Natural Selection in Large Populations

2020 ◽  
pp. 109-146
Author(s):  
Daniel L. Hartl
Keyword(s):  
Natural Selection ◽  
Balancing Selection ◽  
Large Population ◽  
Natural Populations ◽  
Meiotic Drive ◽  
Gene Drive ◽  
Background Selection ◽  
Large Populations ◽  
Gametic Selection ◽  
Soft Selective Sweeps

This chapter includes selection in haploid and diploid organisms, hard and soft selective sweeps, background selection, and the probability of ultimate survival of a new favorable mutation in a large population. It considers overdominance and heterozygote inferiority in detail as well as different types of equilibria and the fundamental theorem of natural selection. Various types of balancing selection are examined including mutation–selection balance, migration–selection balance, meiotic drive and gametic selection, and the theory of CRISPR-mediated gene drive to control natural populations. It closes with a discussion of other modes of selection and their implications.

scholarly journals The Temporal Dynamics of Background Selection in Nonequilibrium Populations

Genetics ◽  
2020 ◽  
Vol 214 (4) ◽  
pp. 1019-1030 ◽  
Author(s):  
Raul Torres ◽  
Markus G. Stetter ◽  
Ryan D. Hernandez ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Natural Selection ◽  
Temporal Dynamics ◽  
Direct Action ◽  
Demographic History ◽  
Empirical Studies ◽  
Natural Populations ◽  
Background Selection ◽  
Size Change ◽  
Demographic Models ◽  
Classical Models

Neutral genetic diversity across the genome is determined by the complex interplay of mutation, demographic history, and natural selection. While the direct action of natural selection is limited to functional loci across the genome, its impact can have effects on nearby neutral loci due to genetic linkage. These effects of selection at linked sites, referred to as genetic hitchhiking and background selection (BGS), are pervasive across natural populations. However, only recently has there been a focus on the joint consequences of demography and selection at linked sites, and some empirical studies have come to apparently contradictory conclusions as to their combined effects. To understand the relationship between demography and selection at linked sites, we conducted an extensive forward simulation study of BGS under a range of demographic models. We found that the relative levels of diversity in BGS and neutral regions vary over time and that the initial dynamics after a population size change are often in the opposite direction of the long-term expected trajectory. Our detailed observations of the temporal dynamics of neutral diversity in the context of selection at linked sites in nonequilibrium populations provide new intuition about why patterns of diversity under BGS vary through time in natural populations and help reconcile previously contradictory observations. Most notably, our results highlight that classical models of BGS are poorly suited for predicting diversity in nonequilibrium populations.

scholarly journals Natural selection acts on Atlantic salmon major histocompatibility (MH) variability in the wild

2007 ◽  
Vol 274 (1611) ◽  
pp. 861-869 ◽  
Author(s):  
Elvira de Eyto ◽  
Philip McGinnity ◽  
Sofia Consuegra ◽  
Jamie Coughlan ◽  
Jarle Tufto ◽  
...  
Keyword(s):  
Natural Selection ◽  
Atlantic Salmon ◽  
Balancing Selection ◽  
Natural Populations ◽  
Class Ii ◽  
Major Histocompatibility ◽  
Genotype Frequencies ◽  
Fitness Consequences ◽  
In The Wild ◽  
Class Ii Alpha

Pathogen-driven balancing selection is thought to maintain polymorphism in major histocompatibility (MH) genes. However, there have been few empirical demonstrations of selection acting on MH loci in natural populations. To determine whether natural selection on MH genes has fitness consequences for wild Atlantic salmon in natural conditions, we compared observed genotype frequencies of Atlantic salmon ( Salmo salar ) surviving in a river six months after their introduction as eggs with frequencies expected from parental crosses. We found significant differences between expected and observed genotype frequencies at the MH class II alpha locus, but not at a MH class I-linked microsatellite or at seven non-MH-linked microsatellite loci. We therefore conclude that selection at the MH class II alpha locus was a result of disease-mediated natural selection, rather than any demographic event. We also show that survival was associated with additive allelic effects at the MH class II alpha locus. Our results have implications for both the conservation of wild salmon stocks and the management of disease in hatchery fish. We conclude that natural or hatchery populations have the best chance of dealing with episodic and variable disease challenges if MH genetic variation is preserved both within and among populations.

scholarly journals Natural Selection and Y-Linked Polymorphism

Genetics ◽  
1987 ◽  
Vol 115 (3) ◽  
pp. 569-577 ◽  
Author(s):  
Andrew G Clark
Keyword(s):  
Natural Selection ◽  
Sequence Variation ◽  
Natural Populations ◽  
Meiotic Drive ◽  
Stable Limit ◽  
Interior Equilibrium ◽  
Dna Sequence Variation ◽  
Selection Parameters ◽  
Stable Limit Cycles ◽  
Two Equilibria

ABSTRACT Several population genetic models allowing natural selection to act on Y-linked polymorphism are examined. The first incorporates pleiotropic effects of a Y-linked locus, such that viability, segregation distortion, fecundity and sexual selection can all be determined by one locus. It is shown that no set of selection parameters can maintain a stable Y-linked polymorphism. Interaction with the X chromosome is allowed in the next model, with viabilities determined by both X- and Y-linked factors. This model allows four fixation equilibria, two equilibria with X polymorphism and a unique point with both X- and Y-linked polymorphism. Stability analysis shows that the complete polymorphism is never stable. When X- and Y-linked loci influence meiotic drive, it is possible to have all fixation equilibria simultaneously unstable, and yet there is no stable interior equilibrium. Only when viability and meiotic drive are jointly affected by both X- and Y-linked genes can a Y-linked polymorphism be maintained. Unusual dynamics, including stable limit cycles, are generated by this model. Numerical simulations show that only a very small portion of the parameter space admits Y polymorphism, a result that is relevant to the interpretation of levels of Y-DNA sequence variation in natural populations.

scholarly journals Weakly deleterious natural genetic variation amplifies probability of resistance in multiplexed gene drive systems

2021 ◽  
Author(s):  
Bhavin S Khatri ◽  
Austin Burt
Keyword(s):  
De Novo ◽  
Large Population ◽  
Stochastic Simulations ◽  
Gene Drive ◽  
End Joining ◽  
Single Nucleotide ◽  
Major Barrier ◽  
Standing Variation ◽  
Large Populations ◽  
Drive Systems

Evolution of resistance is a major barrier to successful deployment of gene drive systems to suppress natural populations. Multiplexed guide RNAs that require resistance mutations in all target cut sites is a promising strategy to overcome resistance. Using novel stochastic simulations that accurately model evolution at very large population sizes, we explore the probability of resistance due to three important mechanisms: 1) non-homologous end-joining mutations, 2) single nucleotide mutants arising de novo or, 3) single nucleotide polymorphisms pre-existing as standing variation. If the fraction of functional end-joining mutants is rare, we show that standing variation dominates, via a qualitatively new phenomenon where weakly deleterious variants significantly amplify the probability of multi-site resistance. This means resistance can be probable even with many target sites in not very large populations. This result has broad application to resistance arising in multi-site evolutionary scenarios including the evolution of vaccine escape mutations in large populations.

scholarly journals Natural selection shaped the rise and fall of passenger pigeon genomic diversity

Science ◽  
2017 ◽  
Vol 358 (6365) ◽  
pp. 951-954 ◽  
Author(s):  
Gemma G. R. Murray ◽  
André E. R. Soares ◽  
Ben J. Novak ◽  
Nathan K. Schaefer ◽  
James A. Cahill ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
North America ◽  
Large Population ◽  
Genomic Diversity ◽  
Vertebrate Genome ◽  
Rapid Extinction ◽  
Neutral Genetic Diversity ◽  
The World ◽  
Large Populations

The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. Although theory predicts that large populations will be more genetically diverse, passenger pigeon genetic diversity was surprisingly low. To investigate this disconnect, we analyzed 41 mitochondrial and 4 nuclear genomes from passenger pigeons and 2 genomes from band-tailed pigeons, which are passenger pigeons’ closest living relatives. Passenger pigeons’ large population size appears to have allowed for faster adaptive evolution and removal of harmful mutations, driving a huge loss in their neutral genetic diversity. These results demonstrate the effect that selection can have on a vertebrate genome and contradict results that suggested that population instability contributed to this species’s surprisingly rapid extinction.

scholarly journals Polymorphism for Y-Linked Suppressors of sex-ratio in Two Natural Populations of Drosophila mediopunctata

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 891-902 ◽  
Author(s):  
Antonio Bernardo Carvalho ◽  
Suzana Casaccia Vaz ◽  
Louis Bernard Klaczko
Keyword(s):  
Population Genetics ◽  
Population Dynamics ◽  
Natural Selection ◽  
Sex Ratio ◽  
Numerical Simulations ◽  
Natural Populations ◽  
Meiotic Drive ◽  
X Chromosomes ◽  
Variable Expression ◽  
Y Chromosomes

In several Drosophila species there is a trait known as “sex-ratio”: males carrying certain X chromosomes (called “SR”) produce female biased progenies due to X-Y meiotic drive. In Drosophila mediopunctata this trait has a variable expression due to Y-linked suppressors of sex-ratio expression, among other factors. There are two types of Y chromosomes (suppressor and nonsuppressor) and two types of SR chromosomes (suppressible and unsuppressible). Sex-ratio expression is suppressed in males with the SRsuppressible/Ysuppressor genotype, whereas the remaining three genotypes produce female biased progenies. Now we have found that ∼10–20% of the Y chromosomes from two natural populations 1500 km apart are suppressors of sex-ratio expression. Preliminary estimates indicate that Ysuppressor has a meiotic drive advantage of 6% over Ynonsuppressor. This Y polymorphism for a nonneutral trait is unexpected under current population genetics theoly. We propose that this polymorphism is stabilized by an equilibrium between meiotic drive and natural selection, resulting from interactions in the population dynamics of X and Y alleles. Numerical simulations showed that this mechanism may stabilize nonneutral Y polymorphisms such as we have found in D. mediopunctata.

scholarly journals Natural selection shaped the rise and fall of passenger pigeon genomic diversity

2017 ◽  
Author(s):  
Gemma G. R. Murray ◽  
André E. R. Soares ◽  
Ben J. Novak ◽  
Nathan K. Schaefer ◽  
James A. Cahill ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
North America ◽  
Large Population ◽  
Genomic Diversity ◽  
Vertebrate Genome ◽  
Rapid Extinction ◽  
Neutral Genetic Diversity ◽  
The World ◽  
Large Populations

AbstractThe extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. While theory predicts that large populations will be more genetically diverse and respond more efficiently to selection, passenger pigeon genetic diversity was surprisingly low. To investigate this we analysed 41 mitochondrial and 4 nuclear genomes from passenger pigeons, and 2 genomes from band-tailed pigeons, passenger pigeons’ closest living relatives. We find that passenger pigeons’ large population size allowed for faster adaptive evolution and removal of harmful mutations, but that this drove a huge loss in neutral genetic diversity. These results demonstrate how great an impact selection can have on a vertebrate genome, and invalidate previous results that suggested population instability contributed to this species’ surprisingly rapid extinction.

scholarly journals The temporal dynamics of background selection in non-equilibrium populations

2019 ◽  
Author(s):  
Raul Torres ◽  
Markus G Stetter ◽  
Ryan D Hernandez ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Natural Selection ◽  
Temporal Dynamics ◽  
Direct Action ◽  
Demographic History ◽  
Empirical Studies ◽  
Natural Populations ◽  
Background Selection ◽  
Size Change ◽  
Demographic Models ◽  
Non Equilibrium

ABSTRACTNeutral genetic diversity across the genome is determined by the complex interplay of mutation, demographic history, and natural selection. While the direct action of natural selection is limited to functional loci across the genome, its impact can have effects on nearby neutral loci due to genetic linkage. These effects of selection at linked sites, referred to as genetic hitchhiking and background selection (BGS), are pervasive across natural populations. However, only recently has there been a focus on the joint consequences of demography and selection at linked sites, and empirical studies have sometimes come to apparently contradictory conclusions as to their combined effects. In order to understand the relationship between demography and selection at linked sites, we conducted an extensive forward simulation study of BGS under a range of demographic models. We found that the relative levels of diversity in BGS and neutral regions vary over time and that the initial dynamics after a population size change are often in the opposite direction of the long-term expected trajectory. Our detailed observations of the temporal dynamics of neutral diversity in the context of selection at linked sites in non-equilibrium populations provides new intuition about why patterns of diversity under BGS vary through time in natural populations and help reconcile previously contradictory observations. Most notably, our results highlight that classical models of BGS are poorly suited for predicting diversity in non-equilibrium populations.

scholarly journals Genome-wide polymorphisms show unexpected targets of natural selection

2011 ◽  
Vol 279 (1732) ◽  
pp. 1412-1420 ◽  
Author(s):  
Melissa H. Pespeni ◽  
David A. Garfield ◽  
Mollie K. Manier ◽  
Stephen R. Palumbi
Keyword(s):  
Gene Expression ◽  
Natural Selection ◽  
Genetic Differentiation ◽  
Gene Function ◽  
Sea Urchins ◽  
Balancing Selection ◽  
Disease Incidence ◽  
Natural Populations ◽  
Marine Species ◽  
Genome Wide

Natural selection can act on all the expressed genes of an individual, leaving signatures of genetic differentiation or diversity at many loci across the genome. New power to assay these genome-wide effects of selection comes from associating multi-locus patterns of polymorphism with gene expression and function. Here, we performed one of the first genome-wide surveys in a marine species, comparing purple sea urchins, Strongylocentrotus purpuratus , from two distant locations along the species' wide latitudinal range. We examined 9112 polymorphic loci from upstream non-coding and coding regions of genes for signatures of selection with respect to gene function and tissue- and ontogenetic gene expression. We found that genetic differentiation ( F ST ) varied significantly across functional gene classes. The strongest enrichment occurred in the upstream regions of E3 ligase genes, enzymes known to regulate protein abundance during development and environmental stress. We found enrichment for high heterozygosity in genes directly involved in immune response, particularly NALP genes, which mediate pro-inflammatory signals during bacterial infection. We also found higher heterozygosity in immune genes in the southern population, where disease incidence and pathogen diversity are greater. Similar to the major histocompatibility complex in mammals, balancing selection may enhance genetic diversity in the innate immune system genes of this invertebrate. Overall, our results show that how genome-wide polymorphism data coupled with growing databases on gene function and expression can combine to detect otherwise hidden signals of selection in natural populations.

Specific features of long-term domestication of australian crayfish Cherax quadricarinatus in conditions of the western part of Russian Federation

2018 ◽  
Vol 194 ◽  
pp. 188-192
Author(s):  
D. I. Shokasheva
Keyword(s):  
Natural Selection ◽  
Russian Federation ◽  
Natural Populations ◽  
Cherax Quadricarinatus ◽  
Local Environments ◽  
Local Species ◽  
Adaptive Ability

Natural populations of crayfish are in depression in Russia and local species are not cultivated. In this situation, experimental cultivation of allochtonous australian crayfish Cherax quadricarinatus is conducted. This species is distinguished by high reproductive abilities and good consumer properties. It has domesticated in Russia spontaneously and produced 9–10 generations in Astrakhan Region. Certain natural selection in the process of domestication provides adaptive ability of this species to local environments and its capabil­ity to reproduce a viable progeny, so there is no doubts in good prospects of its cultivation in industrial conditions.

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