scholarly journals Evolutionary rescue by beneficial mutations in environments that change in space and time

2013 ◽  
Vol 368 (1610) ◽  
pp. 20120082 ◽  
Author(s):  
Mark Kirkpatrick ◽  
Stephan Peischl
Keyword(s):  
Branching Processes ◽  
Selective Advantage ◽  
Maximum Speed ◽  
Selection Coefficient ◽  
Beneficial Mutations ◽  
Changing Environments ◽  
Classic Theory ◽  
Evolutionary Rescue ◽  
Effective Selection ◽  
Establishment Probability

A factor that may limit the ability of many populations to adapt to changing conditions is the rate at which beneficial mutations can become established. We study the probability that mutations become established in changing environments by extending the classic theory for branching processes. When environments change in time, under quite general conditions, the establishment probability is approximately twice the ‘effective selection coefficient’, whose value is an average that gives most weight to a mutant's fitness in the generations immediately after it appears. When fitness varies along a gradient in a continuous habitat, increased dispersal generally decreases the chance a mutation establishes because mutations move out of areas where they are most adapted. When there is a patch of favourable habitat that moves in time, there is a maximum speed of movement above which mutations cannot become established, regardless of when and where they first appear. This critical speed limit, which is proportional to the mutation's maximum selective advantage, represents an absolute constraint on the potential of locally adapted mutations to contribute to evolutionary rescue.

scholarly journals A Branching Process Model of Evolutionary Rescue

2021 ◽  
Author(s):  
Peter Olofsson ◽  
Ricardo B. R. Azevedo
Keyword(s):  
Population Growth ◽  
Mutation Rate ◽  
Discrete Time ◽  
Growth Curve ◽  
Process Model ◽  
Branching Process ◽  
Selective Advantage ◽  
Population Declines ◽  
Beneficial Mutations ◽  
Evolutionary Rescue

Evolutionary rescue is the process whereby a declining population may start growing again, thus avoiding extinction, via an increase in the frequency of beneficial genotypes. These genotypes may either already be present in the population in small numbers, or arise by mutation as the population declines. We present a simple two-type discrete-time branching process model and use it to obtain results such as the probability of rescue, the shape of the population growth curve of a rescued population, and the time until the first rescuing mutation occurs. Comparisons are made to existing results in the literature in cases where both the mutation rate and the selective advantage of the beneficial mutations are small.

scholarly journals Evolutionary Rescue and Drug Resistance on Multicopy Plasmids

Genetics ◽  
2020 ◽  
Vol 215 (3) ◽  
pp. 847-868
Author(s):  
Mario Santer ◽  
Hildegard Uecker
Keyword(s):  
Copy Number ◽  
Gene Dosage ◽  
Branching Processes ◽  
Plasmid Copy Number ◽  
Wild Type ◽  
Plasmid Copy ◽  
Gene Dosage Effects ◽  
Dosage Effects ◽  
Evolutionary Rescue ◽  
Establishment Probability

Bacteria often carry “extra DNA” in the form of plasmids in addition to their chromosome. Many plasmids have a copy number greater than one such that the genes encoded on these plasmids are present in multiple copies per cell. This has evolutionary consequences by increasing the mutational target size, by prompting the (transitory) co-occurrence of mutant and wild-type alleles within the same cell, and by allowing for gene dosage effects. We develop and analyze a mathematical model for bacterial adaptation to harsh environmental change if adaptation is driven by beneficial alleles on multicopy plasmids. Successful adaptation depends on the availability of advantageous alleles and on their establishment probability. The establishment process involves the segregation of mutant and wild-type plasmids to the two daughter cells, allowing for the emergence of mutant homozygous cells over the course of several generations. To model this process, we use the theory of multitype branching processes, where a type is defined by the genetic composition of the cell. Both factors—the availability of advantageous alleles and their establishment probability—depend on the plasmid copy number, and they often do so antagonistically. We find that in the interplay of various effects, a lower or higher copy number may maximize the probability of evolutionary rescue. The decisive factor is the dominance relationship between mutant and wild-type plasmids and potential gene dosage effects. Results from a simple model of antibiotic degradation indicate that the optimal plasmid copy number may depend on the specific environment encountered by the population.

scholarly journals Evolutionary rescue and drug resistance on multicopy plasmids

2019 ◽  
Author(s):  
Mario Santer ◽  
Hildegard Uecker
Keyword(s):  
Copy Number ◽  
Gene Dosage ◽  
Branching Processes ◽  
Plasmid Copy Number ◽  
Wild Type ◽  
Plasmid Copy ◽  
Gene Dosage Effects ◽  
Dosage Effects ◽  
Evolutionary Rescue ◽  
Establishment Probability

AbstractBacteria often carry “extra DNA” in form of plasmids in addition to their chromosome. Many plasmids have a copy number greater than one such that the genes encoded on these plasmids are present in multiple copies per cell. This has evolutionary consequences by increasing the mutational target size, by prompting the (transitory) co-occurrence of mutant and wild-type alleles within the same cell, and by allowing for gene dosage effects. We develop and analyze a mathematical model for bacterial adaptation to harsh environmental change if adaptation is driven by beneficial alleles on multicopy plasmids. Successful adaptation depends on the availability of advantageous alleles and on their establishment probability. The establishment process involves the segregation of mutant and wild-type plasmids to the two daughter cells, allowing for the emergence of mutant-homozygous cells over the course of several generations. To model this process, we use the theory of multi-type branching processes, where a type is defined by the genetic composition of the cell. Both factors – the number of adaptive alleles and their establishment probability – depend on the plasmid copy number, and they often do so antagonistically. We find that in the interplay of various effects, a lower or higher copy number may maximize the probability of evolutionary rescue. The decisive factor is the dominance relationship between mutant and wild-type plasmids and potential gene dosage effects. Results from a simple model of antibiotic degradation indicate that the optimal plasmid copy number may depend on the specific environment encountered by the population.

scholarly journals Time to fixation in changing environments

Genetics ◽  
2021 ◽  
Author(s):  
Sachin Kaushik ◽  
Kavita Jain
Keyword(s):  
Fixation Time ◽  
Natural Environments ◽  
Theoretical Studies ◽  
Selection Coefficient ◽  
Diploid Population ◽  
Changing Environment ◽  
Conditional Mean ◽  
Changing Environments ◽  
Constant Environment ◽  
Experimental And Theoretical Studies

Abstract Although many experimental and theoretical studies on natural selection have been carried out in a constant environment, as natural environments typically vary in time, it is important to ask if and how the results of these investigations are affected by a changing environment. Here, we study the properties of the conditional fixation time defined as the time to fixation of a new mutant that is destined to fix in a finite, randomly mating diploid population with intermediate dominance that is evolving in a periodically changing environment. It is known that in a static environment, the conditional mean fixation time of a co-dominant beneficial mutant is equal to that of a deleterious mutant with the same magnitude of selection coefficient. We find that this symmetry is not preserved, even when the environment is changing slowly. More generally, we find that the conditional mean fixation time of an initially beneficial mutant in a slowly changing environment depends weakly on the dominance coefficient and remains close to the corresponding result in the static environment. However, for an initially deleterious mutant under moderate and slowly varying selection, the fixation time differs substantially from that in a constant environment when the mutant is recessive. As fixation times are intimately related to the levels and patterns of genetic diversity, our results suggest that for beneficial sweeps, these quantities are only mildly affected by temporal variation in environment. In contrast, environmental change is likely to impact the patterns due to recessive deleterious sweeps strongly.

scholarly journals Mutations of intermediate effect are responsible for adaptation in evolving Pseudomonas fluorescens populations

2006 ◽  
Vol 2 (2) ◽  
pp. 236-238 ◽  
Author(s):  
Rowan D.H Barrett ◽  
R Craig MacLean ◽  
Graham Bell
Keyword(s):  
Pseudomonas Fluorescens ◽  
Sole Carbon Source ◽  
Fundamental Property ◽  
Selective Advantage ◽  
Ancestral Population ◽  
Selection Coefficient ◽  
Beneficial Mutation ◽  
Average Effect ◽  
Stressful Environments ◽  
Intermediate Effect

The fixation of a beneficial mutation represents the first step in adaptation, and the average effect of such mutations is therefore a fundamental property of evolving populations. It is nevertheless poorly characterized because the rarity of beneficial mutations makes it difficult to obtain reliable estimates of fitness. We obtained 68 genotypes each containing a single fixed beneficial mutation from experimental populations of Pseudomonas fluorescens , evolving in medium with serine as the sole carbon source and estimated the selective advantage of each by competition with the ancestor. The distribution of selection coefficients is modal and closely resembles the Weibull distribution. The average selection coefficient (2.1) and beneficial mutation rate (3.8×10 −8 ) are high relative to previous studies, possibly because the ancestral population grows poorly in serine-limited medium. Our experiment suggests that the initial stages of adaptation to stressful environments will involve the substitution of mutations with large effect on fitness.

MODELING THE ROLE OF MUTATIONS AND DENSITY INDEPENDENT DISPERSAL IN EVOLUTIONARY RESCUE

2014 ◽  
Vol 22 (01) ◽  
pp. 123-132
Author(s):  
MELKIOR ORNIK
Keyword(s):  
Experimental Research ◽  
Discrete Time ◽  
Environmental Changes ◽  
Discrete Space ◽  
Time Model ◽  
Beneficial Mutations ◽  
Discrete Time Model ◽  
Population Dispersal ◽  
Evolutionary Rescue

Faced with a strong and sudden deterioration of environment, a population encounters two possible options — adapt or perish. In general, it is not known which of those outcomes the environmental changes will lead to. Building on experimental research, we introduce a discrete-space, discrete-time model for environmental rescue based on the influence of population dispersal, as well as, potentially beneficial mutations. Numerical results obtained by the model are shown to correspond well to experimentally obtained data.

scholarly journals Haldane’s Probability of Mutant Survival is Not the Probability of Allele Establishment

2019 ◽  
Author(s):  
Ivan Krukov ◽  
A.P. Jason de Koning
Keyword(s):  
Odds Ratio ◽  
Short Note ◽  
Selective Advantage ◽  
Fixation Probability ◽  
Probability Of Survival ◽  
Fisher Model ◽  
Large Populations ◽  
Establishment Probability ◽  
Probability Of Fixation ◽  
Over Time

ABSTRACTHaldane notably showed in 1927 that the probability of fixation for an advantageous allele is approximately 2s, for selective advantage s. This widely known result is variously interpreted as either the fixation probability or the establishment probability, where the latter is considered the likelihood that an allele will survive long enough to have effectively escaped loss by drift. While Haldane was concerned with escape from loss by drift in the same paper, in this short note we point out that: 1) Haldane’s ‘probability of survival’ is analogous to the probability of fixation in a Wright-Fisher model (as also shown by others); and 2) This result is unrelated to Haldane’s consideration of how common an allele must be to ‘probably spread through the species’. We speculate that Haldane’s survival probability may have become misunderstood over time due to a conflation of terminology about surviving drift and ‘ultimately surviving’ (i.e., fixing). Indeed, we find that the probability of establishment remarkably appears to have been overlooked all these years, perhaps as a consequence of this misunderstanding. Using straightforward diffusion and Markov chain methods, we show that under Haldane’s assumptions, where establishment is defined by eventual fixation being more likely that extinction, the establishment probability is actually 4s when the fixation probability is 2s. Generalizing consideration to deleterious, neutral, and adaptive alleles in finite populations, if establishment is defined by the odds ratio between eventual fixation and extinction, k, the general establishment probability is (1 + k)/k times the fixation probability. It is therefore 4s when k = 1, or 3s when k = 2 for beneficial alleles in large populations. As k is made large, establishment becomes indistinguishable from fixation, and ceases to be a useful concept. As a result, we recommend establishment be generally defined as when the odds of ultimate fixation are greater than for extinction (k = 1, following Haldane), or when fixation is twice as likely as extinction (k = 2).

scholarly journals Regular bottlenecks and restrictions to somatic fusion prevent the accumulation of mitochondrial defects in Neurospora

2014 ◽  
Vol 369 (1646) ◽  
pp. 20130448 ◽  
Author(s):  
E. Bastiaans ◽  
D. K. Aanen ◽  
A. J. M. Debets ◽  
R. F. Hoekstra ◽  
B. Lestrade ◽  
...  
Keyword(s):  
Detrimental Effect ◽  
Nuclear Dna ◽  
Selective Advantage ◽  
Wild Type ◽  
Selfish Genetic Elements ◽  
Somatic Fusion ◽  
Mtdna Variation ◽  
Effective Selection ◽  
Mitochondrial Defects ◽  
Mtdna Variants

The replication and segregation of multi-copy mitochondrial DNA (mtDNA) are not under strict control of the nuclear DNA. Within-cell selection may thus favour variants with an intracellular selective advantage but a detrimental effect on cell fitness. High relatedness among the mtDNA variants of an individual is predicted to disfavour such deleterious selfish genetic elements, but experimental evidence for this hypothesis is scarce. We studied the effect of mtDNA relatedness on the opportunities for suppressive mtDNA variants in the fungus Neurospora carrying the mitochondrial mutator plasmid pKALILO. During growth, this plasmid integrates into the mitochondrial genome, generating suppressive mtDNA variants. These mtDNA variants gradually replace the wild-type mtDNA, ultimately culminating in growth arrest and death. We show that regular sequestration of mtDNA variation is required for effective selection against suppressive mtDNA variants. First, bottlenecks in the number of mtDNA copies from which a ‘ Kalilo ’ culture started significantly increased the maximum lifespan and variation in lifespan among cultures. Second, restrictions to somatic fusion among fungal individuals, either by using anastomosis-deficient mutants or by generating allotype diversity, prevented the accumulation of suppressive mtDNA variants. We discuss the implications of these results for the somatic accumulation of mitochondrial defects during ageing.

scholarly journals Ecological limits to evolutionary rescue

2020 ◽  
Vol 375 (1814) ◽  
pp. 20190453 ◽  
Author(s):  
Christopher A. Klausmeier ◽  
Matthew M. Osmond ◽  
Colin T. Kremer ◽  
Elena Litchman
Keyword(s):  
Species Interactions ◽  
Interspecific Interactions ◽  
Research Programme ◽  
Species Traits ◽  
Marine Conservation ◽  
Fundamental Limits ◽  
Fitness Functions ◽  
Changing Environments ◽  
Research Perspectives ◽  
Evolutionary Rescue

Environments change, for both natural and anthropogenic reasons, which can threaten species persistence. Evolutionary adaptation is a potentially powerful mechanism to allow species to persist in these changing environments. To determine the conditions under which adaptation will prevent extinction (evolutionary rescue), classic quantitative genetics models have assumed a constantly changing environment. They predict that species traits will track a moving environmental optimum with a lag that approaches a constant. If fitness is negative at this lag, the species will go extinct. There have been many elaborations of these models incorporating increased genetic realism. Here, we review and explore the consequences of four ecological complications: non-quadratic fitness functions, interacting density- and trait-dependence, species interactions and fundamental limits to adaptation. We show that non-quadratic fitness functions can result in evolutionary tipping points and existential crises, as can the interaction between density- and trait-dependent mortality. We then review the literature on how interspecific interactions affect adaptation and persistence. Finally, we suggest an alternative theoretical framework that considers bounded environmental change and fundamental limits to adaptation. A research programme that combines theory and experiments and integrates across organizational scales will be needed to predict whether adaptation will prevent species extinction in changing environments. This article is part of the theme issue ‘Integrative research perspectives on marine conservation’.

Adaptive introgression enables evolutionary rescue from extreme environmental pollution

Science ◽  
2019 ◽  
Vol 364 (6439) ◽  
pp. 455-457 ◽  
Author(s):  
Elias M. Oziolor ◽  
Noah M. Reid ◽  
Sivan Yair ◽  
Kristin M. Lee ◽  
Sarah Guberman VerPloeg ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Environmental Change ◽  
Population Decline ◽  
Pollution Level ◽  
Selection Coefficient ◽  
Fundulus Grandis ◽  
Adaptive Introgression ◽  
Aryl Hydrocarbon ◽  
Evolutionary Rescue ◽  
Recent Selection

Radical environmental change that provokes population decline can impose constraints on the sources of genetic variation that may enable evolutionary rescue. Adaptive toxicant resistance has rapidly evolved in Gulf killifish (Fundulus grandis) that occupy polluted habitats. We show that resistance scales with pollution level and negatively correlates with inducibility of aryl hydrocarbon receptor (AHR) signaling. Loci with the strongest signatures of recent selection harbor genes regulating AHR signaling. Two of these loci introgressed recently (18 to 34 generations ago) from Atlantic killifish (F. heteroclitus). One introgressed locus contains a deletion in AHR that confers a large adaptive advantage [selection coefficient (s) = 0.8]. Given the limited migration of killifish, recent adaptive introgression was likely mediated by human-assisted transport. We suggest that interspecies connectivity may be an important source of adaptive variation during extreme environmental change.

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