Model selection for quantitative trait loci mapping in a full-sib family

Statistical methods for mapping quantitative trait loci (QTLs) in full-sib forest trees, in which the number of alleles and linkage phase can vary from locus to locus, are still not well established. Previous studies assumed that the QTL segregation pattern was fixed throughout the genome in a full-sib family, despite the fact that this pattern can vary among regions of the genome. In this paper, we propose a method for selecting the appropriate model for QTL mapping based on the segregation of different types of markers and QTLs in a full-sib family. The QTL segregation patterns were classified into three types: test cross (1:1 segregation), F₂ cross (1:2:1 segregation) and full cross (1:1:1:1 segregation). Akaike’s information criterion (AIC), the Bayesian information criterion (BIC) and the Laplace-empirical criterion (LEC) were used to select the most likely QTL segregation pattern. Simulations were used to evaluate the power of these criteria and the precision of parameter estimates. A Windows-based software was developed to run the selected QTL mapping method. A real example is presented to illustrate QTL mapping in forest trees based on an integrated linkage map with various segregation markers. The implications of this method for accurate QTL mapping in outbred species are discussed.     

No female mate choice in Mallee dragon lizards, Ctenophorus fordi

Aspects of sexual selection were studied in a sexually monomorphic Australian agamid lizard (Ctenophorus fordi), in particular with respect to the sensory exploitation hypothesis. In enclosure trials, females were offered the choice between large vs. small males and, in a different experiment, males with blue vs. normal head color. The rationale for these experiments was: firstly, to establish if females actively solicit copulations; secondly, if so, do females solicit copulations non-randomly with respect to male size (because large males may have access to food resources); thirdly, if male coloration is manipulated to match traits of congeneric, conspicuous and sexually dimorphic species, do females show preference for this novel trait (in accordance with the sensory exploitation hypothesis). The corresponding manipulations were also made in a free-living population where the distribution of females on the home ranges of color-manipulated males were monitored. Blue-headed males were accepted as mating partners both in the staged mating trials and in the natural population. Females appeared not to express any kind of active or passive mate choice (rejection); in only one out of 62 trials did a female approach a male herself rather than being approached by the male(s). There was no discrimination against any male category regardless of size or color within a female's receptive period and the manipulation of male head color in the natural population did not result in spatial re-distribution of females. Thus, a female appears to mate unselectively within her receptive period. Rejection behaviors were used only outside of the receptive period to communicate, to all males, that the female is not receptive.     

Environment-dependent selection on mate choice in a natural population of birds

Female mate choice acts as an important evolutionary force, yet the influence of the environment on both its expression and the selective pressures acting upon it remains unknown. We found consistent heritable differences between females in their choice of mate based on ornament size during a 25-year study of a population of collared flycatchers. However, the fitness consequences of mate choice were dependent on environmental conditions experienced whilst breeding. Females breeding with highly ornamented males experienced high relative fitness during dry summer conditions, but low relative fitness during wetter years. Our results imply that sexual selection within a population can be highly variable and dependent upon the prevailing weather conditions experienced by individuals.     

Ultra-simple DNA extraction method for marker-assisted selection using microsatellite markers in rice

We prevent an ultra-simple DNA extraction method for microsatellite analysis of rice. Each extraction requires only one microtube, one disposable pipette tip, TE buffer and few pieces (about 5 mm) of rice leaf tissue. This is sufficient for 200 PCR reactions. The extract can be kept in the freezer for long-term storage. Also, DNA can be extracted from 200–300 individuals in a few hours. These features enabled us to perform rapid largescale seedling genotyping required for marker-assisted selection. We have also examined the applicability of this method for other PCR-based markers: RAPDs, nuclear STS, chloroplast STS and chloroplast microsatellites.     

Optimizing purebred selection for crossbred performance using QTL with different degrees of dominance

A method was developed to optimize simultaneous selection for a quantitative trait with a known QTL within a male and a female line to maximize crossbred performance from a two-way cross. Strategies to maximize cumulative discounted response in crossbred performance over ten generations were derived by optimizing weights in an index of a QTL and phenotype. Strategies were compared to selection on purebred phenotype. Extra responses were limited for QTL with additive and partial dominance effects, but substantial for QTL with over-dominance, for which optimal QTL selection resulted in differential selection in male and female lines to increase the frequency of heterozygotes and polygenic responses. For over-dominant QTL, maximization of crossbred performance one generation at a time resulted in similar responses as optimization across all generations and simultaneous optimal selection in a male and female line resulted in greater response than optimal selection within a single line without crossbreeding. Results show that strategic use of information on over-dominant QTL can enhance crossbred performance without crossbred testing.     

Evolutionary study of a potential selection target region in the pig

Domestication, modern breeding and artificial selection have shaped dramatically the genomic variability of domestic animals. In livestock, the so-called FAT1 quantitative trait locus (QTL) in porcine chromosome 4 was the first QTL uncovered although, to date, its precise molecular nature has remained elusive. Here, we characterize the nucleotide variability of 13 fragments of ∼500 bp equally spaced in a 2 Mb region in the vicinity of the FAT1 region in a wide-diversity panel of 32 pigs. Asian and European animals, including local Mediterranean and international pig breeds, were sequenced. Patterns of genetic variability were very complex and varied largely across loci and populations; they did not reveal overall a clear signal of a selective sweep in any breed, although FABP4 fragment showed a significantly higher diversity. We used an approximate Bayesian computation approach to infer the evolutionary history of this SSC4 region. Notably, we found that European pig populations have a much lower effective size than their Asian counterparts: in the order of hundreds vs hundreds of thousands. We show also an important part of extant European variability is actually due to introgression of Asian germplasm into Europe. This study shows how a potential loss in diversity caused by bottlenecks and possible selective sweeps associated with domestication and artificial selection can be counterbalanced by migration, making it much more difficult the identification of selection footprints based on naive demographic assumptions. Given the small fragment analyzed here, it remains to be studied how these conclusions apply to the rest of the genome.     

Multiple cues in mate selection: The sexual interference hypothesis

Animals use multiple cues when choosing mates, but it is not yet clear why a single signal would not suffice. In this paper, drawing support from predation and “noise” effects on mate choice, marketing economics, and multiple signals models, a new hypothesis explaining multiple sexual signals is proposed: the sexual interference hypothesis. The hypothesis is based on three well-supported premises: (1) selectivity decreases when mate assessment costs increase, (2) assessment costs increase when the propagation or reception of sexual signals is more difficult, and (3) males not only exploit such circumstances by courting females when choice is more difficult, but actively interfere with females' preferences by making choice more difficult. The hypothesis argues that additional sexual signals evolve as a way for males to hinder female mate choice by interfering with the propagation and reception of other males' sexual signals. Females respond by evolving the ability to glean meaningful information from signals despite males' attempts at obfuscation. In turn, males respond by producing better interference signals and signals that are not so easily blocked. This co-evolutionary process increases the costs of assessment for females and the costs of signal production for males, and leads to a temporary equilibrium of honest advertising via multiple signals.     

Synergistic selection between ecological niche and mate preference primes diversification

The ecological niche and mate preferences have independently been shown to be important for the process of speciation. Here, we articulate a novel mechanism by which ecological niche use and mate preference can be linked to promote speciation. The degree to which individual niches are narrow and clustered affects the strength of divergent natural selection and population splitting. Similarly, the degree to which individual mate preferences are narrow and clustered affects the strength of divergent sexual selection and assortative mating between diverging forms. This novel perspective is inspired by the literature on ecological niches; it also explores mate preferences and how they may contribute to speciation. Unlike much comparative work, we do not search for evolutionary patterns using proxies for adaptation and sexual selection, but rather we elucidate how ideas from niche theory relate to mate preference, and how this relationship can foster speciation. Recognizing that individual and population niches are conceptually and ecologically linked to individual and population mate preference functions will significantly increase our understanding of rapid evolutionary diversification in nature. It has potential to help solve the difficult challenge of testing the role of sexual selection in the speciation process. We also identify ecological factors that are likely to affect individual niche and individual mate preference in synergistic ways and as a consequence to promote speciation. The ecological niche an individual occupies can directly affect its mate preference. Clusters of individuals with narrow, differentiated niches are likely to have narrow, differentiated mate preference functions. Our approach integrates ecological and sexual selection research to further our understanding of diversification processes. Such integration may be necessary for progress because these processes seem inextricably linked in the natural world.     

Incorporation of genotype effects into animal model evaluations when only a small fraction of the population has been genotyped

The method of Israel and Weller (Estimation of candidate gene effects in dairy cattle populations. Journal of Dairy Science 1998, 81, 1653-1662) to estimate quantitative trait locus (QTL) effects when only a small fraction of the population was genotyped was investigated by simulation. The QTL effect was underestimated in all cases, but bias was greater for extreme allelic frequencies, and increased with the number of generations included in the simulations. Apparently, as the fraction of animals with inferred genotypes increases, the genotype probabilities tend to 'mimic' the effect of relationships. Unbiased estimates of QTL effects were derived by a modified 'cow model' without the inclusion of the relationship matrix on simulated data, even though only a small fraction of the population was genotyped. This method yielded empirically unbiased estimates for the effects of the genes DGAT1 and ABCG2 on milk production traits in the Israeli Holstein population. Based on these results, an efficient algorithm for marker-assisted selection in dairy cattle was proposed. Quantitative trait loci effects are estimated and subtracted from the cows' records. Genetic evaluations are then computed for the adjusted records. Animals are then selected based on the sum of their polygenic genetic evaluations and QTL effects. This scheme differs from a traditional dairy cattle breeding scheme in that all bull calves were considered candidates for selection. At year 10, total genetic gain was 20% greater by the proposed algorithm as compared to the selection based on a standard animal model for a locus with a substitution effect of 0.5 phenotypic standard deviations. The proposed method is easy to apply, and all required software are 'on the shelf.' It is only necessary to genotype breeding males, which are a very small fraction of the entire population. The method is flexible with respect to the model used for routine genetic evaluation. Any number of genetic markers can be easily incorporated into the algorithm, and the reduction in genetic gain due to incorrect QTL determination is minimal.     

Behaviour before beauty: Signal weighting during mate selection in the butterfly Papilio polytes

Mating displays often contain multiple signals. Different combinations of these signals may be equally successful at attracting a mate, as environment and signal combination may influence relative signal weighting by choosy individuals. This variation in signal weighting among choosy individuals may facilitate the maintenance of polymorphic displays and signalling behaviour. One group of animals known for their polymorphic patterning are Batesian mimetic butterflies, where the interaction of sexual selection and predation pressures is hypothesized to influence the maintenance of polymorphic wing patterning and behaviour. Males in the female‐limited polymorphic Batesian mimetic butterfly Papilio polytes use female wing pattern and female activity levels when determining whom to court. They court stationary females with mimetic wing patterns more often than stationary females with non‐mimetic, male‐like wing patterns and active females more often than inactive females. It is unclear whether females modify their behaviour to increase (or decrease) their likelihood of receiving male courtship, or whether non‐mimetic females spend more time in cryptic environments than mimetic females, to compensate for their lack of mimicry‐driven predation protection (at the cost of decreased visibility to males). In addition, relative signal weighting of female wing pattern and activity to male mate selection is unknown. To address these questions, we conducted a series of observational studies of a polymorphic P. polytes population in a large butterfly enclosure. We found that males exclusively courted active females, irrespective of female wing pattern. However, males did court active non‐mimetic females significantly more often than expected given their relative abundance in the population. Females exhibited similar activity levels, and selected similar resting environments, irrespective of wing pattern. Our results suggest that male preference for non‐mimetic females may play an active role in the maintenance of the non‐mimetic female form in natural populations, where males are likely to be in the presence of active, as well as inactive, mimetic and non‐mimetic females.     

Optimal selection on two quantitative trait loci with linkage

A mathematical approach to optimize selection on multiple quantitative trait loci (QTL) and an estimate of residual polygenic effects was applied to selection on two linked or unlinked additive QTL. Strategies to maximize total or cumulative discounted response over ten generations were compared to standard QTL selection on the sum of breeding values for the QTL and an estimated breeding value for polygenes, and to phenotypic selection. Optimal selection resulted in greater response to selection than standard QTL or phenotypic selection. Tight linkage between the QTL (recombination rate 0.05) resulted in a slightly lower response for standard QTL and phenotypic selection but in a greater response for optimal selection. Optimal selection capitalized on linkage by emphasizing selection on favorable haplotypes. When the objective was to maximize total response after ten generations and QTL were unlinked, optimal selection increased QTL frequencies to fixation in a near linear manner. When starting frequencies were equal for the two QTL, equal emphasis was given to each QTL, regardless of the difference in effects of the QTL and regardless of the linkage, but the emphasis given to each of the two QTL was not additive. These results demonstrate the ability of optimal selection to capitalize on information on the complex genetic basis of quantitative traits that is forthcoming.     

Environmental stress increases selection against and dominance of deleterious mutations in inbred families of the Pacific oyster Crassostrea gigas

The deleterious effects of inbreeding are well documented and of major concern in conservation biology. Stressful environments have generally been shown to increase inbreeding depression; however, little is known about the underlying genetic mechanisms of the inbreeding-by-stress interaction and to what extent the fitness of individual deleterious mutations is altered under stress. Using microsatellite marker segregation data and quantitative trait locus (QTL) mapping methods, I performed a genome scan for deleterious mutations affecting viability (viability or vQTL) in two inbred families of the Pacific oyster Crassostrea gigas, reared in a stressful, nutrient-poor diet and a favourable, nutrient-rich diet, which had significant effects on growth and survival. Twice as many vQTL were detected in the stressful diet compared with the favourable diet, resulting primarily from substantially greater mortality of homozygous genotypes. At vQTL, estimates of selection (s) and dominance (h) were greater in the stressful environment (= 0.86 vs. 0.54 and = 0.35 vs. 0.18, in stressful and nonstressful diets, respectively). There was no evidence of interaction between vQTL. Individual vQTL differed across diets in selection only, or in both selection and dominance, and some vQTL were not affected by diet. These results suggest that stress-associated increases in selection against individual deleterious alleles underlie greater inbreeding depression with stress. Furthermore, the finding that inbreeding-by-environment interaction appears, to some extent, to be locus specific, helps to explain previous observations of lineage-specific expression of inbreeding depression and environment-specific purging, which have important implications for conservation and evolutionary biology.     

The diversification of mate preferences by natural and sexual selection

The evolution of sexual display traits or preferences for them in response to divergent natural selection will alter sexual selection within populations, yet the role of sexual selection in ecological speciation has received little empirical attention. We evolved 12 populations of Drosophila serrata in a two‐way factorial design to investigate the roles of natural and sexual selection in the evolution of female mate preferences for male cuticular hydrocarbons (CHCs). Mate preferences weakened in populations evolving under natural selection alone, implying a cost in the absence of their expression. Comparison of the vectors of linear sexual selection revealed that the populations diverged in the combination of male CHCs that females found most attractive, although this was not significant using a mixed modelling approach. Changes in preference direction tended to evolve when natural and sexual selection were unconstrained, suggesting that both processes may be the key to initial stages of ecological speciation. Determining the generality of this result will require data from various species across a range of novel environments.     

Baffling: a condition-dependent alternative mate attraction strategy using self-made tools in tree crickets

Intense sexual selection in the form of mate choice can facilitate the evolution of different alternative reproductive strategies, which can be condition-dependent. Tree cricket males produce long-distance acoustic signals which are used by conspecific females for mate localization and mate choice. Our study shows that baffling, an acoustic call amplification strategy employed by male tree crickets using self-made tools, is a classic example of a condition-dependent alternative strategy. We show that though most males can baffle, less preferred males, such as smaller and lower-amplitude callers, predominantly use this alternative strategy. Baffling allows these males to increase their call amplitude and advertisement range, which attracts a higher number of females. Baffling also gives these males a mating benefit because females mate for longer durations with them. Our results suggest that the advantage of baffling in terms of gain in the number of sperm cells transferred while mating is primarily limited to less preferred males, thus maintaining the polymorphism of calling strategies in the population. We summarize that baffling is a condition-dependent strategy used by less preferred tree cricket males to obtain mating benefits.     

Different mate preferences by parasitized and unparasitized females potentially reduces sexual selection

Parasite‐mediated models of sexual selection predict that females should avoid parasitized mates, thereby generating selection on male traits revealing health. The strength of this selection, however, may depend on the prevalence of parasitism among females if their infection status alters their mate preferences. We evaluated the effects of a socially transmitted parasite on male traits and female behaviour in spadefoot toads. Parasitized males were larger and in better condition than unparasitized males. Moreover, better condition males produced longer calls. Unparasitized females preferred longer calls indicative of good‐condition males that are more likely parasitized. By contrast, parasitized females as a group possessed no preference for call duration. Presumably because of reduced selection by these parasitized females, male mating success was not associated with any measured traits. Thus, when females are parasitized, sexual selection on condition‐dependent traits is potentially reduced.     

A method to optimize selection on multiple identified quantitative trait loci

A mathematical approach was developed to model and optimize selection on multiple known quantitative trait loci (QTL) and polygenic estimated breeding values in order to maximize a weighted sum of responses to selection over multiple generations. The model allows for linkage between QTL with multiple alleles and arbitrary genetic effects, including dominance, epistasis, and gametic imprinting. Gametic phase disequilibrium between the QTL and between the QTL and polygenes is modeled but polygenic variance is assumed constant. Breeding programs with discrete generations, differential selection of males and females and random mating of selected parents are modeled. Polygenic EBV obtained from best linear unbiased prediction models can be accommodated. The problem was formulated as a multiple-stage optimal control problem and an iterative approach was developed for its solution. The method can be used to develop and evaluate optimal strategies for selection on multiple QTL for a wide range of situations and genetic models.     

Finding the one: optimal choosiness under sequential mate choice

When mates are encountered sequentially, each encounter involves a decision whether to reject the current suitor and risk not finding a better mate, or to accept them despite their flaws. I provide a flexible framework for modelling optimal choosiness when mate encounters occur unpredictably in time. The model allows for temporal variation in the fitness benefits of mating, including seasonal breeding conditions, accrual of mate search costs, survival of the choosing individual or senescence of gametes. The basic optimality framework can be applied iteratively to obtain mate choice equilibria in dynamically evolving populations. My model predicts that individuals should be choosier when the average rate of mate encounters is high, but that choosiness should decline over time as the likelihood of future mate encounters decreases. When mate encounters are uncertain, there is a trade‐off between reproductive timing and mate choice (the ‘when’ and the ‘who’). Mate choice may be selected against when reproductive timing is highly important (e.g. when breeding conditions show a narrow peak in time). This can even lead to step‐shaped mate choice functions, where individuals abruptly switch from rejecting to accepting all suitors as peak breeding conditions approach. The model contributes to our understanding of why individuals may not express mate preferences, even when there is substantial variation in mate quality.     

Genetic analysis of extended life span in Drosophila melanogaster II. Replication of the backcross test and molecular characterization of the N14 Locus

We are interested in localizing chromosomal regions that extend life span in Drosophila. Using stocks artificially selected for long life by Luckinbill and his colleagues, we have identified marker loci that are highly divergent in allelic frequencies between replicated long-lived lines and controls (Curtsinger et al., 1998). Several of the most divergent loci have been found to be associated with effects on life span in segregating backcross populations. Here we report an independent replication of the backcross test for the N14 marker locus, previously reported to extend male life spans by 12 days. The life span effect successfully replicates in males. N14 accounts for 30% of the total selection response in males. Life span extension occurs by a decrease in age-specific mortality rates at all ages, and is not attributable to modification of the slope of the age-specific mortality curve. The effect in females is small or nonexistent. Sequencing of the N14 locus shows that it is non-coding and not obviously regulatory, suggesting that the phenotypic effect arises from linkage disequilibrium with another locus or loci that directly affect life span. N14 DNA hybridizes to 63F/64A on the left arm of chromosome 3. The location is consistent with previous whole-chromosome substitution studies, and suggests new candidate genes for life span extension in Drosophila, including ras2. This revised version was published online in July 2006 with corrections to the Cover Date.