scholarly journals Slow recovery from inbreeding depression generated by the complex genetic architecture of segregating deleterious mutations

2019 ◽  
Author(s):  
Paula E. Adams ◽  
Anna L. Crist ◽  
Ellen M. Young ◽  
John H. Willis ◽  
Patrick C. Phillips ◽  
...  
Keyword(s):  
Population Size ◽  
Inbreeding Depression ◽  
Evolutionary Biology ◽  
Large Population ◽  
Genomic Diversity ◽  
List Type ◽  
Reproductive Systems ◽  
Genomic Changes ◽  
Deleterious Alleles ◽  
Sister Mating

AbstractThe deleterious effects of inbreeding have been of extreme importance to evolutionary biology, but it has been difficult to characterize the complex interactions between genetic constraints and selection that lead to fitness loss and recovery after inbreeding. Viruses, bacteria, and the selfing nematode Caenorhabditis elegans have been shown to be capable of rapid recovery from the fixation of novel deleterious mutation, however the potential for fitness recovery from fixation of segregating variation under inbreeding in outcrossing organisms is poorly understood. C. remanei is an outcrossing relative of C. elegans with high polymorphic variation and extreme inbreeding depression. Here we sought to characterize changes C. remanei in patterns of genomic diversity after ∼30 generations of inbreeding via brother-sister mating followed by several hundred generations of recovery at large population size. As expected, inbreeding led to a large decline in reproductive fitness, but unlike results from mutation accumulation experiments, recovery from inbreeding at large populations sizes generated only very moderate recovery in fitness after 300 generations. At the genomic level, we found that while 66% of ancestral segregating SNPs were fixed in the inbred population, this was far fewer than expected under neutral processes. Under recovery, 36 SNPs across 30 genes involved in alimentary, muscular, nervous and reproductive systems changed reproducibly across all replicates, indicating that strong selection for fitness recovery does exist but is likely mutationally limited due to the large number of potential targets. Our results indicate that recovery from inbreeding depression via new compensatory mutations is likely to be constrained by the large number of segregating deleterious variants present in natural populations, limiting the capacity for rapid evolutionary rescue of small populations.Impact SummaryInbreeding is defined as mating between close relatives and can have a large effect on the genetic diversity and fitness of populations. This has been recognized for over 100 years of study in evolutionary biology, but the specific genomic changes that accompany inbreeding and the loss of fitness are still not known. Evolutionary theory predicts that inbred populations lose fitness through the fixation of many deleterious alleles and it is not known if populations can recover fitness after prolonged periods of inbreeding and deleterious fixations, or how long recovery may take. These questions are particularly important for wild populations experiencing declines. In this study we use laboratory populations of the nematode worm Caenorhabditis remanei to analyze the loss of fitness and genomic changes that accompany inbreeding via brother-sister mating, and to track the populations as they recover from inbreeding at large population size over 300 generations. We find that: Total progeny decreased by 65% after inbreedingThere were many nucleotides in the genome that remained heterozygous after inbreedingThere was an excess of inbreeding-resistant nucleotides on the X chromosomeThe number of progeny remained low after 300 generations of recovery from inbreeding30 genes changed significant in allele frequency during recovery, including genes involved in the alimentary, muscular, nervous and reproductive systemsTogether, our results demonstrate that recovery from inbreeding is difficult, likely due to the fixation of numerous deleterious alleles throughout the genome.

scholarly journals Long-term exhaustion of the inbreeding load in Drosophila melanogaster

Heredity ◽  
2021 ◽  
Author(s):  
Noelia Pérez-Pereira ◽  
Ramón Pouso ◽  
Ana Rus ◽  
Ana Vilas ◽  
Eugenio López-Cortegano ◽  
...  
Keyword(s):  
Inbreeding Depression ◽  
Evolutionary Biology ◽  
Gene Action ◽  
Large Population ◽  
Recessive Gene ◽  
Deleterious Alleles ◽  
Sib Mating ◽  
Large Populations ◽  
Great Relevance

AbstractInbreeding depression, the decline in fitness of inbred individuals, is a ubiquitous phenomenon of great relevance in evolutionary biology and in the fields of animal and plant breeding and conservation. Inbreeding depression is due to the expression of recessive deleterious alleles that are concealed in heterozygous state in noninbred individuals, the so-called inbreeding load. Genetic purging reduces inbreeding depression by removing these alleles when expressed in homozygosis due to inbreeding. It is generally thought that fast inbreeding (such as that generated by full-sib mating lines) removes only highly deleterious recessive alleles, while slow inbreeding can also remove mildly deleterious ones. However, a question remains regarding which proportion of the inbreeding load can be removed by purging under slow inbreeding in moderately large populations. We report results of two long-term slow inbreeding Drosophila experiments (125–234 generations), each using a large population and a number of derived lines with effective sizes about 1000 and 50, respectively. The inbreeding load was virtually exhausted after more than one hundred generations in large populations and between a few tens and over one hundred generations in the lines. This result is not expected from genetic drift alone, and is in agreement with the theoretical purging predictions. Computer simulations suggest that these results are consistent with a model of relatively few deleterious mutations of large homozygous effects and partially recessive gene action.

scholarly journals Inbreeding depression due to mildly deleterious mutations in finite populations: size does matter

2000 ◽  
Vol 75 (1) ◽  
pp. 75-81 ◽  
Author(s):  
THOMAS BATAILLON ◽  
MARK KIRKPATRICK
Keyword(s):  
Population Size ◽  
Inbreeding Depression ◽  
Deleterious Mutation ◽  
Large Population ◽  
Genetic Load ◽  
Breeding Systems ◽  
Deleterious Mutations ◽  
Single Locus Analysis ◽  
Population Sizes ◽  
Inbreeding Rate

We studied the effects of population size on the inbreeding depression and genetic load caused by deleterious mutations at a single locus. Analysis shows how the inbreeding depression decreases as population size becomes smaller and/or the rate of inbreeding increases. This pattern contrasts with that for the load, which increases as population size becomes smaller but decreases as inbreeding rate goes up. The depression and load both approach asymptotic limits when the population size becomes very large or very small. Numerical results show that the transition between the small and the large population regimes is quite rapid, and occurs largely over a range of population sizes that vary by a factor of 10. The effects of drift on inbreeding depression may bias some estimates of the genomic rate of deleterious mutation. These effects could also be important in the evolution of breeding systems in hermaphroditic organisms and in the conservation of endangered populations.

scholarly journals Evidence that the rate of strong selective sweeps increases with population size in the great apes

2017 ◽  
Vol 114 (7) ◽  
pp. 1613-1618 ◽  
Author(s):  
Kiwoong Nam ◽  
Kasper Munch ◽  
Thomas Mailund ◽  
Alexander Nater ◽  
Maja Patricia Greminger ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Large Population ◽  
Great Apes ◽  
Genomic Diversity ◽  
Comparative Approach ◽  
Selective Sweeps ◽  
Effective Population ◽  
Intergenic Sequences ◽  
The Right

Quantifying the number of selective sweeps and their combined effects on genomic diversity in humans and other great apes is notoriously difficult. Here we address the question using a comparative approach to contrast diversity patterns according to the distance from genes in all great ape taxa. The extent of diversity reduction near genes compared with the rest of intergenic sequences is greater in a species with larger effective population size. Also, the maximum distance from genes at which the diversity reduction is observed is larger in species with large effective population size. In Sumatran orangutans, the overall genomic diversity is ∼30% smaller than diversity levels far from genes, whereas this reduction is only 9% in humans. We show by simulation that selection against deleterious mutations in the form of background selection is not expected to cause these differences in diversity among species. Instead, selective sweeps caused by positive selection can reduce diversity level more severely in a large population if there is a higher number of selective sweeps per unit time. We discuss what can cause such a correlation, including the possibility that more frequent sweeps in larger populations are due to a shorter waiting time for the right mutations to arise.

scholarly journals Genetic Allee effects and their interaction with ecological Allee effects

2016 ◽  
Author(s):  
Meike J. Wittmann ◽  
Hanna Stuis ◽  
Dirk Metzler
Keyword(s):  
Population Size ◽  
Inbreeding Depression ◽  
Survival Probability ◽  
Allee Effect ◽  
Extinction Risk ◽  
List Type ◽  
Small Populations ◽  
Allee Effects ◽  
Deleterious Mutations ◽  
Lethal Equivalents

SummaryIt is now widely accepted that genetic processes such as inbreeding depression and loss of genetic variation can increase the extinction risk of small populations. However, it is generally unclear whether extinction risk from genetic causes gradually increases with decreasing population size or whether there is a sharp transition around a specific threshold population size. In the ecological literature, such threshold phenomena are called “strong Allee effects” and they can arise for example from mate limitation in small populations.In this study, we aim to a) develop a meaningful notion of a “strong genetic Allee effect”, b) explore whether and under what conditions such an effect can arise from inbreeding depression due to recessive deleterious mutations, and c) quantify the interaction of potential genetic Allee effects with the well-known mate-finding Allee effect.We define a strong genetic Allee effect as a genetic process that causes a population’s survival probability to be a sigmoid function of its initial size. The inflection point of this function defines the critical population size. To characterize survival-probability curves, we develop and analyze simple stochastic models for the ecology and genetics of small populations.Our results indicate that inbreeding depression can indeed cause a strong genetic Allee effect, but only if individuals carry sufficiently many deleterious mutations (lethal equivalents) on average and if these mutations are spread across sufficiently many loci. Populations suffering from a genetic Allee effect often first grow, then decline as inbreeding depression sets in, and then potentially recover as deleterious mutations are purged. Critical population sizes of ecological and genetic Allee effects appear to be often additive, but even superadditive interactions are possible.Many published estimates for the number of lethal equivalents in birds and mammals fall in the parameter range where strong genetic Allee effects are expected. Unfortunately, extinction risk due to genetic Allee effects can easily be underestimated as populations with genetic problems often grow initially, but then crash later. Also interactions between ecological and genetic Allee effects can be strong and should not be neglected when assessing the viability of endangered or introduced populations.

scholarly journals Small population size and low genomic diversity have no effect on fitness in experimental translocations of a wild fish

2019 ◽  
Vol 286 (1916) ◽  
pp. 20191989 ◽  
Author(s):  
M. C. Yates ◽  
E. Bowles ◽  
D. J. Fraser
Keyword(s):  
Genetic Diversity ◽  
Body Size ◽  
Population Size ◽  
Brook Trout ◽  
Habitat Degradation ◽  
Species Conservation ◽  
Empirical Work ◽  
Genomic Diversity ◽  
Effective Population ◽  
Isolated Populations

Little empirical work in nature has quantified how wild populations with varying effective population sizes and genetic diversity perform when exposed to a gradient of ecologically important environmental conditions. To achieve this, juvenile brook trout from 12 isolated populations or closed metapopulations that differ substantially in population size and genetic diversity were transplanted to previously fishless ponds spanning a wide gradient of ecologically important variables. We evaluated the effect of genome-wide variation, effective population size ( N e ), pond habitat, and initial body size on two fitness correlates (survival and growth). Genetic variables had no effect on either fitness correlate, which was determined primarily by habitat (pond temperature, depth, and pH) and initial body size. These results suggest that some vertebrate populations with low genomic diversity, low N e , and long-term isolation can represent important sources of variation and are capable of maintaining fitness in, and ultimately persisting and adapting to, changing environments. Our results also reinforce the paramount importance of improving available habitat and slowing habitat degradation for species conservation.

scholarly journals Selection, Load and Inbreeding Depression in a Large Metapopulation

Genetics ◽  
2002 ◽  
Vol 160 (3) ◽  
pp. 1191-1202 ◽  
Author(s):  
Michael C Whitlock
Keyword(s):  
Population Structure ◽  
Inbreeding Depression ◽  
Population Subdivision ◽  
Response To Selection ◽  
Mutation Load ◽  
Deleterious Alleles ◽  
Subdivided Population ◽  
Soft Selection ◽  
Mean Fitness ◽  
The Mean

Abstract The subdivision of a species into local populations causes its response to selection to change, even if selection is uniform across space. Population structure increases the frequency of homozygotes and therefore makes selection on homozygous effects more effective. However, population subdivision can increase the probability of competition among relatives, which may reduce the efficacy of selection. As a result, the response to selection can be either increased or decreased in a subdivided population relative to an undivided one, depending on the dominance coefficient FST and whether selection is hard or soft. Realistic levels of population structure tend to reduce the mean frequency of deleterious alleles. The mutation load tends to be decreased in a subdivided population for recessive alleles, as does the expected inbreeding depression. The magnitude of the effects of population subdivision tends to be greatest in species with hard selection rather than soft selection. Population structure can play an important role in determining the mean fitness of populations at equilibrium between mutation and selection.

scholarly journals Macroeconomic Impacts of Climate Change Driven by Changes in Crop Yields

2018 ◽  
Vol 10 (10) ◽  
pp. 3673 ◽  
Author(s):  
Shinichiro Fujimori ◽  
Toshichika Iizumi ◽  
Tomoko Hasegawa ◽  
Jun’ya Takakura ◽  
Kiyoshi Takahashi ◽  
...  
Keyword(s):  
Climate Change ◽  
Land Use ◽  
Population Size ◽  
Large Population ◽  
Food Prices ◽  
Production Volume ◽  
Total Uncertainty ◽  
Indicator Value ◽  
Macroeconomic Impacts ◽  
Macroeconomic Indicator

Changes in agricultural yields due to climate change will affect land use, agricultural production volume, and food prices as well as macroeconomic indicators, such as GDP, which is important as it enables one to compare climate change impacts across multiple sectors. This study considered five key uncertainty factors and estimated macroeconomic impacts due to crop yield changes using a novel integrated assessment framework. The five factors are (1) land-use change (or yield aggregation method based on spatially explicit information), (2) the amplitude of the CO2 fertilization effect, (3) the use of different climate models, (4) socioeconomic assumptions and (5) the level of mitigation stringency. We found that their global impacts on the macroeconomic indicator value were 0.02–0.06% of GDP in 2100. However, the impacts on the agricultural sector varied greatly by socioeconomic assumption. The relative contributions of these factors to the total uncertainty in the projected macroeconomic indicator value were greater in a pessimistic world scenario characterized by a large population size, low income, and low yield development than in an optimistic scenario characterized by a small population size, high income, and high yield development (0.00%).

POPULATION DYNAMICS OF SEX-DETERMINING ALLELES IN HONEY BEES AND SELF-INCOMPATIBILITY ALLELES IN PLANTS

Genetics ◽  
1979 ◽  
Vol 91 (3) ◽  
pp. 609-626 ◽  
Author(s):  
Shozo Yokoyama ◽  
Masatoshi Nei
Keyword(s):  
Population Dynamics ◽  
Population Size ◽  
Honey Bee ◽  
Honey Bees ◽  
Finite Population ◽  
Large Population ◽  
Allele Frequencies ◽  
Self Incompatibility ◽  
Overdominant Selection ◽  
Incompatibility Alleles

ABSTRACT Mathematical theories of the population dynamics of sex-determining alleles in honey bees are developed. It is shown that in an infinitely large population the equilibrium frequency of a sex allele is l/n, where n is the number of alleles in the population, and the asymptotic rate of approach to this equilibrium is 2/(3n) per generation. Formulae for the distribution of allele frequencies and the effective and actual numbers of alleles that can be maintained in a finite population are derived by taking into account the population size and mutation rate. It is shown that the allele frequencies in a finite population may deviate considerably from l/n. Using these results, available data on the number of sex alleles in honey bee populations are discussed. It is also shown that the number of self-incompatibility alleles in plants can be studied in a much simpler way by the method used in this paper. A brief discussion about general overdominant selection is presented.

Evaluation of several initialization methods on arithmetic optimization algorithm performance

2021 ◽  
Vol 31 (1) ◽  
pp. 70-94
Author(s):  
Jeffrey O. Agushaka ◽  
Absalom E. Ezugwu
Keyword(s):  
Population Size ◽  
Optimization Algorithm ◽  
Beta Distribution ◽  
Random Number ◽  
Large Population ◽  
Latin Hypercube Sampling ◽  
Rayleigh Distribution ◽  
Population Based ◽  
Algorithm Performance ◽  
Number Of Iterations

Abstract Arithmetic optimization algorithm (AOA) is one of the recently proposed population-based metaheuristic algorithms. The algorithmic design concept of the AOA is based on the distributive behavior of arithmetic operators, namely, multiplication (M), division (D), subtraction (S), and addition (A). Being a new metaheuristic algorithm, the need for a performance evaluation of AOA is significant to the global optimization research community and specifically to nature-inspired metaheuristic enthusiasts. This article aims to evaluate the influence of the algorithm control parameters, namely, population size and the number of iterations, on the performance of the newly proposed AOA. In addition, we also investigated and validated the influence of different initialization schemes available in the literature on the performance of the AOA. Experiments were conducted using different initialization scenarios and the first is where the population size is large and the number of iterations is low. The second scenario is when the number of iterations is high, and the population size is small. Finally, when the population size and the number of iterations are similar. The numerical results from the conducted experiments showed that AOA is sensitive to the population size and requires a large population size for optimal performance. Afterward, we initialized AOA with six initialization schemes, and their performances were tested on the classical functions and the functions defined in the CEC 2020 suite. The results were presented, and their implications were discussed. Our results showed that the performance of AOA could be influenced when the solution is initialized with schemes other than default random numbers. The Beta distribution outperformed the random number distribution in all cases for both the classical and CEC 2020 functions. The performance of uniform distribution, Rayleigh distribution, Latin hypercube sampling, and Sobol low discrepancy sequence are relatively competitive with the Random number. On the basis of our experiments’ results, we recommend that a solution size of 6,000, the number of iterations of 100, and initializing the solutions with Beta distribution will lead to AOA performing optimally for scenarios considered in our experiments.

Anadromous Sturgeons: Habitats, Threats, and Management

2007 ◽  
Keyword(s):  
Growth Rate ◽  
Population Size ◽  
Yellow River ◽  
Large Population ◽  
Leading Edge ◽  
The Yellow River ◽  
Gulf Sturgeon ◽  
Successful Recruitment ◽  
Viable Population ◽  
Size Growth

<em>Abstract.</em>—The Gulf sturgeon <em>Acipenser oxyrinchus desotoi</em> is an anadromous species listed as threatened under the Endangered Species Act in 1991. We conducted a 3year tagging study to estimate population size, growth, mortality, and age composition for sturgeon in the Yellow River. Capture probabilities and population size were estimated using Program MARK and a Cormack-Jolly–Seber model. Total mortality of Gulf sturgeon was estimated using a Beverton–Holt mortality equation. Growth rate was determined from annuli on the leading edge of pectoral fin-ray. A total of 522 Gulf sturgeon captures were made, and 399 individual fish were tagged. The population estimates for the Gulf sturgeon over 3 years ranged from 500 to 911 fish. The age structure of the population suggests successful recruitment and a viable population. The total annual mortality estimate for Yellow River Gulf sturgeon was 11.9%. Growth rate for the Yellow River population was comparable to other populations of Gulf sturgeon. The Yellow River Gulf sturgeon population is a dynamic population based upon consistent age-classes as an indicator of successful recruitment, a large population size relative to most rivers where Gulf sturgeon are found, and estimates of mortality below the reported range for the species.

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