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PubMed2006

Adaptive evolution of the spike gene of SARS coronavirus: changes in positively selected sites in different epidemic groups.

BACKGROUND: It is believed that animal-to-human transmission of severe acute respiratory syndrome (SARS) coronavirus (CoV) is the cause of the SARS outbreak worldwide. The spike (S) protein is one of the best characterized proteins of SARS-CoV, which plays a key role in SARS-CoV overcoming species barrier and accomplishing interspecies transmission from animals to humans, suggesting that it may be the major target of selective pressure. However, the process of adaptive evolution of S protein and the exact positively selected sites associated with this process remain unknown. RESULTS: By investigating the adaptive evolution of S protein, we identified twelve amino acid sites (75, 239, 244, 311, 479, 609, 613, 743, 765, 778, 1148, and 1163) in the S protein under positive selective pressure. Based on phylogenetic tree and epidemiological investigation, SARS outbreak was divided into three epidemic groups: 02-04 interspecies, 03-early-mid, and 03-late epidemic groups in the present study. Positive selection was detected in the first two groups, which represent the course of SARS-CoV interspecies transmission and of viral adaptation to human host, respectively. In contrast, purifying selection was detected in 03-late group. These indicate that S protein experiences variable positive selective pressures before reaching stabilization. A total of 25 sites in 02-04 interspecies epidemic group and 16 sites in 03-early-mid epidemic group were identified under positive selection. The identified sites were different between these two groups except for site 239, which suggests that positively selected sites are changeable between groups. Moreover, it was showed that a larger proportion (24%) of positively selected sites was located in receptor-binding domain (RBD) than in heptad repeat (HR)1-HR2 region in 02-04 interspecies epidemic group (p = 0.0208), and a greater percentage (25%) of these sites occurred in HR1-HR2 region than in RBD in 03-early-mid epidemic group (p = 0.0721). These suggest that functionally different domains of S protein may not experience same positive selection in each epidemic group. In addition, three specific replacements (F360S, T487S and L665S) were only found between 03-human SARS-CoVs and strains from 02-04 interspecies epidemic group, which reveals that selective sweep may also force the evolution of S genes before the jump of SARS-CoVs into human hosts. Since certain residues at these positively selected sites are associated with receptor recognition and/or membrane fusion, they are likely to be the crucial residues for animal-to-human transmission of SARS-CoVs, and subsequent adaptation to human hosts. CONCLUSION: The variation of positive selective pressures and positively selected sites are likely to contribute to the adaptive evolution of S protein from animals to humans.

Amino Acid Sequence↗
PubMed1990

Genetic implications of a simulation model of litter size in swine based on ovulation rate, potential embryonic viability and uterine capacity: II. Simulated selection.

Direct selection for ovulation rate, uterine capacity, litter size and embryo survival and selection for indexes of ovulation rate with each of the remaining traits were simulated for a swine population. The relationships among these traits were determined from a simulation model that assumed that litter size was always less than or equal to both ovulation rate and uterine capacity. Heritabilities of ovulation rate and uterine capacity were assumed to be .25 and .20, respectively, and uncorrelated genetically and phenotypically. No additional genetic variation was assumed. Responses to weak selection pressure were simulated by recurrent updating of phenotypic variances and covariances combined with the heritabilities of ovulation rate and uterine capacity. Two indexes of ovulation rate and uterine capacity each resulted in 37% greater increase in litter size than direct selection for litter size. Indexes of ovulation rate and either litter size or embryo survival increased litter size by 21% more than direct selection for litter size. Selection for ovulation rate, uterine capacity or embryo survival was 6, 35 and 79%, respectively, less effective than direct selection for litter size. Responses to intense selection pressure were determined by direct simulation of genotypes and phenotypes of individuals. The two indexes of ovulation rate and uterine capacity exceeded direct selection for litter size by 39 and 27%. The indexes of ovulation rate and either litter size or embryo survival exceeded direct selection for litter size by 19 and 13%, respectively. Intense selection for ovulation rate or uterine capacity decreased selection response by 26 and 67%, respectively, relative to direct selection for litter size. Intense selection for embryo survival decreased litter size slightly.

Animals↗
PubMed1991

Selective uptake of cholesteryl esters from low density lipoproteins in vitro and in vivo.

Evidence for the direct uptake ("selective uptake") of cholesteryl esters (CE) from low density lipoproteins (LDL) by perfused luteinized rat ovaries (Azhar, S., A. Cooper, L. Tsai, W. Maffe, and E. Reaven. 1988. J. Lipid Res. 29: 869-882) led to this examination of LDL selective uptake in cultured cells and in rats using LDL doubly labeled with intracellularly trapped tracers of the CE and apoB moieties. Studies in vitro demonstrated LDL selective uptake by human fibroblasts at a low rate relative to LDL particle uptake; the fractional rate of this selective uptake increased with decreasing LDL particle size. Mouse Y1-BS1 adrenal cortical tumor cells also selectively took up LDL CE; on ACTH treatment, LDL selective uptake increased in parallel with high density lipoproteins (HDL) selective uptake, and accounted for the majority of LDL CE uptake. Metabolism of doubly labeled LDL was examined in rats. Adrenal gland and liver selectively took up CE from rat LDL, as did lung and adipose tissue. Selective uptake from human LDL was at a lower fractional rate than from rat LDL, and could not be demonstrated in as many organs. Although selective uptake from LDL by ovaries of adult rats was not significant, ovaries of immature rats consistently exhibited LDL selective uptake; on treatment of these rats with hormones to produce superovulated, luteinized ovaries, LDL selective uptake increased in the ovaries and nowhere else. Selective uptake was also apparent in liver, where it accounted for 27% of total hepatic uptake of rat LDL CE. These studies indicate a significant contribution of selective uptake to LDL CE metabolism in rats, suggesting the possibility of a role in other animals as well.

Adrenocorticotropic Hormone↗
PubMed2000

Body weight and tail length divergence in mice selected for rate of development.

A series of mouse lines has been produced by 19 generations of restricted index selection for rate of development during early and late ontogeny. The selection program was based on an index with the following four replicated selection treatments: E(+) and E(-) were selected to alter birth to 10-day body weight gain while holding late gain for both selection lines constant; correspondingly, L(+) and L(-) were selected to alter 28- to 56-day body weight gain holding early gain for both lines constant. Herein, we characterize response to selection for growth rate by analyzing age-specific mouse body weight and tail lengths and for growth curves using a logistics model. Selection on developmental rate has resulted in divergence in both age-specific and growth curve traits. E(+) and L(+) lines reached identical weights during the late selection interval, then diverged to unique mature weights. E(-) and L(-) lines similarly achieved identical weights during late selection and diverged to unique mature weights. However, the shapes of early and late growth curves were significantly divergent, and at least two distinct growth patterns are shown to result from selection. Response in body weight gain was accompanied by similar, though less pronounced, change in tail length traits. Significant response during intervals of restricted growth was also found, especially in lines selected for late gain. The evolution of the growth trajectory under restricted index selection is discussed in terms of drift and available additive genetic variation and covariation.

Aging↗
PubMed2003

Positive assortative mating with selection restrictions on group coancestry enhances gain while conserving genetic diversity in long-term forest tree breeding.

Selection and mating principles in a closed breeding population (BP) were studied by computer simulation. The BP was advanced, either by random assortment of mates (RAM), or by positive assortative mating (PAM). Selection was done with high precision using clonal testing. Selection considered both genetic gain and gene diversity by "group-merit selection", i.e. selection for breeding value weighted by group coancestry of the selected individuals. A range of weights on group coancestry was applied during selection to vary parent contributions and thereby adjust the balance between gain and diversity. This resulted in a series of scenarios with low to high effective population sizes measured by status effective number. Production populations (PP) were selected only for gain, as a subset of the BP. PAM improved gain in the PP substantially, by increasing the additive variance (i.e. the gain potential) of the BP. This effect was more pronounced under restricted selection when parent contributions to the next generation were more balanced with within-family selection as the extreme, i.e. when a higher status effective number was maintained in the BP. In that case, the additional gain over the BP mean for the clone PP and seed PPs was 32 and 84% higher, respectively, for PAM than for RAM in generation 5. PAM did not reduce gene diversity of the BP but increased inbreeding, and in that way caused a departure from Hardy-Weinberg equilibrium. The effect of inbreeding was eliminated by recombination during the production of seed orchard progeny. Also, for a given level of inbreeding in the seed orchard progeny or in a mixture of genotypes selected for clonal deployment, gain was higher for PAM than for RAM. After including inbreeding depression in the simulation, inbreeding was counteracted by selection, and the enhancement of PAM on production population gain was slightly reduced. In the presence of inbreeding depression the greatest PP gain was achieved at still higher levels of status effective number, i.e. when more gene diversity was conserved in the BP. Thus, the combination of precise selection and PAM resulted in close to maximal short-term PP gain, while conserving maximal gene diversity in the BP.

Computer Simulation↗
PubMed2005

Trends in population parameters and best linear unbiased prediction of progeny performance in a European F(2) maize population under modified recurrent full-sib selection.

Recurrent selection is a cyclic breeding procedure designed to improve the mean of a population for the trait(s) under selection. Starting from an F(2) population of European flint maize (Zea mays L.) intermated for three generations, we conducted seven cycles of a modified recurrent full-sib (FS) selection scheme. The objectives of our study were to (1) monitor trends across selection cycles in the estimates of the population mean, additive and dominance variances, (2) compare predicted and realized selection responses, and (3) investigate the usefulness of best linear unbiased prediction (BLUP) of progeny performance under the recurrent FS selection scheme applied. Recurrent FS selection was conducted at three locations using a selection rate of 25% for a selection index, based on grain yield and grain moisture. Recombination was performed according to a pseudo-factorial mating scheme, where the selected FS families were divided into an upper-ranking group of parents mated to the lower-ranking group. Variance components were estimated with restricted maximum likelihood. Average grain yield increased 9.1% per cycle, average grain moisture decreased 1.1% per cycle, and the selection index increased 11.2% per cycle. For the three traits we observed, no significant changes in additive and dominance variances occurred, suggesting future selection response at or near current rates of progress. Predictions of FS family performance in Cn+1 based on mean performance of parental FS families in Cn were of equal or higher precision as those based on the mean additive genetic BLUP of their parents, and corresponding correlations were of moderate size only for grain moisture. The significant increase in grain yield combined with the decrease in grain moisture suggest that the F(2) source population with use of a pseudo-factorial mating scheme is an appealing alternative to other types of source materials and random mating schemes commonly used in recurrent selection.

Breeding↗
PubMed2005

Diverse evolutionary trajectories characterize a community of RNA-cleaving deoxyribozymes: a case study into the population dynamics of in vitro selection.

Two parallel in vitro selections (denoted Selection A and Selection B) were conducted under different selection-pressure regimes, yielding a diverse community of RNA-cleaving deoxyribozymes. In Selection A, the reaction time was reduced four times (from 5 h to 5 s) over the course of 24 generations, while in Selection B the reaction time was maintained at 5 h for 30 rounds of selective amplification. Sequence alignment was conducted on more than 800 clones assembled from 18 generations that span both selections. Many prominent catalytic sequence classes, including some that extend across both selections, were identified and used to construct fitness landscapes depicting their rise and fall over time. The landscapes from both selections exhibit similar global trends despite differences in population dynamics. Some deoxyribozymes were predominant in the early rounds of selection but gave way to other species that dominated in the middle rounds. Ultimately, these middle classes disappeared from the landscape in favor of new and presumably more fit deoxyribozyme sequence classes. The shape of these landscapes alludes to the presence of many latent deoxyribozymes in the initial library, which can only be accessed by changes in the selection pressure and/or by adaptive mutations. Basic computer simulations provide theoretical corroboration of the experimentally observed pattern of staggered sequence-class transitions across the fitness landscapes. These simulations model the influence of one or more contributing factors, including catalytic rate, folding efficiency, PCR amplification efficiency, and random mutagenesis. This is the first study which thoroughly documents the topography of a deoxyribozyme fitness landscape over many generations of in vitro selection.

Base Sequence↗
PubMed2001

MDR1 bicistronic vectors: analysis of selection stringency, amplified gene expression, and vector stability in cell lines.

The human multidrug resistance-1 gene (MDR1) is a dominant selectable and amplifiable marker in mammalian tissue culture cells. MDR1 is also being investigated as a gene therapy tool, both to protect normal cells against chemotherapy-related toxicity and to serve as an in vivo selectable marker for the overexpression of non-selectable therapeutic genes. The success of these strategies will depend on whether MDR1 expression can be sustained at levels high enough to confer a survival advantage on target cells. However, the MDR1 selection system is quite stringent, requiring high gene expression for transduced cells to survive in the presence of drug. The current report is a detailed molecular analysis of MDR1 selection stringency compared with the common neo selectable marker. A bicistronic vector encoding MDR1 and neo genes linked through an internal ribosome entry site was transferred into NIH 3T3 mouse fibroblasts and K562 human leukemia cells; cells were then exposed to colchicine (to select for MDR1 expression) or to G418 (to select for neo expression). Surviving populations and individual clones of cells were analyzed for expression levels of MDR1 and neo gene products; resistance to colchicine, paclitaxel, and G418; level and integrity of bicistronic mRNA; and structural integrity, integration number, and copy number of vector DNA. These studies provide direct evidence that colchicine selection is more stringent than G418 selection; that increased selection pressure with colchicine leads to increased gene expression; that increased gene expression can be accommodated primarily by gene amplification, even within an individual transduced clone and starting from a single-copy proviral integration event; and that the clonal diversity of a transduced population of cells is influenced significantly by the stringency of selection. Taken together, these results have important implications for the potential utility of MDR1 as a selectable marker and as a gene therapy tool in hematopoietic cells.

3T3 Cells↗
PubMed2006

Optimal multiple trait selection for multiple linked quantitative trait loci.

A method was developed to optimize selection on multiple traits with multiple quantitative trait loci (QTLs) over multiple generations. The basis of the method was to replace in the objective function the genotypic value of a single trait with an aggregate genotypic value of multiple traits weighted by their corresponding economic weight, and to maximize the weighted sum of the selection response in the planning horizon. The optimization was formulated as a multiple stage optimal control problem and solved by a forward and backward iteration cycle. The practical utility of this method was illustrated in an example of pig breeding population, in which the number born alive (NBA) and days to 100 kg (D100) were used as parameters. The selection response of this method was compared with standard QTL selection and regular best linear unbiased prediction (BLUP) selection. Results showed that optimal selection achieved greater selection response than either standard QTL or regular BLUP selections. The influence of economic weight to optimal selection was significant, and the optimization was better as the economic weight of D100 increased. Optimal selection increased the total selection response by two ways: 1) it sacrificed some QTL responses during early generations and 2) it put more emphasis on D100. Optimal cumulative discounted selection gave more weight to D100 than optimal terminal selection in the longer generations.

Algorithms↗
PubMed2004

Power, selection bias and predictive performance of the Population Pharmacokinetic Covariate Model.

Identification and quantification of covariate relations is often an important part of population pharmacokinetic/pharmacodynamic (PK/PD) modelling. The covariate model is regularly built in a stepwise manner. With such methods, selection bias may be a problem if only statistically significant covariates are accepted into the model. Competition between multiple covariates may further increase selection bias, especially when there is a moderate to high correlation between the covariates. This can also result in a loss of power to find the true covariates. The aim of this simulation study was to investigate the effect on power, selection bias and predictive performance of the covariate model, when altering study design and system-related quantities. Data sets with 20-1000 subjects were investigated. Five covariates were created by sampling from a multivariate standard normal distribution. The true covariate was set up to have no, low, moderate and high correlation to the other four covariates, respectively. Data sets, in which each individual had two or three PK observations, were simulated using a one-compartment i.v. bolus model. The true covariate influenced clearance according to one of several magnitudes. Different magnitudes of residual error and inter-individual variability in the structural model parameters were also introduced to the simulation model. A total of 7400 replicate data sets were simulated independently for each combination of the above conditions. Models with one of the five simulated covariates influencing clearance and the model without any covariate were fitted to the data. The probability of selecting (according to a pre-specified P-value) the different covariates, along with the estimated covariate coefficient, was recorded. The results show that selection bias is very high for small data sets (< or = 50 subjects) simulated with a weak covariate effect. If selected under these circumstances, the covariate coefficient is on average estimated to be more than twice its true value, making the covariate model useless for predictive purposes. Surprisingly, even though competition from false covariates caused substantial loss in the power of selecting the true covariate, the already high selection bias increased only marginally. This means that the bias due to competition is negligible if statistical significance is also required for covariate selection. Bias and predictive performance are direct functions of power, only indirectly affected by study design and system-related quantities. Mainly because of selection bias, low-powered covariates can be expected to harm the predictive performance when selected. For the same reason these low-powered covariates may falsely appear to be clinically relevant when selected. If the aim of an analysis is predictive modelling, we do not recommend stepwise selection or significance testing of covariates to be performed on small or moderately sized data sets (<50-100 subjects).

Computer Simulation↗
PubMed1999

The direct response of Drosophila melanogaster to selection on knockdown temperature.

We selected on knockdown temperature, the upper temperature at which insects lose the ability to cling to an inclined surface, in replicate populations of Drosophila melanogaster for 32 generations (46 generations of rearing). Knockdown temperature (Tkd) was initially bimodally distributed in both control and selected lines, and a similar pattern was found in several populations surveyed from two other continents. Within 20 generations of selection, the Up-selected lines (top 25% each generation) had lost the lower mode and the Low-selected lines (selected to fall out at approximately 37 degrees C) had largely lost the upper mode. The realized heritability of Tkd computed over the first 10 selection episodes was approximately 0.12 in the Up-selected and approximately 0.19 in the Low-selected lines. Realized heritability rose dramatically in the Low-selected lines over the first 20 generations of selection. The two modes, plus this rise in heritability, suggest that knockdown temperature is the product of one or two genes of large effect. The global polymorphism for knockdown temperature, coupled with the ease of selective removal of either mode, suggests that genetic variation for knockdown temperature may be maintained by natural selection.

Animals↗
PubMed1999

Effect of selection against deleterious mutations on the decline in heterozygosity at neutral loci in closely inbreeding populations.

Transition matrices for selfing and full-sib mating were derived to investigate the effect of selection against deleterious mutations on the process of inbreeding at a linked neutral locus. Selection was allowed to act within lines only (selection type I) or equally within and between lines (type II). For selfing lines under selection type I, inbreeding is always retarded, the retardation being determined by the recombination fraction between the neutral and selected loci and the inbreeding depression from the selected locus, irrespective of the selection coefficient (s) and dominance coefficient (h) of the mutant allele. For selfing under selection type II or full-sib mating under both selection types, inbreeding is delayed by weak selection (small s and sh), due to the associative overdominance created at the neutral locus, and accelerated by strong selection, due to the elevated differential contributions between alternative alleles at the neutral locus within individuals and between lines (for selection type II). For multiple fitness loci under selection, stochastic simulations were run for populations with selfing, full-sib mating, and random mating, using empirical estimates of mutation parameters and inbreeding load in Drosophila. The simulations results are in general compatible with empirical observations.

Animals↗
PubMed1974

An experimental comparison of individual, family and combination selection.

Two selection experiments comparing the relative efficiencies of individual, family, and combination selection were conducted. The expected results for larval weight of Tribolium (h(2) = 0.20) and for pupal weight (h(2) = 0.40) were that combination selection would be a more efficient method than family selection, and that family selection would exceed individual selection. In experiment I, individual selection produced more response (P < 0.05) than did combination or family, which was not in agreement with expectation. There was confounding of inbreeding levels and random drift due to differential effective population sizes in the lines selected by different methods. Experiment II consisted of ten single-generation selection tests. An advantage of this approach is that it eleminates the inherent problems of differential inbreeding levels and differential rates of genetic drift due to unequal population sizes among the methods of selection. There were no statistically significant differences in efficiency among the three methods of selection for both traits. This was contrary to theoretical expectations but does suggest that with traits of 20% h(2) or higher, and where feasible, one may be justified in basing selection decisions on the phenotype of the individual only. Other advantages of single generation testing are that it allows more precise testing of selection theory and unbiased standard errors for estimates of realized heritability.

Animals↗
PubMed1975

Direct response to selection for postweaning gain in the rat.

The effectiveness of selection for 3-9 week gain was examined in a population of rats with a history of past selection for high 3-9 week gain. Lines were selected for high (U line) and low (D line) 3-9 week gain with two replicates of each line. Two randomly selected lines were also kept, one originating from the same base population as the two selected lines (R line) and the other originating from a population that had been randomly mated for the previous 27 generations (C line). Two replicates of each of these lines were kept. After seven generations of selection, a randomly selected line (relaxed line) was formed from each of the two upward- and each of the two downward- selected lines. Results have been presented for 13 generations of selection. The environmental trend for 3-9-week gain, as indicated by the randomly selected R and C lines, was consistently negative in all four lines. Realized heritabilities calculated by deviating the response to selection from the trend in the R or C lines resulted in non-significantly higher values in the D lines than the U lines. Six generations of relaxation of selection indicated no effect of natural selection in the U lines or the D lines. The relative magnitude of the drift, error and common environmental variances were estimated by the methods given by HILL (1971). The estimates of these parameters then led to calculation of the degree of bias in the sampling variances of the realized heritability estimates. As was predicted by HILL (1971), estimates of the variance of realized heritabilities obtained by using standard regression techniques were less than those obtained using HILL'S formulae. The results are discussed in relation to other similar studies with rats and mice.

Analysis of Variance↗
PubMed2005

Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level.

Detecting positive Darwinian selection at the DNA sequence level has been a subject of considerable interest. However, positive selection is difficult to detect because it often operates episodically on a few amino acid sites, and the signal may be masked by negative selection. Several methods have been developed to test positive selection that acts on given branches (branch methods) or on a subset of sites (site methods). Recently, Yang, Z., and R. Nielsen (2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19:908-917) developed likelihood ratio tests (LRTs) based on branch-site models to detect positive selection that affects a small number of sites along prespecified lineages. However, computer simulations suggested that the tests were sensitive to the model assumptions and were unable to distinguish between relaxation of selective constraint and positive selection (Zhang, J. 2004. Frequent false detection of positive selection by the likelihood method with branch-site models. Mol. Biol. Evol. 21:1332-1339). Here, we describe a modified branch-site model and use it to construct two LRTs, called branch-site tests 1 and 2. We applied the new tests to reanalyze several real data sets and used computer simulation to examine the performance of the two tests by examining their false-positive rate, power, and robustness. We found that test 1 was unable to distinguish relaxed constraint from positive selection affecting the lineages of interest, while test 2 had acceptable false-positive rates and appeared robust against violations of model assumptions. As test 2 is a direct test of positive selection on the lineages of interest, it is referred to as the branch-site test of positive selection and is recommended for use in real data analysis. The test appeared conservative overall, but exhibited better power in detecting positive selection than the branch-based test. Bayes empirical Bayes identification of amino acid sites under positive selection along the foreground branches was found to be reliable, but lacked power.

Bayes Theorem↗
PubMed2000

Genetics of growth and reproduction in the turkey. 14. Changes in genetic parameters over thirty generations of selection for increased body weight.

A line (F) of turkeys was selected over 30 generations for increased 16-wk BW. The base population for the F line was a randombred control population (RBC2) that was maintained without conscious selection and used to remove yearly environmental variation in the F line. Selection was effective in increasing 16-wk BW in the F line. Selection differentials based on the mean of selected parents minus mean of entire population (intended) and intended selection differentials weighted for number of offspring produced (actual) did not consistently differ, indicating that natural selection was not significantly opposing artificial selection. The realized heritability (h2) of 16-wk BW in the F line, based on the linear regression of the selection response on accumulated actual selection differentials, declined with selection; the decline appeared to be slightly different for males than females. For both sexes combined, the realized h2 was 0.309+/-0.022 (SE), 0.268+/-0.033, 0.242+/-0.026, and 0.254+/-0.007, respectively, for Generations 1 to 10, 11 to 20, 21 to 30, and 1 to 30. Genetic increases in 16-wk BW in the F line were positively associated with BW at other ages (8, 20, and 24 wk of age and at 50% production), days from stimulatory lighting to production of the first egg, and egg weight. Genetic increases were negatively associated with egg production, intensity of lay (maximum and average clutch length and rate of lay), and hatch of fertile eggs. There was no significant relationship between 16-wk BW and total days lost from broodiness or fertility. The genetic changes in some correlated traits were not consistent in all generation intervals studied, indicating that the genetic correlation between the selected trait (16 wk BW) and the correlated trait changed with selection.

Animals↗
PubMed2001

Social causes of correlational selection and the resolution of a heritable throat color polymorphism in a lizard.

When selection acts on social or behavioral traits, the fitness of an individual depends on the phenotypes of its competitors. Here, we describe methods and statistical inference for measuring natural selection in small social groups. We measured selection on throat color alleles that arises from microgeographic variation in allele frequency at natal sites of side-blotched lizards (Uta stansburiana). Previous game-theoretic analysis indicates that two color morphs of female side-blotched lizards are engaged in an offspring quantity-quality game that promotes a density- and frequency-dependent cycle. Orange-throated females are r-strategists. They lay large clutches of small progeny, which have poor survival at high density, but good survival at low density. In contrast, yellow-throated females are K-strategists. They lay small clutches of large progeny, which have good survival at high density. We tested three predictions of the female game: (1) orange progeny should have a fitness advantage at low density; (2) correlational selection acts to couple color alleles and progeny size; and (3) this correlational selection arises from frequency-dependent selection in which large hatchling size confers an advantage, but only when yellow alleles are rare. We also confirmed the heritability of color, and therefore its genetic basis, by producing progeny from controlled matings. A parsimonious cause of the high heritability is that three alleles (o, b, y) segregate as one genetic factor. We review the physiology of color formation to explain the possible genetic architecture of the throat color trait. Heritability of color was nearly additive in our breeding study, allowing us to compute a genotypic value for each individual and thus predict the frequency of progeny alleles released on 116 plots. Rather than study the fitness of individual progeny, we studied how the fitness of their color alleles varied with allele frequency on plots. We confirmed prediction 1: When orange alleles are present in female progeny, they have higher fitness at low density when compared to other alleles. Even though the difference in egg size of the female morphs was small (0.02 g), it led to knife-edged survival effects for their progeny depending on local social context. Selection on hatchling survival was not only dependent on color alleles, but on a fitness interaction between color alleles and hatchling size, which confirmed prediction 2. Sire effects, which are not confounded by maternal phenotype, allowed us to resolve the frequency dependence of correlational selection on egg size and color alleles and thereby confirmed prediction 3. Selection favored large size when yellow sire alleles were rare, but small size when they were common. Correlational selection promotes the formation of a self-reinforcing genetic correlation between the morphs and life-history variation, which causes selection in the next density and frequency cycle to be exacerbated. We discuss general conditions for the evolution of self-reinforcing genetic correlations that arise from social selection associated with frequency-dependent sexual and natural selection.

Alleles↗
PubMed2002

Temporal variation in divergent selection on spine number in threespine stickleback.

Short-term temporal cycles in ecological pressures, such as shifts in predation regime, are widespread in nature yet estimates of temporal variation in the direction and intensity of natural selection are few. Previous work on threespine stickleback (Gasterosteus aculeatus) has revealed that dorsal and pelvic spines are a defense against gape-limited predators but may be detrimental against grappling insect predators. In this study, we examined a 15-year database from an endemic population of threespine stickleback to look for evidence of temporal shifts in exposure to these divergent predation regimes and correlated shifts in selection on spine number. For juveniles, we detected selection for increased spine number during winter when gape-limited avian piscivores were most common but selection for decreased spine number during summer when odonate predation was more common. For subadults and adults, which are taken primarily by avian piscivores, we predicted selection should generally be for increased spine number in all seasons. Among 59 comparisons, four selection differentials were significant (Bonferroni corrected) and in the predicted direction. However, there was also substantial variability in remaining differentials, including two examples with strong selection for spine reduction. These reversals were associated with increased tendency of the fish to shift to a benthic niche, as determined from examination of stomach contents. These dietary data suggest that increased encounter rates with odonate predation select for spine reduction. Strong selection on spine number was followed by changes in mean spine number during subsequent years and a standard quantitative genetic formula revealed that spine number has a heritable component. Our results provide evidence of rapid morphological responses to selection from predators and suggest that temporal variation in selection may help maintain variation within populations. Furthermore, our findings indicate that variable selection can be predicted if the agents of selection are known.

Animals↗