scholarly journals Accumulation and maintenance of information in evolution

2021 ◽  
Author(s):  
Michal Hledik ◽  
Nick H Barton ◽  
Gasper Tkacik
Keyword(s):  
Accumulation Rate ◽  
Genetic Load ◽  
Population Level ◽  
Relative Fitness ◽  
Actual Distribution ◽  
Genotype Frequencies ◽  
Information Sets ◽  
Level Information ◽  
Single Allele ◽  
The Cost

Selection accumulates information in the genome - it guides stochastically evolving populations towards states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback-Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright-Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation and recombination. Finally, the cost of maintaining information depends on how it is encoded: specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap.

scholarly journals Process noise distinguishes between indistinguishable population dynamics

2019 ◽  
Author(s):  
Matthew J. Simpson ◽  
Jacob M. Ryan ◽  
James M. McGree ◽  
Ruth E. Baker
Keyword(s):  
Model Selection ◽  
Stochastic Models ◽  
Population Level ◽  
Logistic Growth ◽  
Summary Statistics ◽  
Process Noise ◽  
Level Information ◽  
Improved Model ◽  
The Cost ◽  
Stochastic Setting

AbstractModel selectionis becoming increasingly important in mathematical biology. Model selection often involves comparing a set of observations with predictions from a suite of continuum mathematical models and selecting the model that provides the best explanation of the data. In this work we consider the more challenging problem of model selection in a stochastic setting. We consider five different stochastic models describing population growth. Through simulation we show that all five stochastic models gives rise to classical logistic growth in the limit where we consider a large number of identically prepared realisations. Therefore, comparing mean data from each of the models gives indistinguishable predictions and model selection based on population-level information is impossible. To overcome this challenge we extractprocess noisefrom individual realisations of each model and identify properties in the process noise that differ between the various stochastic models. Using a Bayesian framework, we show how process noise can be used successfully to make a probabilistic distinction between the various stochastic models. The relative success of this approach depends upon the identification of appropriate summary statistics and we illustrate how increasingly sophisticated summary statistics can lead to improved model selection, but this improvement comes at the cost of requiring more detailed summary statistics.

scholarly journals Increase in Zucchini yellow mosaic virus Symptom Severity in Tolerant Zucchini Cultivars Is Related to a Point Mutation in P3 Protein and Is Associated with a Loss of Relative Fitness on Susceptible Plants

2003 ◽  
Vol 93 (12) ◽  
pp. 1478-1484 ◽  
Author(s):  
C. Desbiez ◽  
A. Gal-On ◽  
M. Girard ◽  
C. Wipf-Scheibel ◽  
H. Lecoq
Keyword(s):  
Mosaic Virus ◽  
Point Mutation ◽  
Zucchini Yellow Mosaic Virus ◽  
Genetic Load ◽  
Yellow Mosaic Virus ◽  
Relative Fitness ◽  
Interspecific Crosses ◽  
Mixed Infections ◽  
Wild Type ◽  
Sequence Comparisons

Zucchini yellow mosaic virus (ZYMV, Potyvirus) is a very damaging cucurbit virus worldwide. Interspecific crosses with resistant Cucurbita moschata have led to the release of “resistant” zucchini squash (C. pepo) F1 hybrids. However, although the resistance is almost complete in C. moschata, the commercial C. pepo hybrids are only tolerant. ZYMV evolution toward increased aggressiveness on tolerant hybrids was observed in the field and was obtained experimentally. Sequence comparisons and recombination experiments revealed that a point mutation in the P3 protein of ZYMV was enough to induce tolerance breaking. Competition experiments were performed between quasi-isogenic wild-type, and aggressive variants of ZYMV distinguished by monoclonal antibodies. The aggressive mutants were more fit than wild-type strains in mixed infections of tolerant zucchini, but they presented a drastic fitness loss in mixed infections of susceptible zucchini or melon. Thus, the ability to induce severe symptoms in tolerant zucchini is related to a genetic load in susceptible zucchini, but also on other susceptible hosts. This represents the first quantitative study of the fitness cost associated with tolerance breaking for a plant virus. Thus, although easily broken, the tolerance might prove durable in some conditions if the aggressive variants are counterselected in susceptible crops.

Overt and Concealed Genetic Loads Revealed by QTL Mapping of Genotype-dependent Viability in the Pacific Oyster Crassostrea gigas

Genetics ◽  
2021 ◽  
Author(s):  
Xiaoshen Yin ◽  
Dennis Hedgecock
Keyword(s):  
Genetic Diversity ◽  
Crassostrea Gigas ◽  
Pacific Oyster ◽  
Genetic Load ◽  
High Density ◽  
High Genetic Diversity ◽  
High Fecundity ◽  
Recessive Mutations ◽  
Genotype Frequencies ◽  
The Pacific

Abstract Understanding the genetic bases of inbreeding depression, heterosis, and genetic load is integral to understanding how genetic diversity is maintained in natural populations. The Pacific oyster Crassostrea gigas, like many long-lived plants, has high fecundity and high early mortality (type-III survivorship), manifesting a large, overt, genetic load; the oyster harbors an even greater concealed genetic load revealed by inbreeding. Here, we map viability QTL (vQTL) in six interrelated F2 oyster families, using high-density linkage maps of single nucleotide polymorphisms generated by genotyping-by-sequencing (GBS) methods. Altogether, we detect 70 vQTL and provisionally infer 89 causal mutations, 11 to 20 per family. Genetic mortality caused by independent (unlinked) vQTL ranges from 94.2% to 97.8% across families, consistent with previous reports. High-density maps provide better resolution of genetic mechanisms, however. Models of one causal mutation present in both identical-by-descent (IBD) homozygotes and heterozygotes fit genotype frequencies at 37 vQTL; consistent with the mutation-selection balance theory of genetic load, 20 are highly deleterious, completely recessive mutations and 17 are less deleterious, partially dominant mutations. Another 22 vQTL require pairs of recessive or partially dominant causal mutations, half showing selection against recessive mutations linked in repulsion, producing pseudo-overdominance. Only eight vQTL appear to support the overdominance theory of genetic load, with deficiencies of both IBD homozygotes, but at least four of these are likely caused by pseudo-overdominance. Evidence for epistasis is absent. A high mutation rate, random genetic drift, and pseudo-overdominance may explain both the oyster’s extremely high genetic diversity and a high genetic load maintained primarily by mutation-selection balance.

scholarly journals A narrative review on HPV vaccination among boys and men

2020 ◽  
pp. 9-12
Author(s):  
Vinod K Ramani ◽  
Radheshyam Naik
Keyword(s):  
Hpv Vaccine ◽  
Hpv Vaccination ◽  
Herd Immunity ◽  
Population Level ◽  
Hpv Infection ◽  
Level Control ◽  
Anogenital Warts ◽  
Indian Context ◽  
Present Generation ◽  
The Cost

Apart from cervical cancer, Human papillomavirus (HPV) infection is associated with head and neck as well as other anogenital cancers such as vulva, vagina, anus, and penis. HPV vaccine provides specific protection against the disease and its subsequent manifestations.Vaccination programs for men tend to improve population-level control of HPV infection and directly prevent HPV related disease such as anogenital warts and oropharyngeal cancers in males. HPV vaccine does not treat existing infection or lesions/cancer and is intended for individuals before initiation fo sexual activity or any other form of exposure to HPV.Many programs across the globe do not include vaccination for boys because of the cost and little recognition of the emerging epidemic of HPV associated cancers in men. In the Indian context, as screening is not feasible for non-cervical HPV associated cancers, its incidence mostly among men will continue to rise until the present generation of vaccinated adolescents reaches their middle-age.Vaccination will reduce transmission rates and increase herd immunity. This in-turn, will prevent not just cervical cancers but also other HPV-associated malignancies among men and women.

Estimation of genotype distributions and posterior genotype probabilities for beta-mannosidosis in Salers cattle.

Genetics ◽  
1993 ◽  
Vol 135 (3) ◽  
pp. 855-868
Author(s):  
J F Taylor ◽  
B Abbitt ◽  
J P Walter ◽  
S K Davis ◽  
J T Jaques ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Medical Diagnostics ◽  
Relative Fitness ◽  
Model Parameters ◽  
Genotype Distribution ◽  
Lysosomal Storage ◽  
Genotypic Distribution ◽  
Genotype Assignment ◽  
Genotype Frequencies ◽  
Systematic Effects

Abstract beta-Mannosidosis is a lethal lysosomal storage disease inherited as an autosomal recessive in man, cattle and goats. Laboratory assay data of plasma beta-mannosidase activity represent a mixture of homozygous normal and carrier genotype distributions in a proportion determined by genotype frequency. A maximum likelihood approach employing data transformations for each genotype distribution and assuming a diallelic model of inheritance is described. Estimates of the transformation and genotype distribution parameters, gene frequency, genotype fitness and carrier probability were obtained simultaneously from a sample of 2,812 observations on U.S. purebred Salers cattle with enzyme activity, age, gender, month of pregnancy, month of testing, and parents identified. Transformations to normality were not required, estimated gene and carrier genotype frequencies of 0.074 and 0.148 were high, and the estimated relative fitness of heterozygotes was 1.36. The apparent overdominance in fitness may be due to a nonrandom sampling of progeny genotypes within families. The mean of plasma enzyme activity was higher for males than females, higher in winter months, lower in summer months and decreased with increased age. Estimates of carrier probabilities indicate that the test is most effective when animals are sampled as calves, although effectiveness of the plasma assay was less for males than females. Test effectiveness was enhanced through averaging repeated assays of enzyme activity on each animal. Our approach contributes to medical diagnostics in several ways. Rather than assume underlying normality for the distributions comprising the mixture, we estimate transformations to normality for each genotype distribution simultaneously with all other model parameters. This process also excludes potential biases due to data preadjustment for systematic effects. We also provide a method for partitioning phenotypic variation within each genotypic distribution which allows an assessment of the value of repeat measurements of the predictive variable for genotype assignment.

scholarly journals The consequences of polyandry for population viability, extinction risk and conservation

2013 ◽  
Vol 368 (1613) ◽  
pp. 20120053 ◽  
Author(s):  
Luke Holman ◽  
Hanna Kokko
Keyword(s):  
Population Dynamics ◽  
Extinction Risk ◽  
Population Level ◽  
Female Fitness ◽  
Male Care ◽  
Negative Effect ◽  
Adverse Environmental Conditions ◽  
The Cost ◽  
Cost Of Sex ◽  
Population Fitness

Polyandry, by elevating sexual conflict and selecting for reduced male care relative to monandry, may exacerbate the cost of sex and thereby seriously impact population fitness. On the other hand, polyandry has a number of possible population-level benefits over monandry, such as increased sexual selection leading to faster adaptation and a reduced mutation load. Here, we review existing information on how female fitness evolves under polyandry and how this influences population dynamics. In balance, it is far from clear whether polyandry has a net positive or negative effect on female fitness, but we also stress that its effects on individuals may not have visible demographic consequences. In populations that produce many more offspring than can possibly survive and breed, offspring gained or lost as a result of polyandry may not affect population size. Such ecological ‘masking’ of changes in population fitness could hide a response that only manifests under adverse environmental conditions (e.g. anthropogenic change). Surprisingly few studies have attempted to link mating system variation to population dynamics, and in general we urge researchers to consider the ecological consequences of evolutionary processes.

scholarly journals Advances in research on the impacts of anti-submarine sonar on beaked whales

2019 ◽  
Vol 286 (1895) ◽  
pp. 20182533 ◽  
Author(s):  
Y. Bernaldo de Quirós ◽  
A. Fernandez ◽  
R. W. Baird ◽  
R. L. Brownell ◽  
N. Aguilar de Soto ◽  
...  
Keyword(s):  
Canary Islands ◽  
Decompression Sickness ◽  
Current Knowledge ◽  
Population Level ◽  
Mitigation Measures ◽  
Individual Outcomes ◽  
Spatial Management ◽  
Level Information ◽  
Beaked Whales ◽  
The 1960S

Mass stranding events (MSEs) of beaked whales (BWs) were extremely rare prior to the 1960s but increased markedly after the development of naval mid-frequency active sonar (MFAS). The temporal and spatial associations between atypical BW MSEs and naval exercises were first observed in the Canary Islands, Spain, in the mid-1980s. Further research on BWs stranded in association with naval exercises demonstrated pathological findings consistent with decompression sickness (DCS). A 2004 ban on MFASs around the Canary Islands successfully prevented additional BW MSEs in the region, but atypical MSEs have continued in other places of the world, especially in the Mediterranean Sea, with examined individuals showing DCS. A workshop held in Fuerteventura, Canary Islands, in September 2017 reviewed current knowledge on BW atypical MSEs associated with MFAS. Our review suggests that the effects of MFAS on BWs vary among individuals or populations, and predisposing factors may contribute to individual outcomes. Spatial management specific to BW habitat, such as the MFAS ban in the Canary Islands, has proven to be an effective mitigation tool and mitigation measures should be established in other areas taking into consideration known population-level information.

A Bird's-Eye View of Pollination: Biotic Interactions as Drivers of Adaptation and Community Change

2019 ◽  
Vol 50 (1) ◽  
pp. 477-502 ◽  
Author(s):  
Anton Pauw
Keyword(s):  
Community Composition ◽  
Bird Species ◽  
Biotic Interactions ◽  
Population Level ◽  
Community Change ◽  
Plant Evolution ◽  
Relative Fitness ◽  
Fitness Advantage ◽  
Bird Evolution ◽  
Composition I

Nectarivorous birds and bird-pollinated plants are linked by a network of interactions. Here I ask how these interactions influence evolution and community composition. I find near complete evidence for the effect of birds on plant evolution. Experiments show the process in action—birds select among floral phenotypes in a population—and comparative studies find the resulting pattern—bird-pollinated species have long-tubed, red flowers with large nectar volumes. Speciation is accomplished in one “magical” step when adaptation for bird pollination brings about divergent morphology and reproductive isolation. In contrast, evidence that plants drive bird evolution is fragmentary. Studies of selection on population-level variation are lacking, but the resulting pattern is clear—nectarivorous birds have evolved a remarkable number of times and often have long bills and brush-tipped or tubular tongues. At the level of the ecological guild, birds select among plant species via an effect on seed set and thus determine plant community composition. Plants simultaneously influence the relative fitness of bird species and thus determine the composition of the bird guild. Interaction partners may give one guild member a constant fitness advantage, resulting in competitive exclusion and community change, or may act as limiting resources that depress the fitness of frequent species, thus stabilizing community composition and allowing the coexistence of diversity within bird and plant guilds.

scholarly journals Single-Cell Microbiology: Tools, Technologies, and Applications

2004 ◽  
Vol 68 (3) ◽  
pp. 538-559 ◽  
Author(s):  
Byron F. Brehm-Stecher ◽  
Eric A. Johnson
Keyword(s):  
Single Cell ◽  
Population Level ◽  
Cellular Heterogeneity ◽  
Food Preservatives ◽  
Complex Processes ◽  
Biocide Resistance ◽  
Level Data ◽  
Level Information ◽  
Or Gene ◽  
Tools And Techniques

SUMMARY The field of microbiology has traditionally been concerned with and focused on studies at the population level. Information on how cells respond to their environment, interact with each other, or undergo complex processes such as cellular differentiation or gene expression has been obtained mostly by inference from population-level data. Individual microorganisms, even those in supposedly “clonal” populations, may differ widely from each other in terms of their genetic composition, physiology, biochemistry, or behavior. This genetic and phenotypic heterogeneity has important practical consequences for a number of human interests, including antibiotic or biocide resistance, the productivity and stability of industrial fermentations, the efficacy of food preservatives, and the potential of pathogens to cause disease. New appreciation of the importance of cellular heterogeneity, coupled with recent advances in technology, has driven the development of new tools and techniques for the study of individual microbial cells. Because observations made at the single-cell level are not subject to the “averaging” effects characteristic of bulk-phase, population-level methods, they offer the unique capacity to observe discrete microbiological phenomena unavailable using traditional approaches. As a result, scientists have been able to characterize microorganisms, their activities, and their interactions at unprecedented levels of detail.

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