Impact of farmer selection on yam genetic diversity

In the traditional yam agricultural system, by way of an ennoblement practice, farmers select tubers from the wild for cultivation. In order to assess the impact of that practice on the genetic diversity of yam, we studied the genetic structure of yams obtained after at least 3 years of ennoblement, to which farmers gave the name of traditional varieties. Cultivated yams do not always have the same genotype as homonymous traditional varieties. For the first time, we demonstrated selection by farmers through the ennoblement of genotypes found in neighbouring villages. Their adoption has a double impact: it allows an increase in the polyclonality of varieties and an indirect exchange of yam tubers between farmers. We also demonstrated that wild yams and hybrids between wild and cultivated yams are also selected. However, their adoption seems less frequent, suggesting selection and valuation of ennobled yams before integration into the cultivated pool. Finally, the adaptive advantage of wild and hybrid yams and their role in yam agrosystems are discussed.     

Impact of nonrandom mating on genetic variance and gene flow in populations with mass selection

The mechanisms by which nonrandom mating affects selected populations are not completely understood and remain a subject of scientific debate in the development of tractable predictors of population characteristics. The main objective of this study was to provide a predictive model for the genetic variance and covariance among mates for traits subjected to directional selection in populations with nonrandom mating based on the pedigree. Stochastic simulations were used to check the validity of this model. Our predictions indicate that the positive covariance among mates that is expected to result with preferential mating of relatives can be severely overpredicted from neutral expectations. The covariance expected from neutral theory is offset by an opposing covariance between the genetic mean of an individual's family and the Mendelian sampling term of its mate. This mechanism was able to predict the reduction in covariance among mates that we observed in the simulated populations and, in consequence, the equilibrium genetic variance and expected long-term genetic contributions. Additionally, this study provided confirmatory evidence on the postulated relationships of long-term genetic contributions with both the rate of genetic gain and the rate of inbreeding (deltaF) with nonrandom mating. The coefficient of variation of the expected gene flow among individuals and deltaF was sensitive to nonrandom mating when heritability was low, but less so as heritability increased, and the theory developed in the study was sufficient to explain this phenomenon.     

Impact of boar exposure on puberty attainment and breeding outcomes in gilts

We examined the most effective method of boar exposure for the attainment of puberty in 89 gilts. At 160 days of age, we allocated gilts to daily direct contact with a vasectomized boar after movement of pen groups of gilts to a detection-mating area (DGB: n = 30); daily direct contact with boars in the gilt home pens (DBG: n = 31); or daily fenceline contact between boars and gilts housed in individual gilt stalls (FBG: n = 28). DGB gilts were younger (P < or = 0.05) than FBG gilts at puberty. Direct boar contact reduced the interval from initial boar contact to puberty in DGB and DBG gilts, compared to fenceline contact in FBG gilts (P < 0.05). There was no difference (P > or = 0.05) between treatment for pubertal weight, backfat, lifetime growth rate, or duration of first pubertal estrus. Backfat depth and leptin concentration at 160 days of age were positively correlated (P < or = 0.05). We detected no relationships between leptin or IGF-1 concentration at 160 days of age and the interval from initial exposure to a vasectomized boar to puberty (P > 0.05). Based on objective criteria, fenceline contact with a boar (BC) during artificial insemination improved the quality of artificial insemination compared to no boar contact (NC) (P < 0.05).     

Daily selection of habitat in wild boar (Sus scrofa)

Spatial segregation of the sexes is observed in numerous species of ungulates, but are there other forms of segregation in species where spatial segregation is not present, such as in the wild boar? This study investigates the differences in habitat selection between two categories of individuals whose ecological requirements are supposedly divergent: subadult males, and females with dependent piglets. The proportion of the day spent in each category of habitat was used as a parameter representative of daily decisions. The overall results fit with the hypothesis that females with piglets avoid insecure habitats, and that both categories select habitats on the basis of food richness. In addition, it was found that the pattern of habitat selection depends on the total time spent moving slowly. A short duration of slow movement was observed only in males, but the time dedicated to efficient foraging (in rich habitats) was sufficient in all observations of all animals. Subadult males, therefore, do not differ from each other in foraging efficiency, but in the time spent on slow movement in secure habitats. Those spending more time active in secure habitats have the opportunity of performing more potentially beneficial activities such as social interactions and sexual contacts.     

The joint effects of kin, multilevel selection and indirect genetic effects on response to genetic selection

Kin and levels-of-selection models are common approaches for modelling social evolution. Indirect genetic effect (IGE) models represent a different approach, specifying social effects on trait values rather than fitness. We investigate the joint effect of relatedness, multilevel selection and IGEs on response to selection. We present a measure for the degree of multilevel selection, which is the natural partner of relatedness in expressions for response. Response depends on both relatedness and the degree of multilevel selection, rather than only one or the other factor. Moreover, response is symmetric in relatedness and the degree of multilevel selection, indicating that both factors have exactly the same effect. Without IGEs, the key parameter is the product of relatedness and the degree of multilevel selection. With IGEs, however, multilevel selection without relatedness can explain evolution of social traits. Thus, next to relatedness and multilevel selection, IGEs are a key element in the genetical theory of social evolution.     

Impact of founder population, drift and selection on the genetic diversity of a recently translocated tree population

Recently established, temperate tree populations combine a high level of differentiation for adaptive traits, suggesting rapid genetic evolution, with a high level of genetic diversity within population, suggesting a limited impact of genetic drift and purifying selection. To study experimentally the evolutionary forces in a recently established population, we assessed the spatial and temporal patterns of genetic diversity within a disjunct population of Cedrus atlantica established 140 years ago in south-eastern France from a North African source. The population is expanding through natural regeneration. Three generations were sampled, including founder trees. We analysed 12 isozyme loci, three of which were previously found in tight association with selected genes, and quantitative traits. No bottleneck effect was detected in the founder generation, but a simple test of allelic association revealed an initial disequilibrium which disappeared in the following generations. The impact of genetic drift during secondary evolution was limited, as suggested by the weak temporal differentiation. The genetic load was not reduced after 3 generations, and the quantitative variation for adaptive traits did not change either. Thus, initial genetic changes first proceed from a rapid re-organisation of the diversity through mating and recombination, whereas genetic erosion through drift and selection is delayed due to temporal and spatial stochasticity. Two life-history traits of trees contribute to slowing down the processes of genetic erosion: perenniality and large spatial scale. Thus, one would expect recently established tree populations to have a higher diversity than older ones, which seems in accordance with experimental surveys.     

Impact of density and disease on frequency-dependent selection and genetic polymorphism: experiments with stripe rust and wheat

Frequency-dependent disease impacts may contribute to the maintenance of genetic diversity and sexual reproduction in plant populations. In earlier work with experimental wheat (Triticum aestivum) populations at a single density, we found that stripe rust (caused by Puccinia striiformis) created frequency-dependent selection on its host but competitive interactions between host genotypes reduced the potential for disease to maintain genetic polymorphisms in this highly self-pollinated species; the weaker competitor actually exhibited positive disease-mediated frequency-dependent selection. Based on these results we predicted that at low density, where the overall level of competition is lower, disease would have a stronger impact relative to competition and thus be more likely to maintain genetic polymorphisms; at low densities the greatest effect of disease for negative frequency-dependent selection should be seen in the weak competitor. Here we report on results with wheat stripe rust in which we altered both the frequency and density of host genotypes in factorial combinations of two-way mixtures where each host genotype was attacked by its own specialized race of rust. Within each density disease levels increased with genotype frequencies, creating frequency-dependent disease attack at all densities. Similarly, disease created negative frequency-dependent selection on its host at all densities, as a genotype’s fitness was often greater at low than high frequency when disease was present. Disease levels increased with plant density in 1997 but decreased in 1998. While increasing plant density reduced absolute fitness, presumably as a result of increased competition, a genetic polymorphism was not more likely to be maintained at low than high density as we had predicted. Within each density, the impact of disease was insufficient to reverse the slope of the relationship between absolute fitness and planted frequency from positive to negative for the less competitive host genotype, thus preventing the maintenance of a genetic polymorphism.     

The effect of non-additive genetic interactions on selection in multi-locus genetic models

Additive genetic variance might usually be expected to decrease in a finite population because of genetic drift. However, both theoretical and empirical studies have shown that the additive genetic variance of a population could, in some cases, actually increase owing to the action of genetic drift in presence of non-additive effects. We used Monte-Carlo simulations to address a less-well-studied issue: the effects of directional truncation selection on a trait affected by non-additive genetic variation. We investigated the effects on genetic variance and the response to selection. We compared two different genetic models, representing various numbers of loci. We found that the additive genetic variance could also increase in the case of truncation selection, when dominance and epistasis was present. Additive-by-additive epistatic effects generally gave a higher increase in additive variance compared to dominance. However, the magnitude of the increase differed depending on the particular model and on the number of loci.     

Habitat and management influence on a seasonal diet composition of wild boar

The purpose of this study was to compare the diet composition of two wild boar populations living in the Czech Republic, one living in a floodplain, broadleaved, forest (A) and the other in a highland mostly coniferous forest (B). Food consumed by A showed to be mostly of natural origin, while that of B was predominantly supplemented. The diet consisting of natural resources was significantly different than the diet including mainly supplemented food. All diversity indices of food volume were higher in lowland localities compared to highland in all season’s cumulative sample. Similarity of the relative volume and relative frequency gradually decreased from spring to winter. Significant differences were found in wild boar consumption of roots (higher in A), grasses (higher in A), seeds and fruits (higher in B) and cereal husks (higher in B). Differences were also found in body mass of the piglets in A, as piglets were dominant group in both localities. Food supply of the localities and population management by the wildlife managers (supplemented food) were the main factors influencing the diet composition of the wild boar.     

Effect of selection on genetic parameters of correlated traits

Summary Changes in genetic parameters of correlated traits due to the buildup of linkage (gametic phase) disequilibrium from repeated truncation selection on a single trait are studied. After several generations of selection, an equilibrium is approached where there are no further changes in genetic parameters and limiting values are reached. Formulae are derived under an infinitesimal model for these limiting values of genetic variances and covariances, heritabilities, and genetic correlations between traits directly and indirectly selected. Changes from generation zero to the limit in all these parameters become greater as heritability of the trait under direct selection increases and, to a lesser extent, as intensity of selection increases. Change in heritability of a trait under indirect selection also increases as the absolute value of the correlation between the trait under indirect and the trait under direct selection increases. The change is maximum when the initial value of heritability is close to 0.5 and insignificant when the initital value is close to zero or one. Change in the genetic correlation between the trait under direct selection and the trait under indirect selection is maximum when its initial value is close to ±0.6 and insignificant when its initial value is close to zero or ±1. Heritability of the trait indirectly selected and genetic correlation between that trait and the trait directly selected always decrease in absolute value, whereas genetic correlation between two traits indirectly selected can either decrease or increase in absolute value. It is suggested that use be made of formulae at selection equilibrium in the prediction of correlated responses after several generations of selection.     

Impact of human management on the genetic variation of wild pepper, Capsicum annuum var. glabriusculum

Management of wild peppers in Mexico has occurred for a long time without clear phenotypic signs of domestication. However, pre-domestication management could have implications for the population's genetic richness. To test this hypothesis we analysed 27 wild (W), let standing (LS) and cultivated (C) populations, plus 7 samples from local markets (LM), with nine polymorphic microsatellite markers. Two hundred and fifty two alleles were identified, averaging 28 per locus. Allele number was higher in W, and 15 and 40% less in LS and C populations, respectively. Genetic variation had a significant population structure. In W populations, structure was associated with ecological and geographic areas according to isolation by distance. When LM and C populations where included in the analysis, differentiation was no longer apparent. Most LM were related to distant populations from Sierra Madre Oriental, which represents their probable origin. Historical demography shows a recent decline in all W populations. Thus, pre-domestication human management is associated with a significant reduction of genetic diversity and with a loss of differentiation suggesting movement among regions by man. Measures to conserve wild and managed populations should be implemented to maintain the source and the architecture of genetic variation in this important crop relative.     

The effect of simultaneous selection on the genetic correlation

The theoretical effect of simultaneous selection on the genetic correlations between two traits over 20 generations was examined using simulation. For each generation, a population of 50 male and 50 female diploid gen otypes with 15 loci, each with two alleles, was synthesized. None of the loci exhibited dominance. Five loci affected only trait 1, 5 loci only trait 2 and 5 were pleiotropic (affected both traits). Initial allelic frequencies were equal at each locus. Phenotypes were created by adding a random normal deviation for each trait to the genotype. The size of this deviation for each trait determined its heritability (h²). Index selection with h² combinations of (0.15, 0.15), (0.15,0.45) and (0.45,0.45) and relative economic weights of (1, 1) and (1, 3) for each h² combination was employed. In each generation, the highest ranking 25 genotypes of each sex were used to generate the next generation with single-pair matings, each producing two male and two female offspring. One hundred replicates were run for both negative and positive correlations. With a positive initial value, the genetic correlation tended to decline (toward zero). The rates of change were moderately affected by index weights and h². With a negative initial value, the genetic correlation tended to decrease (towards -1). However, unequal heritabilities and unequal relative economic weights slowed the rate of change with the greatest imbalances tending to hold the correlation constant or move it toward zero. These simulations illustrate that changes in parameters over time can affect the selection practiced. Under some of the conditions simulated, the use of initial genetic parameter values without change could have potentially negative effects on overall genetic gain.     

Traditional Amerindian cultivators combine directional and ideotypic selection for sustainable management of cassava genetic diversity

Plant domestication provides striking examples of rapid evolution. Yet, it involves more complex processes than plain directional selection. Understanding the dynamics of diversity in traditional agroecosystems is both a fundamental goal in evolutionary biology and a practical goal in conservation. We studied how Amerindian cultivators maintain dynamically evolving gene pools in cassava. Farmers purposely maintain diversity in the form of phenotypically distinct, clonally propagated landraces. Landrace gene pools are continuously renewed by incorporating seedlings issued from spontaneous sexual reproduction. This poses two problems: agronomic quality may decrease because some seedlings are inbred, and landrace identity may be progressively lost through the incorporation of unrelated seedlings. Using a large microsatellite dataset, we show that farmers solve these problems by applying two kinds of selection: directional selection against inbred genotypes, and counter‐selection of off‐type phenotypes, which maintains high intra‐landrace relatedness. Thus, cultural elements such as ideotypes (a representation of the ideal phenotype of a landrace) can shape genetic diversity.     

Quantitative genetic models of sexual selection

Modeling of R.A. Fisher's ideas about the evolution of male ornamentation using quantitative genetics began in the 1980s. Following an initial period of enthusiasm, interest in these models began to wane when theoretical studies seemed to show that the rapid evolution of ornaments would not occur if there were costs associated with female mate choice. Recent theoretical work has shown, however, that runaway evolution and other kinds of extensive diversification of ornaments and preferences can occur, even when female choice is costly. These new models highlight crucial parameters that profoundly influence evolutionary trajectories, but these parameters have been neglected in empirical studies. Here, we review quantitative genetic models of sexual selection with the aim of fostering communication and synergism between theoretical and empirical enterprises. We also point out several areas in which additional empirical work could distinguish between alternative models of evolution.     

Influence of selection forms on genetic structure of domestic animals

Analysis of genetic structure of pure and crossbred sheep and cattle with the use of genetic-biochemical markers was carried out. Data on breed- and locus-specific genetic traits, stable in the time, were obtained. In sheep, breed-specific peculiarities of genetic structure partly related with the belonging of breeds to breed groups with fine-, semi-fine and coarse wool. The preferable influence of artificial selection at the phenotype complex traits in comparison with natural selection and animal origin on the genetic structure of crossbred sheep was revealed. However, the more profound effects of natural selection on the genetic structure of crossbred cattle were observed.     

Dual selection of a genetic switch by a single selection marker

Forward engineering of synthetic genetic circuits in living cells is expected to deliver various applications in biotechnology and medicine and to provide valuable insights into the design principles of natural gene networks. However, lack of biochemical data and complexity of biological environment complicate rational design of such circuits based on quantitative simulation. Previously, we have shown that directed evolution can complement our weakness in designing genetic circuits by screening or selecting functional circuits from a large pool of nonfunctional ones. Here we describe a dual selection strategy that allows selection of both ON and OFF states of genetic circuits using tetA as a single selection marker. We also describe a successful demonstration of a genetic switch selection from a 2000-fold excess background of nonfunctional switches in three rounds of iterative selection. The dual selection system is more robust than the previously reported selection system employing three genes, with no observed false positive mutants during the simulated selections.