scholarly journals The expected time to cross extended fitness plateaus

2018 ◽  
Author(s):  
Mahan Ghafari ◽  
Daniel Weissman
Keyword(s):  
Fitness Landscape ◽  
Low Frequency ◽  
Linkage Equilibrium ◽  
Expected Time ◽  
Large Populations ◽  
Population Sizes ◽  
Neutral Mutations ◽  
Independent Mutant

AbstractFor a population to acquire a complex adaptation requiring multiple individually neutral mutations, it must cross a plateau in the fitness landscape. We consider plateaus involving three mutations, and show that large populations can cross them rapidly via lineages that acquire multiple mutations while remaining at low frequency. Plateau-crossing is fastest for very large populations. At intermediate population sizes, recombination can greatly accelerate adaptation by combining independent mutant lineages to form triple-mutants. For more frequent recombination, such that the population is kept near linkage equilibrium, we extend our analysis to find simple expressions for the expected time to cross plateaus of arbitrary width.

scholarly journals Population size determines the type of nucleotide variations in humans

2017 ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
High Frequency ◽  
Genetic Diseases ◽  
Large Population ◽  
Low Frequency ◽  
Small Population ◽  
Effective Population ◽  
Large Populations ◽  
Population Sizes

AbstractIt is well known that the effective size of a population (Ne) is one of the major determinants of the amount of genetic variation within the population. Here, we examined whether the types of genetic variations are dictated by the effective population size. Our results revealed that for low frequency variants, the ratio of AT→GC to GC→AT variants (β) was similar across populations, suggesting the similarity of the pattern of mutation in various populations. However, for high frequency variants, β showed a positive correlation with the effective population size of the populations. This suggests a much higher proportion of high frequency AT→GC variants in large populations (e.g. Africans) compared to those with small population sizes (e.g. Asians). These results imply that the substitution patterns vary significantly between populations. These findings could be explained by the effect of GC-biased gene conversion (gBGC), which favors the fixation of G/C over A/T variants in populations. In large population, gBGC causes high β. However, in small populations, genetic drift reduces the effect of gBGC resulting in reduced β. This was further confirmed by a positive relationship between Ne and β for homozygous variants. Our results highlight the huge variation in the types of homozygous and high frequency polymorphisms between world populations. We observed the same pattern for deleterious variants, implying that the homozygous polymorphisms associated with recessive genetic diseases will be more enriched with G or C in populations with large Ne (e.g. Africans) than in populations with small Ne (e.g. Europeans).

scholarly journals The duty cycle of radio galaxies revealed by LOFAR: remnant and restarted radio source populations in the Lockman Hole

2020 ◽  
Vol 496 (2) ◽  
pp. 1706-1717 ◽  
Author(s):  
Stanislav S Shabala ◽  
Nika Jurlin ◽  
Raffaella Morganti ◽  
Marisa Brienza ◽  
Martin J Hardcastle ◽  
...  
Keyword(s):  
Active Galactic Nuclei ◽  
Radio Source ◽  
Low Frequency ◽  
Galactic Nuclei ◽  
Radio Jets ◽  
Modelling Analysis ◽  
Self Consistent ◽  
Large Populations ◽  
Source Populations ◽  
Lockman Hole

ABSTRACT Feedback from radio jets associated with active galactic nuclei (AGNs) plays a profound role in the evolution of galaxies. Kinetic power of these radio jets appears to show temporal variation, but the mechanism(s) responsible for this process are not yet clear. Recently, the LOw Frequency ARray (LOFAR) has uncovered large populations of active, remnant, and restarted radio jet populations. By focusing on LOFAR data in the Lockman Hole, in this work we use the Radio AGNs in Semi-Analytic Environments (RAiSE) dynamical model to present the first self-consistent modelling analysis of active, remnant, and restarted radio source populations. Consistent with other recent work, our models predict that remnant radio lobes fade quickly. Any high (>10 per cent) observed fraction of remnant and restarted sources therefore requires a dominant population of short-lived jets. We speculate that this could plausibly be provided by feedback-regulated accretion.

scholarly journals Repeatability of adaptation in experimental populations of different sizes

2015 ◽  
Vol 282 (1805) ◽  
pp. 20143033 ◽  
Author(s):  
Josianne Lachapelle ◽  
Joshua Reid ◽  
Nick Colegrave
Keyword(s):  
Population Size ◽  
Large Contribution ◽  
Unicellular Alga ◽  
Effective Population ◽  
Fitness Level ◽  
Relative Contribution ◽  
Large Populations ◽  
Population Sizes ◽  
Evolutionary Trajectories ◽  
Experimental Populations

The degree to which evolutionary trajectories and outcomes are repeatable across independent populations depends on the relative contribution of selection, chance and history. Population size has been shown theoretically and empirically to affect the amount of variation that arises among independent populations adapting to the same environment. Here, we measure the contribution of selection, chance and history in different-sized experimental populations of the unicellular alga Chlamydomonas reinhardtii adapting to a high salt environment to determine which component of evolution is affected by population size. We find that adaptation to salt is repeatable at the fitness level in medium ( N e = 5 × 10 4 ) and large ( N e = 4 × 10 5 ) populations because of the large contribution of selection. Adaptation is not repeatable in small ( N e = 5 × 10 3 ) populations because of large constraints from history. The threshold between stochastic and deterministic evolution in this case is therefore between effective population sizes of 10 3 and 10 4 . Our results indicate that diversity across populations is more likely to be maintained if they are small. Experimental outcomes in large populations are likely to be robust and can inform our predictions about outcomes in similar situations.

scholarly journals Evolution of Drift Robustness in Small Populations

2016 ◽  
Author(s):  
Thomas LaBar ◽  
Christoph Adami
Keyword(s):  
Mathematical Modeling ◽  
Experimental Evolution ◽  
Small Population ◽  
Small Populations ◽  
Mutational Load ◽  
Deleterious Mutations ◽  
Mutational Robustness ◽  
Large Populations ◽  
Slightly Deleterious Mutations ◽  
Population Sizes

AbstractMost mutations are deleterious and cause a reduction in population fitness known as the mutational load. In small populations, weakened selection against slightly-deleterious mutations results in an additional fitness reduction. Many studies have established that populations can evolve a reduced mutational load by evolving mutational robustness, but it is uncertain whether small populations can evolve a reduced susceptibility to drift-related fitness declines. Here, using mathematical modeling and digital experimental evolution, we show that small populations do evolve a reduced vulnerability to drift, or “drift robustness”. We find that, compared to genotypes from large populations, genotypes from small populations have a decreased likelihood of small-effect deleterious mutations, thus causing small-population genotypes to be drift-robust. We further show that drift robustness is not adaptive, but instead arises because small populations preferentially adapt to drift-robust fitness peaks. These results have implications for genome evolution in organisms with small population sizes.

scholarly journals A silent disco: Persistent entrainment of low-frequency neural oscillations underlies beat-based, but not memory-based temporal expectations

2020 ◽  
Author(s):  
Fleur L. Bouwer ◽  
Johannes J. Fahrenfort ◽  
Samantha K. Millard ◽  
Heleen A. Slagter
Keyword(s):  
Neuronal Activity ◽  
Beat Frequency ◽  
Low Frequency ◽  
Neural Oscillations ◽  
Expected Time ◽  
Low Frequency Oscillations ◽  
Eeg Data ◽  
Predictable Pattern ◽  
Temporal Intervals ◽  
Multivariate Pattern

AbstractTemporal expectations (e.g., predicting “when”) facilitate sensory processing, and are suggested to rely on entrainment of low frequency neural oscillations to regular rhythmic input. However, temporal expectations can be formed not only in response to a regular beat, such as in music (“beat-based” expectations), but also based on a predictable pattern of temporal intervals of different durations (“memory-based” expectations). Here, we examined the neural mechanisms underlying beat-based and memory-based expectations, by assessing EEG activity and behavioral responses during silent periods following rhythmic auditory sequences that allowed for beat-based or memory-based expectations, or had random timing. In Experiment 1 (N = 32), participants rated how well probe tones at various time points fitted the previous rhythm. Beat-based expectations affected fitness ratings for at least two beat-cycles, while the effects of memory-based expectations subsided after the first expected time point in the silence window. In Experiment 2 (N = 27), using EEG, we found a CNV following the final tones of memory-based and random, but not beat-based sequences, suggesting that climbing neuronal activity may specifically reflect memory-based expectations. Moreover, we found enhanced power in the EEG signal at the beat frequency for beat-based sequences both during listening and the silence. For memory-based sequences, we found enhanced power at a frequency inherent to the memory-based pattern only during listening, but not during the silence, suggesting that ongoing entrainment of low frequency oscillations may be specific to beat-based expectations. Finally, using multivariate pattern decoding on the raw EEG data, we could classify above chance from the silence which type of sequence participants had heard before. Together, our results suggest that beat-based and memory-based expectations rely on entrainment and climbing neuronal activity, respectively.

scholarly journals Similar patterns of genetic diversity and linkage disequilibrium in Western chimpanzees (Pan troglodytes verus) and humans indicate highly conserved mechanisms of MHC molecular evolution

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Christelle Vangenot ◽  
José Manuel Nunes ◽  
Gaby M. Doxiadis ◽  
Estella S. Poloni ◽  
Ronald E. Bontrop ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Molecular Diversity ◽  
Selective Sweep ◽  
Balancing Selection ◽  
Substantial Effect ◽  
Human Populations ◽  
Large Set ◽  
Large Populations ◽  
Population Sizes

Abstract Background Many species are threatened with extinction as their population sizes decrease with changing environments or face novel pathogenic threats. A reduction of genetic diversity at major histocompatibility complex (MHC) genes may have dramatic effects on populations’ survival, as these genes play a key role in adaptive immunity. This might be the case for chimpanzees, the MHC genes of which reveal signatures of an ancient selective sweep likely due to a viral epidemic that reduced their population size a few million years ago. To better assess how this past event affected MHC variation in chimpanzees compared to humans, we analysed several indexes of genetic diversity and linkage disequilibrium across seven MHC genes on four cohorts of chimpanzees and we compared them to those estimated at orthologous HLA genes in a large set of human populations. Results Interestingly, the analyses uncovered similar patterns of both molecular diversity and linkage disequilibrium across the seven MHC genes in chimpanzees and humans. Indeed, in both species the greatest allelic richness and heterozygosity were found at loci A, B, C and DRB1, the greatest nucleotide diversity at loci DRB1, DQA1 and DQB1, and both significant global linkage disequilibrium and the greatest proportions of haplotypes in linkage disequilibrium were observed at pairs DQA1 ~ DQB1, DQA1 ~ DRB1, DQB1 ~ DRB1 and B ~ C. Our results also showed that, despite some differences among loci, the levels of genetic diversity and linkage disequilibrium observed in contemporary chimpanzees were globally similar to those estimated in small isolated human populations, in contrast to significant differences compared to large populations. Conclusions We conclude, first, that highly conserved mechanisms shaped the diversity of orthologous MHC genes in chimpanzees and humans. Furthermore, our findings support the hypothesis that an ancient demographic decline affecting the chimpanzee populations – like that ascribed to a viral epidemic – exerted a substantial effect on the molecular diversity of their MHC genes, albeit not more pronounced than that experienced by HLA genes in human populations that underwent rapid genetic drift during humans’ peopling history. We thus propose a model where chimpanzees’ MHC genes regenerated molecular variation through recombination/gene conversion and/or balancing selection after the selective sweep.

scholarly journals Population size influences the type of nucleotide variations in humans

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
High Frequency ◽  
Genetic Diseases ◽  
Large Population ◽  
Low Frequency ◽  
Small Population ◽  
Effective Population ◽  
Genome Data ◽  
Large Populations

Abstract Background It is well known that the effective size of a population (Ne) is one of the major determinants of the amount of genetic variation within the population. However, it is unclear whether the types of genetic variations are also dictated by the effective population size. To examine this, we obtained whole genome data from over 100 populations of the world and investigated the patterns of mutational changes. Results Our results revealed that for low frequency variants, the ratio of AT→GC to GC→AT variants (β) was similar across populations, suggesting the similarity of the pattern of mutation in various populations. However, for high frequency variants, β showed a positive correlation with the effective population size of the populations. This suggests a much higher proportion of high frequency AT→GC variants in large populations (e.g. Africans) compared to those with small population sizes (e.g. Asians). These results imply that the substitution patterns vary significantly between populations. These findings could be explained by the effect of GC-biased gene conversion (gBGC), which favors the fixation of G/C over A/T variants in populations. In large population, gBGC causes high β. However, in small populations, genetic drift reduces the effect of gBGC resulting in reduced β. This was further confirmed by a positive relationship between Ne and β for homozygous variants. Conclusions Our results highlight the huge variation in the types of homozygous and high frequency polymorphisms between world populations. We observed the same pattern for deleterious variants, implying that the homozygous polymorphisms associated with recessive genetic diseases will be more enriched with G or C in populations with large Ne (e.g. Africans) than in populations with small Ne (e.g. Europeans).

scholarly journals The effect of population size on effective population size: an empirical study in the red flour beetle Tribolium castaneum

1996 ◽  
Vol 68 (2) ◽  
pp. 151-155 ◽  
Author(s):  
Leslie A. Pray ◽  
Charles J. Goodnight ◽  
Lori Stevens ◽  
James M. Schwartz ◽  
Guiyun Yan
Keyword(s):  
Population Size ◽  
Tribolium Castaneum ◽  
Evolutionary Biology ◽  
Negative Relationship ◽  
Red Flour Beetle ◽  
Published Data ◽  
Effective Population ◽  
Flour Beetle ◽  
Large Populations ◽  
Population Sizes

SummaryDespite the increasing number of studies on the magnitude of Ne/N ratios, much remains unknown about the effects of demographic and environmental variables on Ne/N. We determined Ne/N for seven population size treatments, ranging from N = 2 to N = 960, in the red flour beetle Tribolium castaneum. Ne/N decreased with increasing N, as evidenced by a significant negative relationship between log N and Ne/N. Our results are consistent with other published data on the relationship between Ne/N and N. Effective population sizes in large populations may be much smaller than previously recognized. These results have important implications for conservation and evolutionary biology.

scholarly journals Predictions of response to artificial selection from new mutations

1982 ◽  
Vol 40 (3) ◽  
pp. 255-278 ◽  
Author(s):  
William G. Hill
Keyword(s):  
Large Population ◽  
Mutant Gene ◽  
Gene Effects ◽  
Bristle Number ◽  
Large Populations ◽  
Breeding Programmes ◽  
Population Sizes ◽  
The Difference ◽  
Mutant Genes

SUMMARYThe pattern of response expected from fixation of mutant genes for quantitative traits in finite populations is investigated for a range of distributions of mutant gene effects. The eventual rate depends on the total variance of mutant effects per generation, but the initial rate and the variance of response is higher if the distribution of mutant effects has a large standard deviation or is leptokurtic. The difference between initial and eventual rates of response is greater with large population sizes.For a range of assumptions, new mutants are unlikely to have much influence on response for 20 or so generations, but then may contribute substantially, such that no plateaux are obtained. However, information on the variance contributed by mutants is almost entirely on bristle number in Drosophila.It is argued that the role of new mutants should be considered in designing breeding programmes, in particular in utilizing large populations.

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