing Selection ◽  
Allelic Diversity ◽  
Hla Class I ◽  
Significant Negative Correlation ◽  
Evolutionary Strategies ◽  
Hla Genes ◽  
Geographical Distances

Human leucocyte antigen (HLA) loci have a complex evolution where both stochastic (e.g. genetic drift) and deterministic (natural selection) forces are involved. Owing to their extraordinary level of polymorphism, HLA genes are useful markers for reconstructing human settlement history. However, HLA variation often deviates significantly from neutral expectations towards an excess of genetic diversity. Because HLA molecules play a crucial role in immunity, this observation is generally explained by pathogen-driven-balancing selection (PDBS). In this study, we investigate the PDBS model by analysing HLA allelic diversity on a large database of 535 populations in relation to pathogen richness. Our results confirm that geographical distances are excellent predictors of HLA genetic differentiation worldwide. We also find a significant positive correlation between genetic diversity and pathogen richness at two HLA class I loci (HLA-A and -B), as predicted by PDBS, and a significant negative correlation at one HLA class II locus (HLA-DQB1). Although these effects are weak, as shown by a loss of significance when populations submitted to rapid genetic drift are removed from the analysis, the inverse relationship between genetic diversity and pathogen richness at different loci indicates that HLA genes have adopted distinct evolutionary strategies to provide immune protection in pathogen-rich environments.

scholarly journals Genetic drift from the out-of-Africa bottleneck leads to biased estimation of genetic architecture and selection

2020 ◽  
Author(s):  
Bilal Ashraf ◽  
Daniel John Lawson
Keyword(s):  
Sensitivity Analysis ◽  
Genetic Drift ◽  
Effect Size ◽  
Complex Traits ◽  
Joint Distribution ◽  
Genetic Architecture ◽  
Balancing Selection ◽  
1000 Genomes ◽  
Selection Parameter ◽  
Out Of Africa

AbstractMost complex traits evolved in the ancestors of all modern humans and have been under negative or balancing selection to maintain the distribution of phenotypes observed today. Yet all large studies mapping genomes to complex traits occur in populations that have experienced the Out-of-Africa bottleneck. Does this bottleneck affect the way we characterise complex traits? We demonstrate using the 1000 Genomes dataset and hypothetical complex traits that genetic drift can strongly affect the joint distribution of effect size and SNP frequency. Characterisations that rely on this distribution therefore conflate genetic drift and selection. We provide a model to identify the underlying selection parameter in the presence of drift, and demonstrate that a simple sensitivity analysis may be enough to validate existing characterisations. We conclude that biobanks characterising more worldwide diversity would benefit studies of complex traits.

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