Stabilizing selection and linkage disequilibrium

An approach to the investigation of the evolution of quantitative traits on the basis of analysis of two-locus marginal systems dynamics has been developed. It has been shown that under stabilizing selection the "quasi-stationary" state is quickly reached and maintained continuously. The "quasi-stationary" state is characterized by small changes in allele frequencies and by linkage disequilibrium that significantly decreases genotypic variance. Equations defining the role of linkage disequilibrium in the stationary state of mutation-selection balance are derived.     

Optimizing selection for function-valued traits

We consider a function-valued trait z(t) whose pre-selection distribution is Gaussian, and a fitness function W that models optimizing selection, subject to certain natural assumptions. We show that the post-selection distribution of z(t) is also Gaussian, compute the selection differential, and derive an equation that expresses the selection gradient in terms of the parameters of W and of the pre-selection distribution. We make no assumptions on the nature of the “time” parameter t.      

Stabilizing sexual selection for female ornaments in a dance fly

Ornamental traits function by improving attractiveness and are generally presumed to experience directional selection for mating success. However, given the greater investment of females in offspring than males, female-specific ornaments can in theory signal fecundity yet be constrained by fecundity costs. Theoretical work predicts that such constraints can lead to stabilizing selection via male choice for intermediately ornamented females. Female dance flies Rhamphomyia longicauda (Diptera: Empididae) display two female-specific ornaments in mating swarms - inflatable abdominal sacs and pinnate tibial scales. We investigated the intensity and form of sexual selection on female traits including ornaments and found no evidence for directional sexual selection. Instead, we found marginally nonsignificant quadratic selection for all three measures of ornament expression. Canonical analysis confirmed that the strongest vectors of nonlinear selection were associated with ornamental traits, although the significance of the quadratic coefficients associated with these vectors depended on the statistical approach. Direct Mitchell-Olds and Shaw tests for the location of the maximum fitted fitness value for both raw morphological traits and canonical axes revealed only one marginally nonsignificant result for the multivariate axis loading most heavily on pinnate leg scales. Together, these results provide the first tentative support for stabilizing selection on female-specific ornaments.     

Stabilizing and directional selection on facial paedomorphosis

Averageness is purportedly the result of stabilizing selection maintaining the population mean, whereas facial paedomorphosis is a product of directional selection driving the population mean towards an increasingly juvenile appearance. If selection is predominantly stabilizing, intermediate phenotypes reflect high genetic quality and mathematically average faces should be found attractive. If, on the other hand, directional selection is strong enough, extreme phenotypes reflect high genetic quality and juvenilized faces will be found attractive. To compare the effects of stabilizing and directional selection on facial paedomorphosis (juvenilization), graphic morphing and editing techniques were used to alter the appearance of composite faces to make them appear more or less juvenile. Both facial models and judges of attractiveness were from the CSU-Long Beach campus. Although effect sizes for both preferences were large, the effect for averageness was nearly twice that found for juvenilization, an indication that stabilizing selection influences preferences for facial paedomorphosis more so than directional selection in contemporary humans.     

Stabilizing selection in the dog-whelk (Nucella lapillus)

The amount of stabilizing selection undergone by a population of animals at different times of its life can be estimated by comparing the variances of different age samples. This paper describes an investigation into the intensities of selection experienced by populations of the common dog-whelk, Nucella lapillus (L.) exposed on different shores to different degrees of wave action. It was found that the variance of more exposed populations was reduced during life by up to 90%. There was a positive correlation between the intensity of stabilizing selection and the amount of wave action experienced by the whelks. Most of this selection took place during the first year or two of the life of the animals.     

Simultaneous marker-assisted selection for multiple traits in autogamous crops

A method is presented for the selection of parents with the aim of obtaining improved genotypes in the progeny of a cross. The procedure is designed to select in several unrelated traits simultaneously and is based on the selection of molecular markers that are linked to QTLs. The method was compared with conventional phenotypic selection in simulation experiments for a number of genetic structures underlying the traits and several types of parental populations. Although the method in general provides good results, some of the underlying assumptions may be violated quite easily, thereby reducing the applicability of the procedure in practice. Received: 10 September 1999 / Accepted: 24 August 2000     

Responses to selection for milk traits in dairy buffaloes

The aim of the present study was to estimate the index and individual responses to selection for milk (MY), fat (FY) and protein (PY) yields for different breeding goals for two commercial buffalo milk production systems in S?o Paulo State characterized by: 1) all milk produced is sold to the industry (MILK) and 2) all milk produced is used in the mozzarella cheese-making process at the farm (MOZZARELLA). The current payment policy is based exclusively on milk volume. The mozzarella price refers to the wholesale selling price. Index responses to selection (IR) were calculated for three different breeding goals (BG): 1) MY exclusively (BG(1)); 2) FY + PY (BG(2)) and 3) MY + FY + PY (BG(3)). IR for the MILK system were 41.79 US dollars (BG(1)), 5.91 US dollars (BG(2)) and 38.22 US dollars (BG(3)). For the MOZZARELLA system, IR were 179.50 US dollars (BG(1)), 262.85 US dollars (BG(2)) and 402.41 US dollars (BG(3)). The results suggest that for the present circumstances, selection for milk components is not advantageous when milk is produced for sale to the industry. However, when mozzarella making is added to the system, the selection for components and milk volume is the most economically beneficial.     

Molecular marker-assisted selection for malting quality traits in barley

Selection for malting quality in breeding programs by micromalting and micromashing is time-consuming, and resource-intensive. More efficient and feasible approaches for identifying genotypes with good malting quality would be highly desirable. With the advent of molecular markers, it is possible to map and tag the loci affecting malting quality. The objective of this study was to assess the effectiveness of molecular marker assisted selection for malting quality traits. Two major quantitative trait loci (QTL) regions in six-row barley for malt extract percentage, -amylase activity, diastatic power, and malt -glucan content on chromosomes 1 (QTL1) and 4 (QTL2) have been previously identified. The flanking markers, Brz and Amy2, and WG622 and BCD402B, for these two major QTL regions were used in marker-assisted selection. Four alternative selection strategies; phenotypic selection, genotypic selection, tandem genotypic and phenotypic selection, and combined phenotypic and genotypic selection, were compared for both single and multiple trait selection in a population consisting of 92 doubled haploid lines derived from Steptoe × Morex crosses. Marker assisted selection for QTL1 (tandem genotypic and phenotypic selection, and combined phenotypic and genotypic selection) was more effective than phenotypic selection, but for QTL2 was not as effective as phenotypic selection due to a lack of QTL2 effects in the selection population. The effectiveness of tandem genotypic and phenotypic selection makes marker assisted selection practical for traits which are extremely difficult or expensive to measure such as most malting quality traits. It can substantially eliminate undesirable genotypes by early genotyping and keeping only desirable genotypes for later phenotypic selection.     

Stabilizing selection of protein function and distribution of selection coefficient among sites

In this study, I take a new approach to modeling the evolutionary constraint of protein sequence, introducing the stabilizing selection of protein function into the nearly-neutral theory. In other words, protein function under stabilizing selection generates the evolutionary conservation at the sequence level. With the help of random mutational effects of nucleotides on protein function, I have derived the distribution of selection coefficient among sites, called the S-distribution whose parameters have clear biological interpretations. Moreover, I have studied the inverse relationship between the evolutionary rate and the effective population size, showing that the number of molecular phenotypes of protein function, i.e., independent components in the fitness of the organism, may play a key role for the molecular clock under the nearly-neutral theory. These results are helpful for having a better understanding of the underlying evolutionary mechanism of protein sequences, as well as human disease-related mutations.     

Synergistic selection and graded traits

Fitness interactions where benefits are shared only between individuals with similar traits are often referred to as synergistic. Examples include defence characters, like insect warning colouration and plant unpalatability, and joint activities needing the active participation of all group members, such as cooperative hunting. Previous analyses, assuming discrete variation in the trait, have shown that synergistic selection can be a sufficient explanation for the evolutionary stability of such traits. Here, we investigate the consequences of graded variation in the trait responsible for synergistic effects. Classifying the synergism as unbiased when an individual receives maximum associational benefit by having the same trait value as its neighbours, and letting a positive (negative) bias represent the maximum above (below) this value, we show that only positively biased synergistic selection can enhance a graded trait. Thus for graded traits, a synergistic benefit is not in itself sufficient for evolutionary stability. We study possible reasons for synergistic bias in a simple model of plant defences against herbivores, and suggest that the processes of herbivore avoidance learning and diet selection are probable causes of positive bias. We propose that mammalian herbivores exposed to a given level of toxicity will show stronger feeding aversion to higher toxicity, resulting in positively biased synergistic selection of plant defence traits. Positive bias produced by avoidance learning may, in a similar way, also select for defence signals.     

Bull selection and use in northern Australia. Part 2. Semen traits

Detailed semen evaluations were carried out on approximately 363 Santa Gertrudis, 5/8 Brahman and Brahman bulls on 12 different properties across northern Australia, as part of systematic breeding soundness examinations. A subset of bulls (n=245) were subsequently mated in groups, to cows and heifers at bull:female ratios of 2.5-6.0%, with the paternity of resulting calves being determined by microsatellite DNA testing. Motility traits of semen and spermatozoa were moderately repeatable and correlated with each other, but were unrelated to calf output. The percentage of morphologically normal spermatozoa in ejaculates was moderately to highly repeatable (e.g. r=0.10-0.64). The most common morphological abnormalities seen were mid-piece abnormalities, in particular, distal mid-piece reflex associated with a cytoplasmic droplet. Semen quality, particularly percent normal spermatozoa, was consistently related to calf output. In general, bulls with <50% normal spermatozoa sired few calves while bulls with the highest calf outputs had >70% normal spermatozoa. The presence or absence of heparin binding proteins in semen did not influence calf output. Semen from 93% of tested bulls was positive for heparin binding proteins. These results confirm that examination of semen, in particular, evaluation of percent morphologically normal spermatozoa, should be included in the breeding soundness examination of bulls.     

Stabilizing selection on body mass in the sociable weaver Philetairus socius

The survival of small birds is often believed to increase with increasing body mass, despite some evidence that body mass is usually maintained below the physiological maximum and that there are costs associated with high body mass, such as increased energetic expenditure and predation risk. In this study, we used an eight-year dataset to investigate survival in relation to body mass in a wild population of sociable weavers (Philetairus socius), a savannah-dwelling passerine bird. We present evidence for strong stabilizing selection on body mass, verifying the prediction that body mass probably results from a trade-off between the risks of starvation at low mass and predation at high mass.     

Genomic selection for grain yield and quality traits in durum wheat

The prediction accuracies of genomic selection depend on several factors, including the genetic architecture of target traits, the number of traits considered at a given time, and the statistical models. Here, we assessed the potential of single-trait (ST) and multi-trait (MT) genomic prediction models for durum wheat on yield and quality traits using a breeding panel (BP) of 170 varieties and advanced breeding lines, and a doubled-haploid (DH) population of 154 lines. The two populations were genotyped with the Infinium iSelect 90K SNP assay and phenotyped for various traits. Six ST-GS models (RR-BLUP, G-BLUP, BayesA, BayesB, Bayesian LASSO, and RKHS) and three MT prediction approaches (MT-BayesA, MT-Matrix, and MT-SI approaches which use economic selection index as a trait value) were applied for predicting yield, protein content, gluten index, and alveograph measures. The ST prediction accuracies ranged from 0.5 to 0.8 for the various traits and models and revealed comparable prediction accuracies for most of the traits in both populations, except BayesA and BayesB, which better predicted gluten index, tenacity, and strength in the DH population. The MT-GS models were more accurate than the ST-GS models only for grain yield in the BP. Using BP as a training set to predict the DH population resulted in poor predictions. Overall, all the six ST-GS models appear to be applicable for GS of yield and gluten strength traits in durum wheat, but we recommend the simple computational models RR-BLUP or G-BLUP for predicating single trait and MT-SI for predicting yield and protein simultaneously.     

Heritability and expected selection response for yield traits in blanched asparagus

Despite the continuous breeding that has been conducted with asparagus (Asparagus officinalis L.) since the beginning of the last century, there is little information on parameters for predicting direct and indirect selection response. Yield traits for blanched asparagus production were studied along a two-year period in a half-sib family population planted in Zavalla, Argentina. Half-sib family mean heritability values were low for total yield and marketable spear number (0.31 and 0.35), intermediate for marketable yield and total spear number (0.55 and 0.64), and relatively high for spear diameter and spear weight (0.75 and 0.74). An average increase in marketable yield of 15.9% is expected after each cycle of selection of the top 5% of the families. Total yield failed to express significant genetic correlations with any of the yield components; meanwhile marketable yield showed highly significant relations with market spear number (0.96) and spear weight (0.89). Indirect selection response over yield components (CRx) failed to be advantageous over direct selection (Rx), since the ratio CRx/Rx was always equal or below unity.     

The natural selection of altruistic traits

Proponents of the standard evolutionary biology paradigm explain human “altruism” in terms of either nepotism or strict reciprocity. On that basis our underlying nature is reduced to a function of inclusive fitness: human nature has to be totally selfish or nepotistic. Proposed here are three possible paths to giving costly aid to nonrelatives, paths that are controversial because they involve assumed pleiotropic effects or group selection. One path is pleiotropic subsidies that help to extend nepotistic helping behavior from close family to nonrelatives. Another is “warfare”—if and only if warfare recurred in the Paleolithic. The third and most plausible hypothesis is based on the morally based egalitarian syndrome of prehistoric hunter-gatherers, which reduced phenotypic variation at the within-group level, increased it at the between-group level, and drastically curtailed the advantages of free riders. In an analysis consistent with the fundamental tenets of evolutionary biology, these three paths are evaluated as explanations for the evolutionary development of a rather complicated human social nature. This paper (in a series of drafts) has profited from comments by Michael Boehm, Donald T. Campbell, Bruce Knauft, Jane Lancaster, Martin Muller, Peter J. Richerson, Gary Seaman, Craig Stanford, George Williams, Edward O. Wilson, David Sloan Wilson, and two reviewers for Human Nature. Christopher Boehm is a professor of anthropology and the director of the Jane Goodall Research Center, University of Southern California. His research interests in political anthropology concern egalitarianism, feuding, warfare, and conflict resolution (humans and chimpanzees). In biosocial anthropology he is interested in altruism, group selection, and decisions.     

Artificial selection on phenotypically plastic traits

Many phenotypes respond physiologically or developmentally to continuously distributed environmental variables such as temperature and nutritional quality. Information about phenotypic plasticity can be used to improve the efficiency of artificial selection. Here we show that the quantitative genetic theory for 'infinite-dimensional' traits such as reaction norms provides a natural framework to accomplish this goal. It is expected to improve selection responses by making more efficient use of information about environmental effects than do conventional methods. The approach is illustrated by deriving an index for mass selection of a phenotypically plastic trait. We suggest that the same approach could be extended directly to more general and efficient breeding schemes, such as those based on general best linear unbiased prediction. Methods for estimating genetic covariance functions are reviewed.