Selection strategies for developing smooth bromegrass cell wall ideotypes

Summary A random sample of 80 families of the B8HD smooth bromegrass (Bromus inermis Leyss.) population were tested in three environments for forage yield and cell wall constituents. Expected progress from one cycle of family selection was computed for single-trait selection and multiple-trait restricted selection. Expected gains were compared to desired goals and actual results from one cycle of phenotypic selection. Desired goals were: Model I = reduced lignin and cellulose, with increased hemicellulose, resulting in no change in cell wall content; Model II = reduced lignin and cellulose with no change in hemicellulose; or Model III = reduced lignin, cellulose, and hemicellulose. Single-trait selection for high hemicellulose in first harvest or low cellulose in second harvest had the best expected responses, of any single trait, for Model I. Possible undesirable effects of selection for low cellulose would be a reduction in forage yield potential. Multiple-trait restricted selection was judged to be more effective, with responses all in the desired direction, by specifying increased hemicellulose in index development. Selection in second harvest was expected to have similar responses as first harvest, except for a greater increase in forage yield. Development of Models II or III is expected to be difficult due to a negative correlation estimate between first and second harvest cell wall concentration.     

A comparison of restricted selection index and linear programming in sire selection

Summary The objective of restricted selection index is to enhance genetic change in one trait while restricting to zero change in a second trait. Linear programming is another, yet conceptually different, technique to maximize one function while enforcing limits on others. The objective of this research was to compare restricted selection index and linear programming in ability to maximize performance in one trait while limiting change in a second trait to zero. Results of a numerical study demonstrate that linear programming is a more effective method to limit correlated response than restricted selection index. On average, both methods limited response in a correlated trait to zero. However, the squared deviation of actual response in the restricted trait from zero was smaller with linear programming than with restricted selection index. Response to selection in the unrestricted trait is greater with restricted selection index than with linear programming.     

Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites

The impact of synonymous nucleotide substitutions on fitness in mammals remains controversial. Despite some indications of selective constraint, synonymous sites are often assumed to be neutral, and the rate of their evolution is used as a proxy for mutation rate. We subdivide all sites into four classes in terms of the mutable CpG context, nonCpG, postC, preG, and postCpreG, and compare four-fold synonymous sites and intron sites residing outside transposable elements. The distribution of the rate of evolution across all synonymous sites is trimodal. Rate of evolution at nonCpG synonymous sites, not preceded by C and not followed by G, is approximately 10% below that at such intron sites. In contrast, rate of evolution at postCpreG synonymous sites is approximately 30% above that at such intron sites. Finally, synonymous and intron postC and preG sites evolve at similar rates. The relationship between the levels of polymorphism at the corresponding synonymous and intron sites is very similar to that between their rates of evolution. Within every class, synonymous sites are occupied by G or C much more often than intron sites, whose nucleotide composition is consistent with neutral mutation-drift equilibrium. These patterns suggest that synonymous sites are under weak selection in favor of G and C, with the average coefficient s approximately 0.25/Ne approximately 10(-5), where Ne is the effective population size. Such selection decelerates evolution and reduces variability at sites with symmetric mutation, but has the opposite effects at sites where the favored nucleotides are more mutable. The amino-acid composition of proteins dictates that many synonymous sites are CpGprone, which causes them, on average, to evolve faster and to be more polymorphic than intron sites. An average genotype carries approximately 10(7) suboptimal nucleotides at synonymous sites, implying synergistic epistasis in selection against them.     

Robustness of Selection Procedures

In the article Bechhofers Indifference-zone formulation for selecting the t populations with the t highest means is considered in a set of non-normal distributions. Selection rules based on the sample mean, the 10% and the 20% trimmed means, two estimators proposed by Tiku (1981) for valuating the smallest and highest accepted sample values higher, the sample median and a linear combination of quantile estimators, two adaptive procedures and a ranksum procedure are investigated in a large scale simulation experiment in respect of their robustness against deviations from an assumed distribution. Robustness is understood as a small percentage of the difference β_A-β between the actual probability of incorrect selection β_A and the nominal β-value. We obtained a relatively good robustness for the classical sample mean selection rule and useful derivations for the employment of other selection rules in an area of practical importance.     

Selection for high gamete encounter rates explains the evolution of anisogamy using plausible assumptions about size relationships of swimming speed and duration

A previous general model describing physical constraints on gamete encounter rates was modified to incorporate assumptions that increased size causes decreased swimming speed and increased fertile period (or other proportional enhancement to gamete fertility). The analysis indicates that with moderately strong size dependence of fertile period and a range of speed dependencies, selection for high encounter rates pressures mating systems that develop any heritable difference in size between the gametes of different mating types to exaggerate the difference and evolve from isogamy to anisogamy. The smaller gamete has an optimal size, but the larger faces continuing selection for increased size. This continues to a size that is estimated to be sufficient to make pheromone production of sperm attractants practical. This mechanism then bridges the missing link between isogametes and oogamy in a previous analysis of the effectiveness of pheromones in explaining the success of male-female mating systems. The evolution and success of anisogamy and oogamy can be explained solely on the basis of physical effects on the encounter process.     

Some principles governing selection in self-reproducing macromolecular systems

Summary Starting with Eigen's model we discuss some principles pertaining to the selection of biological macromolecules. The principles have a certain analogy to Fisher's fundamental theorem for natural selection.     

Predation and primate evolution

This paper presents the results of a general review of predation on nonhuman primates as a selective force in primate evolution. Testable hypotheses derived from the literature on predation on primates, concerning sexual dimorphism, male defense, group size, solitaries, transfer, subgrouping, and sex ratio, were applied to the available data on populations with varying predation rates in search of significant correlations. All seven hypotheses were supported, indicating that predation is and has been an important determinant of primate evolutionary history. Suggestions for accumulating a larger and more accurate body of information on predation rates on primates are offered.     

Principles and strategies in breeding for higher salt tolerance

Summary Salinity is an environmental component that usually reduces yield. Recent advances in the understanding of salt effects on plants have not revealed a reliable physiological or biochemical marker that can be used to rapidly screen for salt tolerance. The necessity of measuring salt tolerance based upon growth in saline relative to non-saline environments makes salt tolerance measurements and selection for tolerance difficult. Additionally, high variability in soil salinity and environmental interactions makes it questionable whether breeding should be conducted for tolerance or for high yield. Genetic techniques can be used to identify the components of variation attributable to genotype and environment, and the extent of genetic variation in saline and nonsaline environments can be used to estimate the potential for improving salt tolerance. Absolute salt tolerance can be improved best by increasing both absolute yield and relative salt tolerance.     

Precedence effects and the evolution of chorusing

The structured choruses produced by rhythmically signalling males in many species of acoustic animals have long-captured the imagination of evolutionary biologists. Though various hypotheses have been forwarded to explain the adaptive significance of such chorusing, none have withstood empirical scrutiny. We suggest instead that alternating and synchronous choruses represent collective epiphenomena resulting from individual males competing to jam each other''s signals. These competitions originate in psychoacoustic precedence effects wherein females only orient toward the first call of a sequence, thus selectively favouring males who produce leading calls. Given this perceptual bias, our modelling confirms that a resetting of signal rhythm by neighbours'' signals, which generates either alternation or synchrony, is evolutionarily stable provided that resetting includes a relativity adjustment for the velocity of signal transmission and selective attention toward only a subset of signalling neighbours. Signalling strategies in chorusing insects and anurans are consistent with these predicted features.     

Simulated evolution and artificial selection

A highly simplified evolving system was investigated by computer simulation. The genetic complement of each simulated organism in the population was represented by a single chromosome that consisted of a string of symbols. Individual fitness was measured as the number of symbols that corresponded to a specified rule. Reproduction was simulated with a non-breeding algorithm and two variants of a breeding algorithm, and was subject to random point mutations. In each generation, selection was effected by replacing the less fit members of the population with offspring of the more fit. The size of the population and the fraction replaced, though under experimental control, were constant for each simulation run. It was found that even such a simplified system is able to mimic a variety of properties observed in natural systems. In addition, the effect of the simulation parameters on the course of fitness increase provides a basis for using a genetic algorithm as an optimization technique.     

Selection indices for non-linear profit functions

Summary Conventional selection index theory assumes that the total merit or profitability of animals is a linear function of measurable traits. However, in many cases merit may be a non-linear function of these traits. A linear selection index can still be used in this situation but the optimum index depends on the selection intensity to be used and on the number of generation over which the selection response is to be maximized. Nonlinear selection indices have been suggested but these result in a lower selection response than the best linear index. Linear selection indices suggested in the past are shown to correspond to the optimum linear index for either a very small selection response or, in the case of restricted indices, a very large selection response. The economic value of a trait may depend on management decisions taken by the farmer. In this situation the economic values should be calculated assuming that the management decisions taken maximize profit given the present genetic value of the animals.     

Selection versus random drift: long-term polymorphism persistence in small populations (evidence and modelling)

Our data on a subterranean mammal, Spalax ehrenbergi, and other evidence, indicate that appreciable polymorphism can be preserved in small isolated populations consisting of several dozens of, or a hundred, individuals. Current theoretical models predict fast gene fixation in small panmictic populations without selection, mutation, or gene inflow. Using simple multilocus models, we demonstrate here that moderate stabilizing selection (with stable or fluctuating optimum) for traits controlled by additive genes could oppose random fixation in such isolates during thousands of generations. We also show that in selection-free models polymorphism persists only for a few hundred generations even under high mutation rates. Our multi-chromosome models challenge the hitchhiking hypothesis of polymorphism maintenance for many neutral loci due to close linkage with few selected loci.     

Generalization and the evolution of symmetry preferences

Biological displays are often symmetrical, and there is growing evidence that receivers are sensitive to these symmetries. One explanation for the evolution of such sensitivity is that symmetry reflects the quality of the signaller. An alternative is that the sensitivity may arise as a by-product of general properties of biological recognition systems. In line with the latter idea, simulations of the recognition process based on simple, artificial neural networks have suggested that generalization can give rise to preferences for particular symmetrical stimuli. However, it is not clear from these studies exactly how the preferences emerge, and to what extent the results are relevant to biological recognition systems. Here, we employ a different class of recognition models (gradient interaction models) to demonstrate more clearly how generalization can generate a preference for symmetrical variants of a display. We also point out that the predictions of the gradient interaction and network-based models regarding the effects of generalization closely match the results from empirical studies of stimulus control. Our analysis demonstrates that the effects of generalization cannot be ignored when studying the evolution of symmetry preferences and symmetric signals.     

Correlated responses of growth traits to selection for high and low plasma alkaline phosphatase in mice

Summary The effectiveness of two way selection for plasma alkaline phosphatase (ALP) was investigated in order to determine its influences on growth traits through thirteen generations. The responses of the two lines selected for high (HP) and low (LP) ALP at 45 days of age were compared to that of the mice selected for large (L) and small (SM) body size. The selection responses of plasma ALP were very effective for both HP and LP lines, with average responses per generation calculated from linear regressions of 0.227±0.037 and –0.088±0.022 respectively. The final levels of ALP in HP and LP were 5.54±0.71 and 1.27±0.20 in the thirtheenth generation, while the SM, L and base population had levels of 3.49±0.08, 0.86±0.55 and 2.77±0.56 respectively. The body weight at 45 days of age in LP (31.4±1.4 g) as a correlated response was significantly higher than HP (23.4±1.8 g) at generation 10. The correlated response of milk yield, measured by weight gain up to 12 days of age, was significantly greater in the LP line than in HP, but the correlated response of gains after weaning was not so different as the response of milk yield. The response of litter size and weight in LP showed significant higher levels than that of HP, but pups' birth weight did not differ between LP and HP. It is suggested that the correlated response of milk yield contributed more to the divergence of body size between HP and LP than the gain after weaning.Realized heritabilities of ALP were 0.335±0.059 (HP) and 0.279±0.051 (LP). Realized genetic correlations between ALP and 45 days' body weight were –0.27±0.13 (HP with SM) and –0.52±0.19 (LP with L). Realized genetic correlations between ALP and milk yield were –0.95±0.03 (HP) and –0.37±0.29 (LP). Correlations between ALP and postweaning gains were fairly low.     

Selection of individual tubers in potato breeding

Summary Out of 720 field-grown potato first year seedlings plants with best tuber apearance and large and medium size tubers with best shape were respectively selected. The tuber progeny of each group was evaluated in field experiments. It was demonstrated that the selection of individual tubers was very effective in the elimination of clones with irregular tuber shape and deep eyes. The tuber progeny of selected tubers was not inferior to the tuber progeny of selected plants. Possible applications of the results to practical potato breeding are discussed.     

Subset Selection for Exponential Populations: Determination of the Selection Constant

Given are k(≧2) exponential populations differing only in their location parameter. One wishes to choose the best one, that is the population with the largest value of the location parameter. A possible method for solving this problem is to select a subset of the k populations of size at least one which includes the best population with a required confidence P*(k^?1 ≤ P* ≤1). In this paper the required selection constant is determined for different values of k and P*. Also an approximation for the selection constant is derived. A comparison with the exact results is made.     

Codon Usage and Selection on Proteins

Selection pressures on proteins are usually measured by comparing homologous nucleotide sequences (Zuckerkandl and Pauling 1965). Recently we introduced a novel method, termed volatility, to estimate selection pressures on proteins on the basis of their synonymous codon usage (Plotkin and Dushoff 2003; Plotkin et al. 2004). Here we provide a theoretical foundation for this approach. Under the Fisher-Wright model, we derive the expected frequencies of synonymous codons as a function of the strength of selection on amino acids, the mutation rate, and the effective population size. We analyze the conditions under which we can expect to draw inferences from biased codon usage, and we estimate the time scales required to establish and maintain such a signal. We find that synonymous codon usage can reliably distinguish between negative selection and neutrality only for organisms, such as some microbes, that experience large effective population sizes or periods of elevated mutation rates. The power of volatility to detect positive selection is also modest—requiring approximately 100 selected sites—but it depends less strongly on population size. We show that phenomena such as transient hyper-mutators can improve the power of volatility to detect selection, even when the neutral site heterozygosity is low. We also discuss several confounding factors, neglected by the Fisher-Wright model, that may limit the applicability of volatility in practice. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Lauren Meyers]     

Equivalence or Selection: A Distribution-Free Approach

Using a distribution-free approach, a modification of the usual procedure for selecting the better of two treatments is presented. Here the possibility of no selection when the treatments appear to be ‘equivalent’ is allowed. The sample size and the constant needed to implement the proposed procedure are determined by controlling the probabilities of a correct selection and a wrong selection when the two treatments are not equivalent.     

Restricted selection index in mice designed to change body fat without changing body weight: correlated responses

Summary Correlated responses were studied in lines of mice selected for eight generations based on the criterion of a restricted selection index. Two replicate lines were selected in each treatment as follows: HE, high epididymal fat pad weight (EF) with zero change in body weight (BW) at 12 weeks of age; LE; low EF with zero change in BW; and RS, randomly. Correlated responses showed considerable variation between replicates, suggesting that genetic drift was important. Further, correlated responses for most traits were relatively small, probably because of low selection intensity. The HE line responded as expected in component traits of the restricted index. Associated compositional traits in HE responded as predicted since traits correlated with adiposity increased and hind carcass weight did not change significantly. Feed intake increased and feed efficiency (weight gain/feed intake) decreased in HE, as predicted. In contrast, the LE line did not respond in component traits as predicted since EF did not decrease and BW increased. Consequently, LE exhibited little change in traits associated with adiposity, but hind carcass weight, feed intake and feed efficiency increased. Of the correlated responses scored for fitness traits (littering rate, number of days from pairing of mate to littering, litter size and preweaning pup survival rate), significant effects were found for decreased littering rate in LE and increased prenatal survival rate in HE. In summary, correlated responses to restricted index selection generally agreed with expectation when responses in component traits of the index were considered.The research reported in this publication was funded by the North Carolina Agricultural Research Service (NCARS), Raleigh, NC 27695-7643, USA. The use of trade names in this publication does not imply endorsement by the NCARS, nor criticism of similar ones not mentioned     

In silico modelling of directed evolution: Implications for experimental design and stepwise evolution

We model the process of directed evolution (DE) in silico using genetic algorithms. Making use of the NK fitness landscape model, we analyse the effects of mutation rate, crossover and selection pressure on the performance of DE. A range of values of K, the epistatic interaction of the landscape, are considered, and high- and low-throughput modes of evolution are compared. Our findings suggest that for runs of or around ten generations’ duration—as is typical in DE—there is little difference between the way in which DE needs to be configured in the high- and low-throughput regimes, nor across different degrees of landscape epistasis. In all cases, a high selection pressure (but not an extreme one) combined with a moderately high mutation rate works best, while crossover provides some benefit but only on the less rugged landscapes. These genetic algorithms were also compared with a “model-based approach” from the literature, which uses sequential fixing of the problem parameters based on fitting a linear model. Overall, we find that purely evolutionary techniques fare better than do model-based approaches across all but the smoothest landscapes.