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The Warrior Zero Body Weight Challenge

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The Warrior Zero Body Weight Challenge Summary

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Decomposition of the Fitness Function

The following subsection provides some basic definitions for our discussion of representations for genetic and evolutionary algorithms. We show how every optimization problem that should be solved by using GEAs can be decomposed into a genotype-phenotype fg, and a phenotype-fitness mapping fp. where x is a vector of decision variables (or alleles), and f (x) is the objective or fitness function. The vector x is the global maximum. We have chosen to When using a representation for genetic and evolutionary algorithms we have to introduce - in analogy to nature - phenotypes and genotypes (Lewon-tin 1974 Liepins and Vose 1990). The fitness function f is decomposed into two parts. The first maps the genotypic space

Life History And Fitness

Life history is the progress of an individual throughout his or her life. An individual is first born, then grows into an adult or fails to survive to adulthood. If the individual survives to adulthood, then the individual perhaps mates and reproduces at specific ages and finally dies at some age. In Chapter 11, we defined the fitness components of viability, mating success, and fertility fecundity. To examine life history and its evolutionary implications, we must first make each of these fitness components an explicit function of age. We start with the fitness component of viability. Viability can be measured in an age-specific fashion by the age-specific survivorship, lx, the probability of an individual surviving to age x. Ideally, age should be measured from fertilization in order to cover the diploid individual's entire life history, but in practice a time point well after conception is used in many species. For mammals, and humans in particular, the initial time point is...

Fitness To Dive

Physical fitness is important, especially for the diver who plans to dive in northern European waters where the combination of tidal flow, cold, and the heavy equipment and thermal protection required to survive in such an environment makes such diving physically demanding. In tropical waters, although diving may appear to be less demanding physically, the divers may still be required to exert themselves entering and exiting the water carrying heavy equipment and also if required to rescue another diver. Head injuries account for 5 of the referrals to the Undersea Medicine Division at the Institute of Naval Medicine for an opinion regarding fitness to dive. The concerns with head injuries are twofold first, to ensure that the individual has recovered fully, with normal cognitive function and no residual neurological deficit and, second, to determine the risk of post-traumatic epilepsy. Epilepsy, whether idiopathic or post-traumatic, is an absolute contraindication to diving as sudden...

Outline of the Problem

In order to define dynamics, it is necessary to give the fitness values for each sequence. Having assigned the fitness values, we introduce a fitness landscape on the multidimensional sequences space 12, 13, 23, 24 , The fitness landscape of evolutionary system is similar to the energy landscape of physical systems. The difference is that physical system moves to the minimum energy, and the evolutionary system tends to the maximum fitness. On this language, mutation jumps in the sequences space are constrained by the fitness landscape. What kind of fitness landscape is adequate to the pre-biological evolution This is a rather vague question. For biological evolution, because selection of sequences is provided by specific functions, one can assume that a deterministic algorithm of the landscape introduction should be chosen. For prebiotic evolution, in opposite, one can proceed from an assumption that the fitness landscape is defined by a great number of random factors 23 , The...

Representations for Genetic and Evolutionary Algorithms

The chapter starts with an introduction into genetic representations. We describe the notion of genotypes and phenotypes and illustrate how the fitness function can be decomposed into a genotype-phenotype, and a phenotype-fitness mapping. The section ends with a brief characterization of widely used representations. In Sect. 2.2, we provide the basis for genetic and evolutionary algorithms. After a brief description of the principles of a simple genetic algorithm (GA), we present the underlying theory which explains why and how selectorecombinative GAs using crossover as a main search operator work. The schema theorem tells us that GAs process schemata and the building block hypothesis assumes that many real-world problems are decomposable (or at least quasi-decomposable). Therefore, GAs perform well for these types

Genetic Representations

In Sect 2.1.1, we introduce the notion of genotype and phenotype. We briefly describe how nature creates a phenotype from the corresponding genotype by the use of representations. This more biology-based approach to representations is followed in Sect. 2.1.2 by a more formal description of representations. Every fitness function f which assigns a fitness value to a genotype xg can be decomposed into the genotype-phenotype mapping fg, and the phenotype-fitness mapping fp. Finally, in Sect. 2.1.3 we briefly review the most important types of representations.

Water Deficit Stimulates Leaf Abscission

The total leaf area of a plant (number of leaves x surface area of each leaf) does not remain constant after all the leaves have matured. If plants become water stressed after a substantial leaf area has developed, leaves will senesce and eventually fall off (Figure 25.2). Such a leaf area adjustment is an important long-term change that improves the plant's fitness in a water-limited environment. Indeed, many drought-deciduous, desert plants drop all their leaves during a drought and sprout new ones after a rain. This cycle can occur two or more times in a single season. Abscission during water stress results largely from enhanced synthesis of and responsiveness to the endogenous plant hormone ethylene (see Chapter 22).

Create new populations

In the following paragraphs, we briefly explain the basic elements of a GA. For selecting highly fit individuals for reproduction a large number of different selection schemes have been developed. The most popular are proportionate (Holland 1975) and tournament selection (Goldberg et al. 1989). When using proportionate selection, the expected number of copies an individual has in the next population is proportional to its fitness. The chance of an individual xi of being selected for recombination is calculated as

Reasons for Problem Difficulty

Researchers recognized that there are other possible reasons of problem difficulty besides deception. Based on the structure of the fitness landscape (Weinberger 1990 Manderick et al. 1991), the correlation between the fitness of individuals describes how difficult a specific problem is to solve for GEAs. By the modality of a problem, which is more popular for mutation-based If we count the number of schemata of order o(h) k that have the same fixed positions, there are 2k different competing schemata. Based on their fitness, the different schemata compete against each other and GEAs should increase the number of the high-quality schemata. Identifying the high quality schemata and propagating them properly is the main difficulty of intra-BB difficulty. Goldberg measures intra-BB difficulty with the deceptiveness of a problem. Deceptive problems (Goldberg 1987) are most difficult to solve for GEAs because GEAs are led by the fitness landscape to a deceptive attractor which has maximum...

Three Elements of a Theory of Representations

When assigning phenotypes to genotypes, a representation fg can change the importance of the alleles. For example, if a phenotype is a list of integers, all alleles (integers) are equally relevant for calculating the fitness of a pheno-type. However, when encoding the phenotypic integers using binary strings, the contributions of the genotypic bits to the construction of the phenotypes and to the calculation of the corresponding fitness values are no longer equal as some genotypic bits are more relevant than others. By substituting alleles with building blocks (BBs), the order of scaling of a representation describes how different the contributions of the genotypic BBs are to the construction of the phenotypes. It is well known that if the BBs are uniformly scaled, GEAs solve all BBs implicitly in parallel. In contrast, for non-uniformly scaled BBs, domino convergence occurs and the BBs are solved sequentially starting with the most salient BB (Thierens 1995). As a result, the...

Ecological Aspects In Tree Breeding

Cell and tissue cultures adopted to tree breeding may greatly enhance genetic gains in characters such as wood quality (fiber length, lignin composition, specific gravity, bole straightness, crown form and branchiness, etc.) and wood volume (springwood latewood ratio, growth initiation and cessation, nutrient uptake, drought and cold tolerance, etc.). Manipulation of wood quality and volume, all included in final yield, may, however, be contradictory to tree adaptation in a certain climate additional yield may be at the cost of tree adaptation and fitness. During the past 40 years the world has experienced a considerable reduction of genetic diversity in agroecosystems with the advent of the green revolution with its high-yielding cultivars in rice, wheat, and maize, the three outstanding agricultural staple crops. Its consequences have been duly registered in pest and disease outbreaks.

Definition of Home Range

Why do animals have home ranges Stamps (1995 41) argued that animals have home ranges because individuals learn site-specific serial motor programs, which might be envisioned as near reflex movements that take an animal along well traveled routes to safety. These movements should enhance the animal's ability to maneuver through its environment and thereby to avoid or escape predators. Stamps argued that the willingness of an animal to incur costs to remain in a familiar area implies that being familiar with that area provides a fitness benefit greater than the costs. For animals with small home ranges that live their lives as potential prey, Stamps's hypothesis makes sense. However, many animals, especially predatory mammals and birds, have home ranges too large and use specific places too seldom for site-specific serial motor programs to have an important benefit. Site-specific serial motor patterns of greatest use to a predator would have to match the escape routes of each prey...

Redundant Representations in Evolutionary Computation Research

Following the work of Kimura, some biological studies (Huynen et al. 1996 Huynen 1996 Schuster 1997 Reidys and Stadler 1998) focused on the neutral theory. These studies showed that the connectivity between fitness landscapes can be increased by the introduction of redundant representations and neutral mutations. Different genotypes which are assigned to the same phenotype (neutral sets) allow a population to move through the search space more easily and to find new advantageous areas of the search space that would not have been accessible without neutral mutations. Surprisingly, the neutral theory became even more popular in the field of genetic and evolutionary computation (Banzhaf 1994 Dasgupta 1995). There is great interest in how redundant representations and neutral search spaces influence the behavior, and especially the evolvability of GEAs (Barnett 1997 Barnett 1998 Ship-man 1999 Shipman et al. 2000 Shackleton et al. 2000 Shipman et al. 2000 Ebner et al. 2001 Smith et al....

Comparative Physiology Of Aging

In humans, increases in life expectancy in the past century have been ascribed overwhelmingly to reductions in environmental causes of mortality that are extrinsic to the aging process. Longevity in evolutionary terms is difficult to reconcile with the findings, in recent decades, that, in humans, both mortality and disability rates have dropped for all older men and women, across virtually all social classes and ethnic groups, and in most developed and developing countries. It is possible that other factors, in addition to physical fitness and reproductive capability, may be subject to positive selection such as the grandparents hypothesis, that is, the important contribution of the grandparents in raising the young (Chapters 2 and 5). Comparison of life spans of several species (selective longevity) may show some differences in longevity and allow us to draw some relationships between the life span and the selected physiologic characteristics (physiological correlates of longevity).

Synonymity and Locality of Redundant Representations

Low-locality representations result in low GEA performance as guided search methods like GEAs, that use knowledge gained during search for determining future search steps, can only perform better than random search if on average similar solutions have similar fitness (individuals are similar if there are only a few search steps between them). In general, guided search methods assume that in the neighborhood of high-quality solutions other high-quality solutions can be found (Manderick et al. 1991 Horn 1995 Deb et al. 1997 Christensen and Oppacher 2001). High-quality solutions are grouped together and are not scattered over the whole search space (Radcliffe 1991a Whitley 2002). Therefore, to perform well, guided search methods have to search more often in the neighborhood of already found promising high-quality solutions than around low-quality solutions (compare the optimal allocation of trials for the two-armed bandit problem as discussed in Holland (1975)). This behavior guarantees...

Conclusions and Further Research

In this study, we only considered crossover-based search and neglected the influence of redundant representations on mutation-based search. However, we believe that many of the discussed topics are also relevant when using mutation. According to Sect. 3.1.2, we believe that in analogy to the results from Knowles and Watson (2002), using non-synonymously redundant representations reduces the performance of mutation-based search. As these representations have low locality, mutation will not work properly and the search becomes random. Furthermore, there is some theoretical evidence (Radcliffe 1991a Whitley et al. 1997 Rana and Whitley 1997 Whitley 1999 Whitley 2000a Christensen and Oppacher 2001) that mutation-based search only performs well if the connectivity of the phenotypic search space is preserved by the used representation. If the connectivity is either not preserved, such as for low locality representations, or greatly increased (which results in a reduction of the relevant...

Definitions and Background

Representations assign phenotypes xp consisting of different alleles xP, where i G 0, , lp , to genotypes, which also consist of different alleles xg, where i G 0, ,lg . Furthermore, the function fp assigns to each phenotype xp a corresponding fitness value. Usually, the fitness of a phenotype depends on the values of xp. Therefore, different phenotypic alleles can have a different contribution to the fitness of an individual xp. Representations are defined to be uniformly scaled if the genotype-phenotype mapping fg does not change the contribution of the alleles to the calculation of the fitness function. For example, when all phenotypic alleles xP have an equal contribution to the fitness of an individual, representations are uniformly scaled if the importance of the alleles does not change by the genotype-phenotype mapping, and all genotypic alleles xg also have an equal fitness contribution. Representations can also be uniformly scaled if different phenotypic alleles have a...

Delusions in Habitat Evaluation Measuring Use Selection and Importance

Management of wildlife populations, whether to support a harvest, conserve threatened species, or promote biodiversity, generally entails habitat management. Habitat management presupposes some understanding of species' needs. To assess a species' needs, researchers commonly study habitat use and, based on the results, infer selection and preference. Presumably, species should reproduce or survive better (i.e., their fitness should be higher) in habitats that they tend to prefer. Thus, once habitats can be ordered by their relative preference, they can be evaluated as to their relative importance in terms of fitness. Managers can then manipulate landscapes to contain more high-quality habitats and thus produce more of the targeted species. Habitat manipulations specifically intended to produce more animals have been conducted since at least the days of Kublai Khan (a.d. 1259--1294 Leopold 1933). However, the processes of habitat evaluation are fraught with problems. Some problems are...

Demographic Response Design

Ideally, studies should identify relationships between habitat characteristics and the animal's fitness. Studies employing use availability and site attribute designs assume that certain habitat features are selected because they improve fitness. Demographic response designs attempt to test this more directly. However, although I refer to the measured demographic parameters in these studies as response variables, they really only represent correlates with given habitats.

Low versus High Locality Representations

Investigating the relationship between different representations (how the genotypes are assigned to the phenotypes) and the used mutation operator (which is based on the genotypic metric) reveals that a different assignment of genotypes to phenotypes can be equivalent to the use of a different metric for

Influence on Problem Difficulty

We have seen that the phenotypic difficulty of an optimization problem depends on the metric that is defined on the phenotypes and the function fp which assigns a fitness value to every phenotype. Based on the phenotypic metric a local or crossover-based search operator can be defined (for the phe-notypes). By the use of a representation, which assigns a genotype to every phenotype, a new genotypic metric is introduced which can differ from the phenotypic metric. Therefore, the character of the search operator can also be different for genotypes and phenotypes. If the locality of a representation is high, then the search operator has the same effect on the phenotypes as on the genotypes. As a result, genotypic and phenotypic problem difficulty is the same and the difficulty of a problem remains unchanged by the use of an additional representation fg. Easy phenotypic problems remain genotypically easy (compare the results presented in Fig. 3.21) and difficult phenotypic problems remain...

Modifying BBComplexity for the One Max Problem

Fitness fitness For the one-max, or bit-counting problem, the function fp 0,1 ' R assigns to every individual xp G the fitness value xp. As there are only l fitness values that are assigned to 2l phenotypes the fitness function fp is affected by redundancy (see Sect. 3.1.6). The genotype-phenotype mapping fg is a non-redundant one-to-one mapping, and the genotypic space

Protein Interaction Networks

In contrast to chemical reaction networks, large and self-assembled protein interaction networks do not exist outside living cells. Thus, we can not hope to use arguments from self-assembled networks to argue for or against the role of natural selection in explaining a protein network's degree distribution. However, two different lines of evidence speak to this question for protein networks. The first class of evidence regards a corollary of the hypothesis that the degree distribution observed in genetic networks is a by-product of selection for 'robust compactness'. In networks with a broad-tailed degree distribution, mean path length increases drastically upon removal of highly connected nodes, as opposed to the removal of lowly connected nodes, which does not change dramatically. If it is network compactness that matters to the organism, then removal of highly connected nodes should have more severe effects on the fitness of the organism than removal of less highly connected nodes....

Exponentially Scaled Representations

As illustrated in Sects. 3.2 and 4.2.2 we can use the domino convergence model for estimating the performance of GEAs using exponentially scaled representations. We assume that the alleles are solved strictly in serial and there are no interdependencies between the ls alleles in an exponentially scaled BB. However, it is possible to concatenate m exponentially scaled BBs of length ls. When using exponentially scaled representations the maximum size of BBs is k 1. All schemata of order k 1 that contain the best solution have higher fitness than their competitors. Therefore, it makes no sense to consider the effect of locality on GEA performance when using exponentially scaled representations. Section 4.2.3 has shown that low locality modifies the size of BBs k and results in interdependencies between the alleles. However, if kg 1, the domino convergence model can not be used any more, because we can then not assume that the alleles are still solved sequentially. Therefore, we assume in...

Improving Sample Resolution And Information Content

As should be apparent by now, substantial information on food use patterns of vertebrates has been collected. Yet the ability of biologists to apply this information to understand factors that affect an organism's fitness or role in community structure has been limited. Perhaps the most needed change is to ensure that future investigations have a more complete context associated with them. Rather than partitioning studies into separate efforts to examine food and habitat use, these investigations should occur (and be reported) simultaneously.

Integer Optimization Problems

To be able to make a fair comparison between different representations, the problem must be defined on the integer phenotypes independently of the used binary representation. The difficulty of the problem is determined by the phenotype-fitness mapping fp. The difficulty of the problem can be changed by using an additional genotype-phenotype mapping fg, which assigns binary genotypes to integer phenotypes. When assuming that the fitness function fp assigns a real number to every individual in the phenotypic space, we get for the phenotype-fitness mapping

Redundancy and the Unary Encoding

However, when using the unary encoding for the integer one-max and deceptive trap problem, the integer one-max problem remains genotypically fully easy for recombination-based search (Goldberg 1989b Deb and Goldberg 1993 Deb and Goldberg 1994) as all schemata containing the global optimum are still superior to their competitors (compare also Sects. 3.3.6 and 3.3.7). It also remains easy for mutation as it is a unimodal problem for mutation-based search and the structure of the fitness landscape guides mutation towards the global optimum. Analogously, the fully deceptive trap remains fully difficult. The only real handicap of the unary encoding seems to be the non-uniform redundancy. Therefore, we want to neglect the non-synonymous redundancy and focus on the overrepresentation and underrepresentation of the optimal solution.

Modification of Problem Difficulty and the Gray Encoding

We know that using Gray encoding changes the problem difficulty for GEAs. When using crossover-based search, the schema analysis is an appropriate method to measure problem difficulty (compare Sect. 2.3.2). For both, binary and Gray encoding, dc 0 and genotypic and phenotypic problem difficulty is different when using crossover-based search approaches. The distance distortion dc is high, as the structure of the genotypic and phenotypic search space is different and a phenotype has a lower number of neighbors than a genotype. The following analysis of the schemata fitness reveals for the integer one-max and deceptive trap problem that in comparison to the binary encoding, Gray encoding does not preserve the complexity of BBs as well. This leads to a lower GA performance. To investigate how well BB-complexity is preserved, we analyze the fitness of the schemata for a 3-bit problem (s 23 8) using Gray versus binary encoding. In Table 5.2, we present the binary and Gray-encoded genotypes,...

Definitions of Intelligence

While intelligence tests of some sort appeared in human history as early as the Old Testament book ofJudges (7 3-7, 12 6), which indicates that early Jewish society used questions and observations in personnel selection, the intelligence test as it is known today can be traced to Renaissance Europe. In 1575, the Spanish physician Juan Huarte wrote Examen de Ingenios, a treatise concerning individual differences in mental ability with suggestions for appropriate tests. His work, and that of other investigators and theorists, was the result of the rise of a middle class with aspirations to productive employment. Previously, the aristocracy had controlled everything, and fitness for a position was determined by lineage. Once this monarchical rule began to break down, other means were necessary for determining who was fit for a particular occupation and what might be the most productive use of a person's abilities. When it became apparent that royal blood was no guarantee of competence,...

Summary and Conclusions

Section 5.1 started this chapter by presenting two types of integer problems. Integer one-max problems are fully easy problems, whereas the integer fully deceptive trap is an example of a fully difficult problem. In Sect. 5.2, we presented and examined the binary, Gray and unary encoding, which are common representations for integer phenotypes. This is followed in Sect. 5.3 by a theoretical comparison of the expected performance of GEAs using the three different representations. We showed that using the non-synonymously redundant unary encoding reduces GEA performance if the optimal solution is underrepresented. Therefore, the necessary population size for solving the integer one-max and the integer deceptive trap problem is increased. Using binary encoding results in a more compact, redundancy-free representation, but the alleles are exponentially scaled. Therefore, genetic drift occurs for small and easy problems and larger population sizes are necessary. Due to the problems of the...

Considerations of Physical Disability or Immobility

The complexities of the airport environment should not be underestimated, and must be considered during the assessment of fitness to fly. The formalities of check-in and departure procedures are demanding and can be stressful, and this can be compounded by illness and disability as well as by language difficulties or jet lag. The operational effect of the use of equipment such as wheelchairs, ambulances and stretchers must be taken into account, and the possibility of aircraft delays or diversion to another airport must be considered. It may be necessary to change aircraft and transit between terminals during the course of a long journey, and landside medical facilities will not be available to a transiting passenger. At London's Heathrow Airport, for example, transfer traffic accounts for more than 40 of all passengers.

Schema Analysis for Graphs

When assuming that GEAs process schemata, the analysis of schema fitness is the appropriate method to measure problem difficulty (see Sect. 2.3.2). The BB hypothesis (see Sect. 2.2.3) defines building blocks to be highly fit schemata of short defining length and low order. Consequently, problems are fully easy if all schemata of order one that contain the optimum have higher fitness than their competitors. Problems are difficult if all lower order schemata containing the global optimum are inferior to some of their competitors. The one-max problem is an example of a fully easy problem, whereas the fully deceptive trap of order k is an example for a fully difficult problem. When using schemata for trees, there is the additional restriction that each tree has exactly n 1 links and it must be connected. Therefore, there must be n 1 ones in each solution string, and the string must encode a connected tree. This means that the average fitness of a schema must be calculated only from the...

Practical And Ethical Issues Of Drug Research In Older Populations

What is 'geriatric' Strictly defined, it describes a person aged 65 years or over, but aging is neither a homogeneous nor a linear process. There are very fit 80 year-olds who climb mountains, and young children dying from genetic advanced aging (progeria). The elderly therefore cover a spectrum of fitness. So many of the above concerns can be reduced by selecting 'uncomplicated, healthy' older patients in Phase I studies, who are increasingly available due to the success of medicines and pre-ventative medicine.

Manufacturing Process Controls and Testing

Sion and before they are placed on the scaffold. Release criteria generally ensure that cells remain viable and functioning properly after being attached to the scaffold. Functional evaluations of cells and potency assessments of their fitness for use are performed after cells are combined with (or seeded onto) a scaffold. Taken together, these tests determine whether the final product can be released from the production facility for surgical implantation in the clinical setting.

N Evolutionary Theories of Aging

The evolutionary biology of aging theory postulates that the force of natural selection will always decrease with age with either replacement-level or positive-population growth (124). This is the theoretical basis for the disposable soma theory of aging, named for its analogy with disposable goods with a limiting warranty period. This theory postulates that fitness is maximized at a level of investment in somatic maintenance, which is less than would be required for indefinite survival. The disposable soma theory serves as the conceptual foundation for two population genetic hypotheses of aging. The first is termed negative pleiotropy and is based on the concept that alleles that have beneficial effects on one set of components of fitness also have deleterious effects on other components of fitness (125,126). It is based on the selection for forms of genes that confer beneficial effects early in life, in contrast to the ineffective selection to remove such forms of genes that are...

Some Implications Of Fundamental Equations Of Natural Selection

Natural selection can only operate when there is genetic variation associated with phenotypic variation for fitness in the population. If there were no genetic variation influencing the phenotype of fitness, fitness could not possibly be heritable and therefore equation 11.22 implies no evolution due to natural selection. Likewise, without genetic variation associated with phenotypic variation of fitness, there can be no nonzero average excesses of fitness, and therefore equation 11.5 also implies no evolution by natural selection. 2. The only fitness effects that influence the response to natural selection are those transmissible through a gamete. Equation 11.5 shows that there is no response to selection unless the average excess for fitness is not zero, and equation 11.22 shows that there is no response to selection unless the additive genetic variance for fitness is not zero. The additive genetic variance can only be nonzero if the average effects are nonzero, and the average...

Interaction Of Natural Selection With Mutation And System Of Mating

C alleles, respectively, and with fitnesses as given in Table 11.1 for the malarial environment. With inbreeding, the average excesses of the S and C alleles are (from equation 8.9) Under the initial conditions, almost everyone in the population is AA, so the average fitness is close to 0.89, the fitness of the AA genotype under malarial conditions. Hence, the initial response to selection for the S and C alleles is determined by their initial average excesses of using pA & 1, pS & pa & 0 in the initial gene pool. Recall that the initial average excesses in the random-mating case were 0.11 for S and 0 for a (equations 11.6 and 11.8 in Chapter 11), which is a special case of 12.12 when f 0. As equation 12.12 reveals, inbreeding decreases the average excess of the S allele and increases the average excess of the a allele relative to their values under random mating. When f 0.11 0.8 0.14, equations 12.12 reveal that natural selection always operates to eliminate the S allele and favor...

Interaction Of Natural Selection With Gene Flow

The sign of the component of allele frequency change induced by gene flow in equation 12.13 is determined solely by the initial difference in allele frequencies among the demes, in this case p1 - p2. The sign of the selective component of equation 12.13 is determined solely by the average excess of fitness, which in turn is a function of within-deme allele frequencies, system of mating, and genotypic deviations of fitness in the deme. As a result, there is no biological necessity for the selective and gene flow components to have the same sign. In some cases, selection and gene flow can operate in the same direction, allowing an allele to increase (or decrease) in frequency more rapidly than possible through either selection or gene flow alone in other cases selection and gene flow will be in opposite directions and the evolutionary outcome will depend upon their balance. To illustrate these diverse outcomes, we return to the example of African Americans, a population influenced by...

Interactions Of Natural Selection Genetic Drift And Gene Flow

Wright (1932) felt that in a population with a large effective size there would be virtually no chance for a peak shift. Hence, the population would evolve toward the nearest local peak, and then selection would maintain the population on that local peak, even if a vastly superior adaptive alternative existed. We have already seen an example of this with the j -Hb locus in human populations living in the malarial regions of Africa most such populations have evolved toward the A S polymorphic peak even though the fixation for the C peak seems to be a far superior adaptive outcome in terms of average fitness (Figure 11.8), percentage of the population protected against malaria, degree of protection against malaria, and eliminating deleterious side effects such as hemolytic anemia from the population. Because selection could keep populations on inferior adaptive peaks, Wright regarded natural selection as a potential impediment to adaptation when it dominated over genetic drift. To...

Motivation and Functionality

As the costs of a communication or transportation network strongly depend on the length of the links, network structures that prefer short distance links often tend to have higher fitness. Furthermore, it is useful to run more traffic over the nodes near the gravity center of an area than over nodes at the edge of this area (Kershenbaum 1993 Cahn 1998). Thus, it is desirable to be able to characterize nodes as either interior (some traffic only transits), or leaf nodes (all traffic terminates). As a result, the more important a link is, and the more transit traffic that crosses the node, the higher is, on average, the degree of the node. Nodes near the gravity center tend to have a higher degree than nodes at the edge of the network. Hence, the basic idea of the LNB encoding is to encode the importance of a node or link. The more important the node or link is, the more traffic that should transit over it.

Population Subdivision

Population subdivision with Nm close to 1 was a critical requirement for shifting balance according to Wright. Many species do have subdivided populations. Even humans have an Nm close to 1 (Chapter 6). Our own species is instructive about the potential for shifting balance. Although our overall Nm is close to 1, there is much spatial heterogeneity over our geographical distribution for the amount of local population subdivision. This is often true of other species. For example, the eastern collared lizard (Crotaphytus collaris collaris) shows extreme population subdivision with little to no gene flow among isolated demes in the northeastern Ozarks (a central highland area in North America), gene flow constrained by isolation by distance in the southwestern Ozarks, and less extreme isolation by distance in Texas (Hutchison and Templeton 1999). For many species the necessary degree of subdivision may exist only in a part of the species' range. Therefore, the entire species does not...

Units And Targets Of Selection

This reliance upon single-locus models greatly bothered Ernst Mayr (1959, 1970), one of the major architects of the neo-Darwinian theory of evolution. He called such single-locus population genetic models beanbag genetics in which each bean (locus) is studied independently and then added together in a beanbag to reconstruct the whole. Mayr pointed out that the individual is the target of selection and not a single locus. It is the individual that lives or dies, mates or fails to mate, is fertile or sterile. Any single locus may contribute to the individual's fitness, but because of epistasis and coadapted complexes, that single-locus contribution must be placed into the context of the genotype as a whole. Mayr was strongly influenced by the earlier work of Chetverikov (1926), who suggested that the individual is not divisible into discrete traits coded for by individual genes, but instead the individual is a product of the genotype as a whole. Mayr called this idea the unity of the...

The recipient Table 166 Preoperative assessment

Growing pressure on hospital beds and increasing use of day surgery means that a preoperative assessment should be performed before admission. This allows for efficient use of hospital resources and limits the number of cancelled operations. The key aims are to assess a patient's fitness to undergo surgery and anaesthesia, anticipate complications, arrange for supportive therapy to be available perioperatively and to liaise with the appropriate specialists regarding non-surgical management. This assessment needs to take place at a presurgical clinic at least 1 month before the planned date of surgery. After the clinic, it is imperative that the results are seen so that the necessary action can be taken for each patient.

Targets Of Selection Below Level Of Individual

In Chapters 11 and 12, fitness phenotypes were always regarded as properties of individual organisms. However, even in those chapters, we saw that the fitness values of specific individuals were important only through their contribution to genotypic values that is, the average fitness phenotype for a group of individuals sharing a common genotype. Consequently, to study natural selection, all we need is a group that shares a common genetic state. We can then assign a genotypic value or average fitness deviation to that group. There is nothing about the theory of natural selection or the concept of average excess that requires that the biological units that are pooled together and assigned an average fitness value have to be individual organisms. As long as the group we define has some genetic identity that displays a fitness phenotype and there is variation in the population for those genetic identities, natural selection can occur. The genetic identities do not have to correspond to...

Targets Of Selection Above Level Of Individual

Many phenotypes emerge at the level of interactions between two or more individuals. If these interactions are recurrent across generations, they will have continuity over time and can be targets of selection. Targets emerging from interactions among individuals are not difficult to find. For example, of the three major fitness components outlined in Chapter 11, two in general are more appropriately assigned to an interacting pair of individuals mating success and fertility fecundity. An individual in a dioecious species does not truly have a phenotype of mating success or fertility such phenotypes take on biological reality only in the context of an interaction with another individual. Another common target of selection is intraspecific competition, a phenotype emphasized by Darwin as being important in his theory of natural selection. But competition also takes on biological reality only in the context of interactions among individuals. It is always possible to assign an average...

Evolution Of Sociality

The diverse relationships of individuals in a social network interact to create complex emergent patterns. These patterns, like the vortex that appears in an emptying sink, is not contained in the structure of a single component. Because a society represents a whole with properties different from those of its component parts, the ultimate consequences of social interactions may be remote from an observed action. This is a fact that evolution by natural selection can take in its stride but that we, as primarily linear cause-and-effect thinkers, may find hard to accommodate. It may be clear that a lion killing a zebra is behaving adaptively, but less clear whether it is adaptive when the same lion prevents a conspecific from feeding at the kill. The immediate effect is that the first lion may have more food to eat, but the ultimate effects reverberate through a stochastically unpredictable system of long-term consequences among the whole pride. Denied food or coalitionary aid by an ally...

Selection In Heterogeneous Environments

Premise 3 (Chapter 1) states that phenotypes emerge out of a genotype-by-environment interaction. In Chapter 11 we saw that natural selection arises from this premise when there is genetic variation in the population to produce heritable variation in the phenotype of fitness. There is often variation not only in genotypes but also in environments. We have already seen this before. For example, in Chapter 8, Fisher's basic quantitative genetic model has an environmental deviation that is modeled as a random variable assigned independently to each individual. Thus, there is both genetic and environmental variation in Fisher's model. We have also seen examples of environmental variation that is not random for each individual. For example, we discussed how the environment changed in wet, tropical Africa after the introduction of the Malaysian agricultural complex and how this environmental change altered the phenotype of fitness associated with genetic variation at the human -globin...

Coarsegrained Temporal Heterogeneity

Just as a population can move through space via the dispersal of its constituent individuals, a population can also move through time via acts of reproduction to create generation after generation. The environment can change as a population moves through time such that different generations experience different environments, and because fitness is a genotype-by-environment interaction, the fitnesses associated with particular genotypes can also change across the generations. Insight into the evolutionary implications of coarse-grained seasonal selection can be obtained through a simple one-locus, two-allele model (Hoekstra 1975). In most models in population genetics, the basic temporal unit is a point in the life cycle at one generation to the corresponding point in the next generation. However, for a cyclical selection model, Hoekstra chose as his basic unit one complete cycle of the environmental changes, which corresponds to more than one generation in the coarse-grained case. The...

Finegrained Heterogeneity

An individual often experiences environmental heterogeneity within its own lifetime. Because an individual can only be at one place at any given time, an individual experiences both spatial and temporal heterogeneity within its own lifetime as a temporal sequence. Hence, for purposes of microevolutionary modeling, no distinction is necessary between fine-grained spatial and temporal heterogeneity. In many situations, fine-grained heterogeneity needs no special consideration as it can be folded into the constant-fitness models given in Chapter 11. To see this, consider two extreme situations the case in which every individual in the population experiences the same temporal sequence of fine-grained heterogeneity and the case in which every individual experiences an independent sample of temporal sequences of environments within its lifetime. The first case would apply to the situation in which an organism has one generation per year but in which seasonal variation influences the...

Classifications Of Behavioral Interactions

How, in practice, can we impartially assign positive or negative implications to behavioral interactions such as proximity or grooming that are ambivalent, without recourse to the very theories we seek to support One solution lies in sequence analysis, using unequivocal behavior patterns as anchors high-intensity attacks are certainly detrimental to the receiver's fitness, whereas allowing mating is usually beneficial to fitness. If transition probabilities revealed grooming as a predictor of attack, then it might usefully be classed as aggressive, but if grooming often precedes acceptance of mating, it is probably amicable. Firm grounding of a behavior in context may justify an interpretative classification. Often, however, it is impossible to establish a uniform link between ambivalent behaviors (e.g., grooming) and anchors (e.g., coalitionary aid or attack) until the whole social network of interactions within the group has been described. Descriptions based on ultimate function...

Selection In Agestructured Populations

Up to now we have assumed discrete generations. Under this assumption, all individuals are born at the same time and then reproduce at the same time followed by complete reproductive senescence or death. Such a model approximates reality for some species. For example, many insects and plants have only one generation per year that is synchronized by the seasons, and the discrete-generation model can approximate their evolution. However, as pointed out in Chapter 2, individuals in many species can reproduce at multiple times throughout their life, can mate with individuals of different ages, can survive beyond their age of reproduction, and can coexist with their offspring and other generations. We do not have to look far to find such a species our own falls into this category of overlapping generations. In species with overlapping generations, an important component of population structure is age structure, the distribution of the ages of the individuals found in the population at a...

Exercise during Pregnancy and Travel

The physician and the pregnant woman should discuss her history, overall fitness, previous level of activity and signs that portend discontinuation of the activity. They should develop a program that is acceptable and enjoyable but not hazardous to the fetus or the mother.

Evolution of evolvability

This minimal constraint scenario has no outside fitness imposed. Also it ignores competition between networks, as it only compares a network with its predecessor. However, the model naturally selects for networks that have high overlap with neighboring mutant networks. This feature is associated with robustness, defined as the requirement that, not only should the present network work, but also mutations of the networks should work. In terms of network topology this means a change in the wiring Aij Aj that takes place on a much slower timescale than the &j updating using the Boolean dynamics itself.

Other Selective Forces on Floral Longevity

In addition to increasing attractiveness to pollinators, flower longevity (either directly or indirectly through floral display size and or duration) may also increase the plant's apparency to flower or seed predators. Such an effect would select for reduced floral longevity, and thus, counter selection acting through pollination success to extend floral longevity (Ashman and Schoen, 1996a). However, few studies have addressed the role of floral longevity in predation or disease risk directly. Stiles (1975) observed that nectar-rich Heliconia flowers were attacked a few hours after anthesis and their ovaries damaged by various non-pollinating nectivores, leading him to suggest that the very short (half-day) lifetime of these tropical flowers might have evolved in response to predation. Another study (Shykoff et al., 1996) reported that the longer-lived female flowers of dioecious Silene latifolia and S. dioica are more prone to a pollinator-transmitted anther smut disease than...

First Level Interactions The Plant Pest Continuum

Protease inhibitory potential or to a reduced fitness of the host plant. In this context, while the identification or the development of an effective PI must take into consideration the degree of affinity between this inhibitor and the pest target proteases,14,15 it also appears important to assess the interactions between the PI and the various proteases found along the plant-pest continuum, which could drastically influence the effects actually observed in vivo (see Fig. 9.1).

Evidence for Unequivocal Genetic Effects

These knock-out models, while of significant interest, are often not based on proven risk factors for health or disease in the natural world. Evolutionary fitness will require actions of both the real and latent variance in several genes and gene products, respiratory system capacity and learning. Understanding the role of genes in normal and pathologic control of ventilation will require approaches that will accommodate the probable collective effects of multiple loci.

Telomeres and Premature Aging

Among the first mouse models to show multiple signs of accelerated aging was the telomerase knockout mouse. These mice completely lack telomerase activity owing to a germ-line disruption in the gene encoding the essential telomerase RNA component, mTR (147). Interestingly, mTR- - mice are asymptomatic for the first three to four generations. Subsequent generations, however, are shorter lived and prematurely develop hair loss and graying, ulcerative skin lesions, delayed wound healing, reduced fertility, reduced stress resistance, and increased cancer. As noted earlier, mice have telomeres that are much longer than humans. It is notable, then, that the reduced longevity and fitness of mTR- - mice were not manifest until the mouse telomeres had substantially shortened to lengths more typical of those found in aged human tissues. Thus, this model demonstrates a critical role for telomere function not only in suppressing cancer, but also in ensuring many other aspects of organismal...

Preflight Assessment and Medical Clearance

The objectives of medical clearance are to provide advice to passengers and their medical attendants on fitness to fly, and to prevent delays and diversions to the flight as a result of deterioration in the passenger's well-being. It depends upon self-declaration by the passenger, and upon the attending physician having an awareness of the flight environment and how this might affect the patient's condition. Most major airlines provide services for those passengers requiring extra help, and most have a medical adviser to assess the fitness for travel of those with medical needs (Bagshaw and Byrne, 1999). Individual airlines work to their own guidelines, but these are generally based on those published by the Aerospace Medical Association (Air Transport Medicine Committee, 1996) on fitness for travel. The International Air Transport Association (IATA) publishes a recommended Medical Information Form (MEDIF) for use by member airlines. The MEDIF should be completed by the passenger's...

Fundamental Equation Of Natural Selection Measured Genotypes

A complete generation transition, ending up in the next generation at a comparable point to the starting generation. In the models used in Chapter 2 we went from parental genotypes to gametes via Mendelian probabilities, then to offspring genotypes through the mechanisms of uniting gametes (population structure). To include natural selection, we need to expand this model by explicitly modeling the life stages measured by the fitness components. In this chapter, we will assume each of the fitness components can be measured as a constant probability that is assigned as a genotypic value to a particular group of individuals sharing a common genotype.

Investigating Food Habits of Terrestrial Vertebrates

Regardless of the specific question being addressed, nearly all investigations of food habits can be distilled to two basic questions. What is the importance of a specific food to the fitness of an organism (especially survival and reproductive success) How does the feeding niche of an organism affect community composition In this chapter I compare the relative effectiveness of methods commonly used to investigate food habits and how appropriate each method is at answering these questions. I also consider several recent innovations and how potential improvements may improve our ability to understand the significance of food usage. Readers interested in learning more about the actual procedures should consult references by Korschegen (1980), Cooper-rider (1986), Reynolds and Aebischer (1991), and Litvaitis et al. (1994).

Development And Evaluation Of Docking And Scoring

Crystallographically observed pose in 79 and 77 of the complexes, respectively. The results highlight one of the main difficulties of docking, that of identifying where possible the correct pose from the sampling phase. GLIDE is thought to outperform GOLD in ranking the poses, as it refines the position of each pose prior to ranking using molecular mechanics-based energy minimisation. A theory supported by the improved performance of GOLD to a level equal to that of GLIDE when an additional step is taken minimising the poses generated through sampling. One rationale for such an improvement lies in the nature of the GOLD fitness function, where a soft repulsive term is used. Soft functions are one approach to accommodating the dynamic nature of the receptor 88 , discussed in more detail below, but they also lead to mis-docked molecules and a higher number of false positives. Energy minimisation counteracts the inadequacies of the soft functions, but at the price of additional...

Experimental Results

For our experiments we concatenate four instances of a deceptive trap problem for trees of size 3 and 4. The size of a sub-problem denotes the number of nodes. Therefore, the problems for the empirical investigation have either n x m 12 (size 3) or m x n 16 nodes (size 4). The minimum fitness of an individual is 0 and the maximum fitness is either 4 x 2 8 (4 instances of the The performance of GAs using different representations for size 3 and 4 trap problems is shown in Table 8.5. We present results for different optimal solutions (Topt is either an arbitrary tree, the MST, or a random star) and show the percentage Psucc of runs that find the optimal solution Topt, the mean and standard deviation of the fitness of the best found solution, and the mean and standard deviation of the number of generations tconv until the population is fully converged or the GA run is stopped after 200 generations. fitness (o) fitness (o)

Adaptation As Polygenic Process

One way humans adapted to malaria in wet, tropical Africa was through the A S polymorphism at the j-Hb locus, an adaptation that confers malarial resistance to only about 20 of the population. In general, many loci can contribute to how an individual responds to its environment in determining the phenotype of fitness. As a consequence, adaptation to a new environment is usually a polygenic process, with genetic variation at many loci If a person does not have the A S genotype at the j-Hb locus in a malarial region, the person could still be protected against malaria through the G6PD A- allele. Thus, the Bantu-speaking peoples adapted to malaria as they expanded into wet, tropical Africa with the Malaysian agricultural complex not only by the C and S alleles at the j - Hb locus but also by the A- allele at the G6PD locus. However, as with the S allele, there are fitness tradeoffs associated with the A- and other G6PD-deficient alleles. Although reducing the red blood cell's capacity to...

Methods applications and concepts of metabolite profiling Secondary metabolism

Glufosinate Metabolism

Plants manufacture a vast array of secondary metabolites natural products for protection against biotic or abiotic environmental challenges. These compounds provide increased fitness due to their antimicrobial, anti-herbivory, and or alleopathic activities. Secondary metabolites also serve fundamental roles as key signaling compounds in mutualistic interactions and plant development. Metabolic profiling and integrated functional genomics are advancing the understanding of these intriguing biosynthetic pathways and the response of these pathways to environmental challenges. This chapter provides an overview of the basic methods, select applications, and future directions of metabolic profiling of secondary metabolism. The emphasis of the application section includes the combination of primary and secondary metabolic profiling. The future directions section describes the need for increased chromatographic and mass resolution, as well as the inevitable need and benefit of spatially and...

Sickle Cell Anemia As Example Of Natural Selection

In Chapter 8, we noted that the sickle cell allele (S) at this locus is a dominant allele for the phenotype of malarial resistance. In contrast, another allele at this locus, C (a mutation in the same codon as S), is a recessive allele for malarial resistance (Cavalli-Sforza and Bodmer 1971). Modiano et al. (2001) suggest that C is not completely recessive, but for now, we will treat it as a recessive allele before turning our attention to the possibility that it is not. Moreover, both the S and Calleles are associated with hemolytic anemia, another source of mortality. Hence, these alleles are expected to influence the phenotype of viability in both the premalarial and the malarial environment of wet, tropical Africa. Cavalli-Sforza and Bodmer (1971) estimated these viabilities for a West African population under malarial conditions, as shown in Table 11.1. Table 11.1 also shows the estimated viabilities under nonmalarial conditions by removing the beneficial effects of the...

Thyroid Cancer from the Perspective of a Patient

On my thyroid, he explained, had been benign, but I was horrified to hear him add that the attached tissue was abnormal - and you don't need a degree in medicine to know what that means. They had found traces of cancer. If Frank Bruno had punched me I would not have been more winded. I had been feeling light-hearted that morning because I had been working hard at my fitness - and with a great deal of success - but now I sat at the desk in my office in a state of shock as Mr Rhys Evans quietly confirmed that a second operation would be necessary. I gently replaced the phone. I was so angry, I felt my whole body was letting me down. Through the office window I could see David washing the car, singing away with the music. I was in tears, and began kicking the bottom of the desk and swearing at my body. How on earth could I tell him or my sons Mark and Paul, I knew they would be devastated. It was all developing into a terrible nightmare and my body felt like it was about to explode.

Unique Features of Plants

Individual longevity may be affected if somatic mutations result in intraorganismal selection. In long-lived plants with multiple meristems, a genetic mosaic may develop within individual plants, and this may have one of two consequences. On the one hand, intraorgan-ismal selection has primarily been seen as a mechanism for eliminating deleterious somatic mutations (cf. Klekowski and Kazarinova-Fukshansky, 1984 Otto and Orive, 1995). Natural selection can act among cells within an individual to eliminate deleterious mutations that appear in a ramet or module, with little or no impact on the fitness of the genet. Conversely, selection may allow the spread of a favorable mutation within a clonal plant, which may result in an evolutionary change if an advantageous mutation goes to fixation (Pineda-Krch and Fagerstrom, 1999). If somatic mutations occur at a level high enough to allow selective changes within the life span of an individual, then this could allow for a closer tracking of an...

Extracellular Proteases in Plant Pathogens

In this perspective, the use of protease inhibitor (Pl)-encoding cDNA sequences may appear of particular interest in the development of plants which are partly resistant to pathogens. Because they can inhibit a wide variety of proteolytic enzymes, PIs were proposed as a tool to control pest and pathogenic organisms as diverse as herbivorous insects, parasitic nematodes and human microbial pathogens (see Chapters 2, 3, 4 and 17, this volume).4-6 Until now little is known about the potential of PIs in the control of plant pathogens, but one can speculate that blocking the activity ofplant fungal or bacterial pathogen proteases could eventually decrease their fitness in planta by the alteration of some yet uncharacterized, but useful physiological functions. Extracellular proteases may be important in many pathogens for basic processes like dietary protein hydrolysis, penetration of host tissues or zymogen activation. While their role during the infection of plant tissues still remains...

Utility Distributions

From location data such as those shown in figure 3.2, most home range estimators produce a utility distribution describing the intensity of use of different areas by an animal. The utility distribution is a concept borrowed from economics. A function, the utility function, assigns a value (the utility, which can be some measure of importance) to each possible outcome (the outcome of a decision, such as the inclusion of a place within an animal's home range Ellner and Real 1989). If the utility distribution maps intensity of use, then it can be transformed to a probability density function that describes the probability of an animal being in any part of its home range (Calhoun and Casby 1958 Hayne 1949 Jennrich and Turner 1969 White and Garrott 1990 van Winkle 1975), as shown in figure 3.2. Utility distributions need not be probability density functions, although they usually are. A utility distribution could map the fitness an animal gains from each place in its home range, or it...

Evolutionary Approaches A Theories of Senescence

Evolutionary theorists have alternatively suggested that senescence may be a non-adaptive trait which has evolved indirectly as a consequence of a selective premium on genes with favorable effects on survival or fecundity early in the life history. The key element to allow the evolution of senescence is the fact that the force of natural selection on survival and fertility necessarily decreases with age because organisms have a nonzero chance of dying from external causes such as predation and accidents. Medawar (1952) provided the foundation for the major theoretical progress on the evolution of senescence. He suggested that, even in the hypothetical complete absence of senescence, if constant fertility is assumed, the reproductive output of each age class declines with age, because survivorship from birth is a decreasing function of age. As a result, the relative importance of traits expressed at late ages, to the lifetime fitness of an individual, is less than the importance of...

Scalable Test Problems for Graphs

For the calculation of the fitness fi of a solution Ti, the distance di,j between two trees Ti and Tj is used (compare Sect. 6.1.2). Using this metric, the fitness fi of a solution Ti depends on the distance diopt between Ti and the optimal solution Topt. We can distinguish two types of problems maximization and minimization problems. When defining a minimization problem the fitness fmin of an individual Ti is defined as the distance diopt to the optimal solution Topt. Therefore, fmin diopt, where fmin 0,1, ,n - 1 . An individual has fitness of n 2 if it only has one link in common with the best solution. If the two individuals do not differ (Ti Topt), the fitness of Ti is fmin 0. If our example tree from Fig. 6.7 is chosen as the optimal solution and we have a minimization problem, the star with center D would have fitness (cost) of 1, because the two trees differ at one edge2 (diopt 1). When defining a maximization problem, the fitness fmax of an individual Ti is defined as the...

Experiments and Empirical Results

The first test example for our empirical investigation is the one-max problem. This problem is very easy to solve for GEAs as the fitness of an individual is simply the number of ones in the binary phenotype. To ensure that recombination results in a proper mixing of the BBs, we use uniform crossover for all experiments with the one-max problem. Furthermore, in all runs we use tournament selection without replacement and a tournament size of 2. For the one-max function the signal difference d equals 1, the size k of the building blocks is 1, and the variance of a building block a2BB 0.25. tions were provided by Deb and Goldberg (1993). Figure 3.6 depicts a 3-bit deceptive trap problem where the size of a BB is k 3. The fitness value of a phenotype xp depends on the number of ones u in the string of length l. The best BB is a string of l ones which has fitness l. Standard GEAs are misled to the deceptive attractor which has fitness l 1. For the 3-bit deceptive trap the signal...

Fundamental Theorem Of Natural Selection Unmeasured Genotypes

Equation 11.5 is the fundamental equation describing natural selection for a measured genotype at a single locus. Given that many adaptive traits are polygenic but with the underlying loci being unknown, Fisher (1930) elucidated many properties of natural selection using the theory of the quantitative genetics of unmeasured genotypes (Chapter 9). His central result is summarized in an equation that is the unmeasured genotype analogue of the measured genotype equation 11.5. Fisher called this equation the fundamental theorem of natural selection, which describes how natural selection operates upon the phenotype of fitness when fitness is regarded as a heritable but genetically unmeasured trait. There are many ways of deriving this theorem, and we will present only one of the simplest. Because we assume that no genotypes are being measured, we must focus exclusively upon phenotypes. This means that we can no longer use the primary definition of fitness in population genetics as a...

Coarsegrained Spatial Heterogeneity

Consider a landscape subdivided into spatial patches or habitats that induce different fitness responses from specific genotypes. We further assume that these genotypes experience only one of these patches in their lifetime (or at least, the selectively relevant portion of their lifetime for the unit of selection of interest). As an example, consider the northern acorn barnacle (Semibalanus balanoides) on the northeastern coast of the United States (Schmidt and Rand 2001). This, as well as many other marine species, has planktonic larval dispersal, resulting in high levels of gene flow and negligible population subdivision at the larval stage. The larvae then settle and enter a completely sessile stage for the remainder of their lives. The intertidal region that they settle in is a mosaic of habitats that greatly differ in environmental parameters that affect barnacle survivorship. A specific individual only experiences the habitat in which it settled, so this is coarse-grained,...

Preventing Establishment By Transgenic Mitigation

If a transgene confers even a small fitness disadvantage, the less fit transgenic volunteers and their own or hybrid progeny should only be able to exist as a very small proportion of the population. Therefore, it should be possible to mitigate volunteer establishment and gene flow by lowering the fitness of transgene recipients below the fitness of competitors, so that the volunteer or hybrid offspring will reproduce with considerably less success than its non-transgenic competitors. A concept of transgenic mitigation (TM) was proposed 22 , in which mitigator genes are linked or fused to the desired primary transgene. Thus, a transgene with a desired trait is directly linked to a transgene that decreases fitness in volunteers (Fig. 1). TM could also be used as a stand-alone procedure with non-transgenic phytoremediating species to reduce the fitness advantage of hybrids and their rare progeny, and thus substantially reduce the risk of exo-feral hybrid volunteer persistence. Dwarfing...

Theoretical Model of Longevity Extension in Social Species

Improved health and increased longevity in societies sets in motion a self-perpetuating system of longevity extension. This positive feedback relationship is based on the demographic tenet that (all else being equal) increased survival from birth to sexual maturity reduces the number of children desired by parents (15). Because of the reduced drain of childbearing and child rearing, parents with fewer children remain healthier longer and thus raise healthier children. The higher survival rate of these children fosters yet further reductions in fertility. Greater longevity of parents also increases the likelihood that they can contribute as grandparents to the fitness of both their children and their grandchildren. And, the self-reinforcing cycle continues.

Evolution Of Senescence

This section, we will see how the fitness measures derived above allow us to address these important questions. Using the life history data in Table 15.1 in equation 15.18, we can calculate the net reproductive rate of bearers of a newly formed Huntington's allele (one that just crossed the threshold repeat number and reached a value of 36 repeats, as discussed in Chapter 13) to be 0.9941 versus the normal net reproductive rate from Table 15.1 of 0.9968. Theneurolog-ical symptoms are relatively mild when they first occur and then get progressively worse, eventually resulting in death. The assumption that all reproduction stops with the onset of symptoms is therefore overly conservative, so the actual difference in net reproductive rates associated with a newly formed Huntington's is even less than that indicated above. Hence, the lethal neurodegeneration of Huntington's disease is essentially neutral with respect to natural selection when an allele reaches the 36 repeat threshold. Of...

Mycorrhizal Fungi As Helping Agents In Phytoremediation Of Degraded And Contaminated Soils

Plant roots were defined from phytoremediation point of view as exploratory, liquidphase extractors that can find, alter and or translocate elements and compounds against large chemical gradients 1 . Since the roots of majority of higher plants live naturally in symbiosis with different types of mycorrhizal fungi 2 , this association should be regarded as an organic component of the phytoremediation systems 3, 4, 5 . However, relatively few studies have focused on the effects of mycorrhiza on phytoremediation and vice versa, despite the widely acknowledged importance of mycorrhizal symbionts for plant growth and fitness particularly in harsh environments.

Definition and Formation of Groups

There are several ways in which people come to join the groups to which they belong. People are born into some groups. Several types of groupings are influenced in large part by birth family, socioeconomic status, class, race, and religion. Other groups are formed largely by happenstance for example, a line of the same people waiting for the 8 05 ferry every day. Some groups, however, are determined more clearly by intentional, goal-oriented factors. For example, a group of people at work who share a concern for well-being, health, and fitness may decide to form an exercise and nutrition group. Students interested in putting on a concert might decide to form a committee to organize bake sales, car washes, and fund drives in order to raise the money needed to achieve this goal. Finally, group memberships are sometimes created or changed as an effort toward self-definition or self-validation. For example, one can try to change one's religion, political orientation, professional...

Stress Physiology

The concept of stress is intimately associated with that of stress tolerance, which is the plant's fitness to cope with an unfavorable environment. In the literature the term stress resistance is often used interchangeably with stress tolerance, although the latter term is preferred. Note that an environment that is stressful for one plant may not be stressful for another. For example, pea (Pisum sativum) and soybean (Glycine max) grow best at about 20 C and 30 C, respectively. As temperature increases, the pea shows signs of heat stress much sooner than the soybean. Thus the soybean has greater heat stress tolerance.

Editors

Einstein received his PhD from the University of Colorado in experimental psychology in 1977. He has taught at Furman University since 1977 and chaired the department from 1994 until 2006. Dr. Einstein won Furman University's Meritorious Teaching Award in 1985 and was the first recipient of Furman University's Excellence in Teaching Award in 2006. He is past president of the Southeastern Workers in Memory, and he has served on the editorial boards of the Journal of Experimental Psychology Learning, Memory, and Cognition and Memory & Cognition. He is a Fellow of Divisions 2, 3 and 20 of the American Psychological Association, and he is a member of the Association of Psychological Science and the Psychonomic Society. His research focuses on the processes involved in prospective remembering, how these processes break down in important real-world situations, and how they are affected by aging. He has published more than 75 articles, chapters, and books, and his research has been...

Organization

Chapter 2 provides the background necessary for understanding the main issues of this work about representations for GEAs. Section 2.1 introduces representations which can be described as a mapping that assigns one or more genotypes to every phenotype. The genetic operators selection, crossover, and mutation are applied on the level of alleles to the genotypes, whereas the fitness of individuals is calculated from the corresponding phenotypes. Section 2.2 illustrates that selectorecombinative GEAs, where only crossover and selection operators are used, are based on the notion of schemata and building blocks. Using schemata and building blocks is an approach to explain why and how GEAs work. This is followed in Sect. 2.3 by a brief review of reasons and measurements for problem difficulty. Measurements of problem difficulty are necessary to be able to compare the influence of different types of representations on the performance of GEAs. The chapter ends with some earlier, mostly...

Schemata

Schemata were first proposed by Holland (1975) to model the ability of GEAs to process similarities between bitstrings. A schema h (hi,h2, ,hi) is defined as a ternary string of length l, where hi G 0,1, * . * denotes the don't care symbol and tells us that the allele at this position is not fixed. The size or order o(h) of a schema h is defined as the number of fixed positions (0s or 1s) in the string. A position in a schema is fixed if there is either a 0 or a 1 at this position. The defining length 5(h) of a schema h is defined as the distance between the two outermost fixed bits. The fitness of a schema is defined as the average fitness of all instances of this schema and can be calculated as

Territories

Defend territories after reproduction has ceased for the year. If bears, hummingbirds, and other animals use food as an index for the potential to produce offspring, then food can legitimately be considered to be at least a proximately limiting resource. Fitness is the ultimate currency in biology, and fitness may be affected by one or more limiting resources that need not be offspring or other direct components of reproduction. Evolution via natural selection requires heritable variation that affects reproductive output among individuals in a population. The effects can be via offspring, or they can be via food, nest sites, tunnel systems, or other potentially limiting resources.

Chemical Libraries

One approach to generating functional small molecules that control stem cell fate involves the use of phenotypic or pathway-specific screens of synthetic chemical or natural product libraries. The size and diversity of a given purified chemical library as well as the selection method determine the chance of finding a desired hit compound. With recent advances in automation and detection technologies, millions of discrete compounds can be screened rapidly and cost-effectively. However, although combinatorial technologies allow for the synthesis of a large number of molecules with immense structural diversity, it is impossible to saturate the chemical space. Because the diversity of chemical libraries is largely constrained by the synthetic tractability, new synthetic technologies are the driving force to expand current chemical diversities for filling the chemical space. In addition, introducing a high level of structural variability to increase the molecular diversity of a chemical...

Scaling

This section provides the second of three elements of a theory of representations and addresses representations which change the importance of alleles when mapping genotypes on phenotypes. Common representations for GEAs often encode the phenotypes by using a sequence of alleles. When assigning phenotypes to genotypes, a representation can change the importance of the alleles. For example, a phenotype is a list of integers and all alleles (integers) are equally relevant for calculating the fitness of a phenotype. We know from previous work that the BBs (alleles) are solved in parallel if all alleles are equally relevant (Goldberg 1989c). The situation that all alleles are equally relevant is equivalent to the situation that the BBs are uniformly scaled. However, when encoding the phenotypic integers using binary strings, the contributions of the genotypic bits to the fitness function are no longer equal and some bits are more relevant than others. When using such non-uniformly scaled...

Lessons

What currencies are best for quantifying home ranges and territories Home ranges should not always be quantified with respect to the time that an animal spends, or is predicted to spend, in different places. Most researchers use time to index importance, but what really counts is fitness. For some questions, home ranges may need to be quantified by probability density functions of energy expenditure or energy acquisition. Ultimately, for much research, home ranges should be quantified as probability density functions for contributions to fitness. How does a person map a home range's contributions to fitness

Cystic Fibrosis

Another common feature of intraclonal evolution in the CF lung is the diversification of morphotype, the hallmarks being the emergence of small colony variants28 29 and mucoid colonies.26 57 The alginate-overexpressing mucoid phenotype is typical for CF isolates and very uncommon in other habitats.26 A subgroup of hyperpiliated small colony variants is prone to biofilm formation and induction of type II and type III secretion2991 which leads to increased virulence in infection models in contrast to the notion that most P. aeruginosa isolates from chronically colonized CF lungs are typically attenuated in virulence (see above). Auxotrophy is common in CF, particularly in those with severe underlying pulmonary disease.87 At this late stage the auxotroph count exceeds more than 50 total CFU. The majority of auxotrophs required methionine as the sole factor.86 In summary, the common conversion of phenotype of P. aeruginosa in CF lungs starts with morphotype diversification and loss of...

Methods

In this section we will describe two examples of miniprotein design. The first example reports on the design of a metal-binding miniprotein that expresses metal specificity for different metals and has been characterized using different spectroscopic techniques to verify its structure and function. The second reports on the design of a mimic of human CD4, which was ultimately optimized to a native-like activity by two different steps, the first used to increase its nativelikeness (after the miniprotein 3D structure was solved by solution 1H-NMR) and the second used to increase the fitness of the miniprotein active surface for the receptor binding surface (after the structure of the mimic receptor complex was modeled).

Verbal tests

Although means for measuring mental ability date as far back as 2000 b.c.e., when the ancient Chinese administered oral tests to determine a candidate's fitness for carrying out the tasks of civil administration, the modern intelligence test has its origins in the nineteenth century, when Jean- tienne-Dominique Esquirol drew a clear distinction between mentally deranged people ( lunatics ) and mentally retarded people ( idiots ). Esquirol believed that it was necessary to devise a means of gauging normal intelligence so that deviations from an agreed-upon norm could be ascertained, and he pointed out that intellectual ability exists on a continuum extending from idiocy to genius. His work coincided with studies in Europe and the United States that were designed to develop a concept of intelligence and to fashion a means of testing this capacity. Work done by Sir Francis Galton in the United Kingdom on hereditary genius, by James McKeen Cattell in the United States on individual...

Assessment Criteria

In determining the passenger's fitness to fly, a basic knowledge of aviation physiology and physics can be applied to the pathology. Any trapped gas will expand in volume by up to 30 during flight, and consideration must be given to the effects of the relative hypoxia encountered at a cabin altitude of 8000 feet (2400 m) above mean sea level. The altitude of the destination airport may also need to be taken into account in deciding the fitness of an individual to undertake a particular journey. The passenger's exercise tolerance can provide a useful guide on fitness to fly if unable to walk a distance greater than about 50 metres without developing dyspnoea, there is a risk that the passenger will be unable to tolerate the relative hypoxia of the pressurised cabin. More specific guidance can be gained from knowledge of the passenger's blood gas levels and haemoglobin value.

Pressure Transducer

The use of reduced preparations and or more technologically advanced approaches are effective as second-order phenotyping strategies. The ideal would be to use a reduced preparation in tandem with studies of natural variation to disclose mechanisms for evolutionary fitness. Simultaneous use of proteomics and expression arrays in such models may efficiently screen many biochemical processes that could contribute to trait variance, and can be useful in locating candidate genes within the regions-of-interest identified through the study of inbred lines. This approach is used to identify genomic elements operating in strain differences in sleep in the mouse 96 . Complementary and parallel studies in animals and humans can be more efficient in understanding the biology of the response.

Summary

We have seen in this section that an encoding which can represent not only valid, but also invalid, solutions encodes a valid phenotype by more than one genotype. Therefore, such an encoding is redundant and the results about redundant encodings from Sect. 3.1 can be used. Redundancy is independent of whether the invalid solutions are repaired, or if they remain untouched in the population. In both situations, it is necessary to evaluate the invalid genotypes and to assign a fitness value to every invalid solution. Furthermore, we have seen that an encoding which can represent invalid solutions is unbiased if the construction of a valid phenotype from an invalid genotype is unbiased and does not favor some phenotypes.

Genetic Architecture

Shifting balance also requires multiple selective equilibria, that is, multiple adaptive peaks that are separated by either fitness valleys or fitness ridges in Wright's metaphor. The shape of the adaptive surface depends in part upon the underlying genetic architecture of fitness. Recall from Chapter 10 that the genetic architecture refers to the number of loci and their linkage relationships and the numbers of alleles per locus that contribute to a trait, along with the mapping of genotype onto phenotype (dominance, recessiveness, pleiotropy, epistasis, etc.). The multiple-peak adaptive surface required for shifting balance arises in part from a genetic architecture characterized by strong interactions between genes (either between alleles at the same locus or between alleles at different loci, that is, epistasis) and or pleiotropy. For example, the two-peak surface shown in Figure 11.8 for the j-Hb A, S, and Cexample in a malarial environment arises in part from the pleiotropic...

Transposons

Transposons are units of selection that can have multiple targets of selection. In addition to selection within cells on their ability to transpose and replicate within genomes, transposons often affect fitness at the individual level (Cooper 1999 Kidwell and Lisch 2000 Prak and Kazazian 2000). Just as we saw for the t complex in mice, the evolutionary dynamics of transposons must take into account multiple targets of selection, and phrasing the evolution of transposons only as selfish DNA that parasitizes the genome is inappropriate and misleading. For example, different types of transposons have inserted into the promoter of the hsp70Ba gene that codes for the stress-inducible molecular chaperone Hsp70 in Drosophila melanogaster (Lerman et al. 2003). These transposon insertions underlie the natural variation found in the expression of this gene, and this in turn directly alters two components of individual fitness, inducible thermotolerance and female reproductive success. Another...

Fertility

Fertility is a fitness component that emerges inherently from the interaction of a mating pair of individuals. A nonselfing individual cannot display this phenotype except in the context of an interaction with a mate. For example, in humans, the ABO blood group locus has three common alleles that determine one's ABO blood type (Chapter 7). Knowing one's ABO blood type is clinically important because transfusing donor blood bearing an antigen (A and or B) not found in the recipient can create a potentially lethal immunological reaction in the recipient. If there is leakage of blood across the placenta, a mother can mount an immunological reaction against a developing fetus that bears antigens not found in the mother. This results in a significant increase in the rate of spontaneous abortions in those couples that have ABO genotypes that yield ABO maternal-fetal incompatible combinations (Takano and Miller 1972). In the ABO system, the same individual genotype can have drastically...

Competition

Darwin identified competition in the struggle for existence as a source of natural selection. Competition inherently involves interactions among individuals who are competing for some resource, and indeed we already saw a form of this in the competition for mates. When two or more individuals compete with one another, what matters is their relative competitive abilities to one another. Indeed, the very phenotype of competitive ability cannot exist at all except in the context of interacting individuals. Hence, the phenotype of competitive ability constitutes another target of selection above the level of the individual. Cockerham et al. (1972) presented a simple one-locus, two-allele model of competition involving pairs of individuals that randomly encounter one another in a random-mating population. The genotype frequencies within a generation are assumed to be in Hardy-Weinberg proportions, and the frequency of an individual competing with another individual of a specified genotype...

W12 W11

Note A random mating population with one locus with two alleles (A and a) with p the frequency of A. When individuals of genotype i (i 0 is aa, i 1 is Aa, and i 2 is AA) compete with individuals of genotype j, the fitness consequence to genotype i is given by Wij. A protected polymorphism occurs when at least one allele at a locus is favored by natural selection when very rare and selected against when very common. The conditions for protection can be derived from either equation 11.5 or the average excess of fitness by taking the limits as the allele frequency approaches 0 and 1. For protection, the change in allele frequency predicted from equation 11.5 or from the average excess must be positive as p 0 (that is, selection causes the allele frequency to increase when it is very rare), and they must be negative as p 1 (that is, selection causes the allele frequency to decrease when it is very common). In such a case, natural selection protects the allele from going to fixation (p 1)...

Kin Family Selection

In both the fertility model and the competitive model, fitness phenotypes emerged from the interactions of individuals who encountered one another (or mated) at random. However, there are many targets of selection that emerge from individuals whose encounters are highly nonrandom from a genetic perspective. For example, genetically related individuals aggregate in many species, at least for some portion of their lives. This occurs in species with some sort of family structure, which places parents and offspring and or siblings into a potentially interactive context. Table 13.7 presents a simple one-locus, two-allele (A and a) family model in a random-mating population (Templeton 1979b). There are two simultaneous targets of selection in this model, the individual and the family. Thus, the fitnesses that we assign to individuals in the context of a family are constants (the wij in Table 13.7). As before, when we assign a fitness to just an individual genotype with no family context...

Beware Teleology

Omnipresent dangers in the study of social behavior are the closely allied traps of teleology and unwitting anthropomorphism. Teleology, or the doctrine of final causes, infers purpose in nature (e.g., to infer the existence of a creator from the works of creation). The teleological conviction that mind and will are the cause of all things in nature is not within the scope of scientific method (Romanes 1881). In the context of animal behavior, teleological explanation would name and account for a behavior by its presumed ultimate effect (e.g., appeasement, submission, or punishment) and not by its proximate causes or physical appearance. It may be convenient to label as punishment the category of attack launched by a dominant meerkat on the only member of her group not to join in a fight with territorial trespassers. The danger lies in (inadvertently) interpreting the functional nuance of this convenient label as the proximate cause of the attacker's behavior. We know only that one...

No Fail Fitness

No Fail Fitness

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