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PubMed2006

Positive selection on nucleotide substitutions and indels in accessory gland proteins of the Drosophila pseudoobscura subgroup.

Genes encoding reproductive proteins often diverge rapidly due to positive selection on nucleotide substitutions. While this general pattern is well established, the extent to which specific reproductive genes experience similar selection in different clades has been little explored, nor have possible targets of positive selection other than nucleotide substitutions, such as indels, received much attention. Here, we inspect for the signature of positive selection in the genes encoding five accessory gland proteins (Acps) (Acp26Aa, Acp32CD, Acp53Ea, Acp62F, and Acp70A) originally described from Drosophila melanogaster but with recognizable orthologues in the D. pseudoobscura subgroup. We compare patterns of selection within the D. psuedoobscura subgroup to those in the D. melanogaster subgroup. Similar patterns of positive selection were found in Acp26Aa and Acp62F in the two subgroups, while Acp53Ea and Acp70A experienced purifying selection in both subgroups. These proteins have thus remained targets for similar types of selection over long (>21-MY) periods of time. We also found several indel substitutions and polymorphisms in Acp26Aa and Acp32CD. These indels occur in the same regions as positively selected nucleotide substitutions for Acp26Aa in the D. pseudoobscura subgroup but not in the D. melanogaster subgroup. Rates of indel substitution within Acp26Aa in the D. pseudoobscura subgroup were up to several times those in noncoding regions of the Drosophila genome. This suggests that indel substitutions may be under positive selection and may play a key role in the divergence of some Acps.

Amino Acid Sequence↗
PubMed1991

Levels of selection, evolution of sex in RNA viruses, and the origin of life.

Multi-component RNA viruses have genomes that are segmented into two or more RNA molecules. A viral particle carries only one RNA molecule. Reproduction of a particle requires complementation by particles carrying other segments of the genome. Complementation is achieved when a group of particles co-infects the same host cell and forms a co-infection group. I have previously proposed the hypothesis that multi-component reproduction evolved in RNA viruses as a form of sex. Multi-component viruses may need sex because, like all RNA viruses, they have very high mutation rates. On the other hand, Nee (1987, J. molec. Biol. 25, 277-281.) has proposed the hypothesis that multi-component genomes evolved because smaller RNA molecules are favored by selection on RNAs within a host cell. Nee (1989, J. theor. Biol. 138, 407-412.) also claimed that selection on RNAs alone can account for the evolution of multi-component viruses. He criticized the viral sex hypothesis because, in his view, co-infection groups are not units of selection and are too transient to be engaged in sex. These two hypotheses were further examined through population genetic models. Three evolutionary agents are assumed to operate in the models. Selection on co-infection groups favors retention of the genome on one large RNA molecule because larger RNAs require less complementation. Selection on RNAs favor segmentation of the viral genome into smaller RNAs, which are replicated and encapsidated more rapidly. Mutation pressure also favors smaller molecules because those molecules are smaller targets for deleterious mutations. Analysis of the models shows that (when parameter values argued to be biologically realistic are used) selection on co-infection groups is necessary for the evolutionary persistence of multi-component viruses. Without selection on co-infections groups to oppose mutation pressure and selection on RNAs, a population of multi-component viruses is displaced by a population of parasitic viral RNAs that are replication and encapsidation specialists. These results support arguments that co-infection groups are units of selection in multi-component viruses. Both mutation pressure and selection on RNAs may be responsible for the evolution of genome segmentation in multi-component viruses because there is good evidence documenting the action of both in RNA viruses.(ABSTRACT TRUNCATED AT 400 WORDS)

Biological Evolution↗
PubMed1997

The role of genotypic heterogeneity in wild type virus populations on the selection of nonnucleoside reverse transcriptase inhibitor-resistant viruses.

Virus populations were selected in cell culture using two widely used protocols in order to evaluate the role of selection methodology on the genotype and phenotype of nonnucleoside reverse transcriptase inhibitor resistant viruses. Selection was performed by serial passage of virus in the presence of gradually increasing concentrations of antiviral compound or passage in the presence of a constant high concentration of compound. Using the CEM-SS cell line, the IIIB strain of HIV-1, and identical nonnucleoside reverse transcriptase inhibitors, resistant viruses were obtained and their phenotypic and genotypic properties were defined. Resistant virus populations containing the Y181C amino acid change in the reverse transcriptase were predominantly selected with each of the tested compounds. Several of the compounds selected secondary amino acid changes using both methods. A comparison of the resistant viruses selected in our laboratory using each of the two protocols with viruses reported by a second laboratory employing one of the two methods suggests that genotypic differences in the selected virus isolates may most likely result from the variation in the genetic composition of the respective wild type virus pools, rather than the specific selection methodology employed. These results imply that HIV may select a wide variety of amino acid changes to avoid the inhibitory effects of the nonnucleoside reverse transcriptase inhibitors and the selection of compounds for clinical use in combination with agents possessing non-overlapping resistance phenotypes will require evaluation of the agents against virus isolates possessing each of the mutations known to confer drug resistance.

Anti-HIV Agents↗
PubMed1997

Developmental selection and self-organization.

Developmental selection is the differential survival and proliferation of developmental units, such as cellular lineages. This type of internal selection has been proposed as an explanation for diverse examples of self-organization, from the wiring of brains to the formation of pores on leaf surfaces. A general understanding of developmental selection has been slowed by failure to understand its relationship to familiar forms of genetical selection and evolution. I show the formal analogies between models of developmental selection and genetical selection. The general method I outline for the analysis of selective systems partitions self-organizing selective systems into generative rules that create variation and selective filters that move the population toward a target design. The method also emphasizes aggregate statistical measures of evolving systems, such as the covariance between particular traits and fitness. The identification of useful aggregate measures is a crucial step in the analysis of selective systems. I apply these concepts to a model of self-organization in ant colonies.

Biological Evolution↗
PubMed2003

Heat-induced expression of a molecular chaperone decreases by selecting for long-lived individuals.

The 70 kDa heat-shock protein (Hsp70) exhibits a broad range of chaperone functions that respond both to internal and external stresses, and its heat-induced expression both declines with age and reduces age-specific mortality rates. Here we test for changes in both longevity and the level of Hsp70-induced expression as correlated responses to selection on both heat-stress resistance and longevity in D. melanogaster. Three replicated H lines were heat-stress selected and compared to their respective non-selected controls (C lines) in the 25th generation of heat-stress selection. The direct response in heat-stress resistance was 56% in males and 38% in females. Heat-stress selection improved longevity in males at normal temperatures. All lines were subsequently subjected to one generation of truncation selection on longevity (selection intensity, i=1.28 for H lines and 1.36 for C lines). The heat-induced Hsp70 expression seems to increase very weakly by heat-stress selection but shows a dramatic and persistent decline by selecting for long-lived flies. A mechanism of longevity selection, involving changes in Hsp70 regulation, is suggested.

Animals↗
PubMed2000

Evolution of reduced pre-adult viability and larval growth rate in laboratory populations of Drosophila melanogaster selected for shorter development time.

Four large (n > 1000) populations of Drosophila melanogaster, derived from control populations maintained on a 3 week discrete generation cycle, were subjected to selection for fast development and early reproduction. Egg to eclosion survivorship and development time and dry weight at eclosion were monitored every 10 generations. Over 70 generations of selection, development time in the selected populations decreased by approximately 36 h relative to controls, a 20% decline. The difference in male and female development time was also reduced in the selected populations. Flies from the selected populations were increasingly lighter at eclosion than controls, with the reduction in dry weight at eclosion over 70 generations of selection being approximately 45% in males and 39% in females. Larval growth rate (dry weight at eclosion/development time) was also reduced in the selected lines over 70 generations, relative to controls, by approximately 32% in males and 24% in females. However, part of this relative reduction was due to an increase in growth rate of the controls populations, presumably an expression of adaptation to conditions in our laboratory. After 50 generations of selection had elapsed, a considerable and increasing pre-adult viability cost to faster development became apparent, with viability in the selected populations being about 22% less than that of controls at generation 70 of selection.

Adaptation, Physiological↗
PubMed1997

The use of selection experiments for detecting quantitative trait loci.

Gene frequency changes following selection may reveal the existence of gene effects on the trait selected. Loci for the selected quantitative trait (SQTL) may thus be detected. Additionally, one can estimate the average effect (alpha) of a marker allele associated with an SQTL from the allele frequency change (delta q) due to selection of given intensity (i). In a sample of unrelated individuals, it is optimal to select the upper and lower 27% for generating delta q in order to estimate alpha. For a given number of individuals genotyped, this estimator is 0.25i2 times more efficient than the classical estimator of alpha, based on the regression of the trait on the genotype at the marker locus. The method is extended to selection criteria using information from relatives, showing that combined selection considerably increases the efficiency of estimation for traits of low heritability. The method has been applied to the detection of SQTL in a selection experiment in which the trait selected was pig litter size averaged over the first four parities, with i = 3. Results for four genes are provided, one of which yielded a highly significant effect. The conditions required for valid application of the method are discussed, including selection experiments over several generations. Additional advantages of the method can be anticipated from determining gene frequencies on pooled samples of blood or DNA.

Animals↗
PubMed1998

Long-term selection for protein amount over 70 generations in mice.

Based on the outbred mouse strain Fzt: Du, which has been obtained by systematic crossing of four inbred and four outbred lines, a long-term selection experiment was carried out for total protein amount (PA) in the carcass, starting in 1975. An unselected control line (CO) was kept under the same management but without continuous protein analysis. The protein amount of male carcasses at 42 days of age (P42) increased from 2.9 g in generation 0 to 5.2 g at generation 70, representing 97% of a theoretical selection limit. The total selection response amounts to 2.3 g, which is about 80% above the initial value and corresponds to 9 sigma p or 12 sigma A. The estimated realized heritability of protein amount decreased from 0.56 to 0.03 at generation 70, which was due to an increase in phenotypic variance from 0.065 to 0.24 g2 and a reduction in genetic variance from 0.04 to 0.01 g2. Half the selection response was obtained after about 18 to 23 generations, a half-life of 0.25 to 0.3 Ne. The maximum selection response was 0.094 g/generation and the response was 0.01 g/generation at generation 70. The measurements of body weights at 0, 10, 21, 42 and 63 days throughout the experiment showed a strong correlated effect for all weights. The PA mice are one of the heaviest lines of mice ever reported, and do not differ significantly in their body composition from control mice at 42 days. The direct selection response was due primarily to increased general growth. Body weight and protein amount are phenotypically and genetically highly correlated (rp = 0.82, rA approximately 1); however, selection for body weight led to fatter animals, whereas selection for protein opposed increased fatness (at least until selection age). This may be of general importance in animal breeding. The comparatively high selection response in this experiment seems due to the heterogeneity of the base population, the relatively high effective population size, and the duration of the experiment.

Age Factors↗
PubMed2000

Breaking through artificial selection limits of an adaptive behavior in mice and the consequences for correlated responses.

Previous divergent selection for nest-building behavior at 22 +/- 1 degrees C resulted in a 40-fold difference between the high and the low lines in amount of cotton used to build a nest. Correlated responses to selection indicated positive genetic correlations with body weight, nest-building at 4 +/- 1 degrees C, and litter size and negative genetic correlations with food consumption. At generation 46, the replicate high-selected (High 1 x High 2), randomly bred control (Control 1 x Control 2), and low-selected (Low 1 x Low 2) lines were crossed and the F1 showed significant heterosis for nest-building behavior. Regression of the F3 on the F2 generation gave heritability estimates of 0.16 +/- 0.10 for the high and 0.07 +/- 0.10 for the low cross, revealing a potential to break the selection limit (at least in the high direction), which had been reached at about 20 generations of selection. Indeed, renewed selection resulted in responses in both the high and the low directions of nesting, yielding realized heritabilities of 0.29 +/- 0.02 and 0.30 +/- 0.004, respectively. Replicated renewed selection, using the F3 generation as the base population, in the high direction of nesting resulted in correlated increases in nest-building at 4 +/- 1 degrees C, litter size, and food consumption. Body weight did not change. The positive correlation with food consumption is opposite in sign compared to the original selection experiment. This indicates that the evolutionary potential of a population to adapt to a changing environment not only depends on its current genetic variability in one adaptive trait, but may be constrained by genetic correlations changing over the course of selection.

Animals↗
PubMed1997

Spurious associations in unreplicated selected lines.

Often a single pair of lines that has been selected for high and low expression of a trait is used as an animal model to study new biobehavioral characters thought to be associated with the selected trait. Because of genetic drift at many loci, comparisons of High and Low lines on the new character will frequently produce significant line differences even when there is no association between the selected trait and the new character being studied. In the absence of replicate lines to estimate the degree of genetic drift, effect size can be used to reduce the number of false-positive associations between the original selected trait and the new character. When the heritability of the new character exceeds .40 and the inbreeding coefficient within the selected lines is moderate, High- and Low-line means on the new character will frequently differ by at least one phenotypic SD, but not often differ by more than two SDs, in the absence of any relationship between the selected trait and the new character. If the selected lines are highly inbred, drift effects are greater, resulting in more false-positive associations. Situations posing special difficulty in the absence of replicate lines include the study of characters with low heritability relative to the selected trait and cases in which the lines do not differ greatly on the original selected trait. Studies using selected lines should always report inbreeding coefficients of the generations being studies, relative to the base population from which the lines were derived.

Animals↗
PubMed2000

Balanced vs. slightly unbalanced selection.

Balanced selection, defined as that all parents have equal contributions to the next generation, is expected to minimize the loss of gene diversity and thereby to allow a steady increase of selection response even at very advanced generations. In this study, balanced selection was compared with two degrees of slightly unbalanced selection (equal contributions from most of the families) and with unrestricted selection (unequal contributions) in terms of the retrieved response and genetic diversity consumed (group coancestry) over 30 generations of selection. A simulation was used varying the heritability and considering two population sizes and two family sizes. Results showed that a slight unbalance can bring a favourable relation between retrieved response and genetic diversity when compared to balanced selection at low and moderate heritabilities, and when small families and population size were assumed. The implicit constraint of a constant number of contributing families imposed in balanced and slightly unbalanced selection reduced the likelihood of gene loss compared to unrestricted selection. I conclude that a slight unbalance often could be more favourable than complete balance regarding selection efficiency, and that gain retrieved per unit of group coancestry declined with further unbalance.

Founder Effect↗
PubMed2003

Sexual selection on morphological and physiological traits and fluctuating asymmetry in the yellow dung fly.

Previous univariate studies of the yellow dung fly (Scathophaga stercoraria) have demonstrated strong sexual selection, in terms of mating success, on male size (estimated as hind tibia length). To identify specific target(s) of selection on body size and possible conflicting selection pressures on particular body parts, two multivariate field studies of sexual selection were conducted. In one study using point samples from three populations, we assessed several morphological traits, including genital traits and measures of fluctuating asymmetry (FA) of all paired traits. There was sexual selection for large male size in general, confirming previous, univariate studies. With the possible exception of thorax width, which was selected in the opposite direction, no main target of selection was identified, as most morphological traits were highly correlated. There was no detectable sexual selection on the male external genital structures assessed. In a second study using multiple samples from one population, we included physiological measures of energy reserves (lipids, glucose and glycogen) known to affect mating success, in addition to trait size and FA of wings and legs. Inclusion of physiological traits is rare in phenomenological studies of selection. This study again confirmed the mating advantage of large males, and additionally showed independent positive influences of lipid and glucose but not glycogen levels. FA in paired traits generally did not affect male mating success, but was negatively correlated with energy reserves. Our study suggests that inclusion of physiological measures and genital traits in phenomenological studies of selection would be fruitful in other species.

Animals↗
PubMed2006

Weak selection and recent mutational changes influence polymorphic synonymous mutations in humans.

Recent large-scale genomic and evolutionary studies have revealed the small but detectable signature of weak selection on synonymous mutations during mammalian evolution, likely acting at the level of translational efficacy (i.e., translational selection). To investigate whether weak selection, and translational selection in particular, plays any role in shaping the fate of synonymous mutations that are present today in human populations, we studied genetic variation at the polymorphic level and patterns of evolution in the human lineage after human-chimpanzee separation. We find evidence that neutral mechanisms are influencing the frequency of polymorphic mutations in humans. Our results suggest a recent increase in mutational tendencies toward AT, observed in all isochores, that is responsible for AT mutations segregating at lower frequencies than GC mutations. In all, however, changes in mutational tendencies and other neutral scenarios are not sufficient to explain a difference between synonymous and noncoding mutations or a difference between synonymous mutations potentially advantageous or deleterious under a translational selection model. Furthermore, several estimates of selection intensity on synonymous mutations all suggest a detectable influence of weak selection acting at the level of translational selection. Thus, random genetic drift, recent changes in mutational tendencies, and weak selection influence the fate of synonymous mutations that are present today as polymorphisms. All of these features, neutral and selective, should be taken into account in evolutionary analyses that often assume constancy of mutational tendencies and complete neutrality of synonymous mutations.

Animals↗
PubMed2002

Effect of selection for improved body weight and composition on muscle and meat characteristics in Muscovy duck.

1. For 25 years, the Muscovy duck has been selected for greater body weight at slaughter age, higher meat yield and lower fat content. The aim of this study was to analyse the effects of such selection on the biochemical and technological characteristics of duck meat. 2. A line which has been maintained without any selection since 1975 (control line) and a heavy line now commercialised (selected line) were reared under the same conditions. We compared growth performances, dressing and dissection yields and biochemical and technological characteristics of duck meat at 8, 10 and 12 weeks of age. 3. Our results showed that an indirect effect of selection was to increase the duck growth rate. At a given age, muscle weights and yields as well as carcase fat content were higher for selected ducks. In the selected line, muscle fibres were larger and the collagen content in muscles lower. 4. The Sartorius muscle in ducks from the selected line exhibited a higher percentage in numbers of white type IIb fibres to the detriment of red type IIa fibres. Its glycolytic enzyme activity was higher and its oxidative enzyme activity lower. 5. In breast muscle, selection decreased the rate of post-mortem decline in pH value, increased protein and mineral contents and decreased moisture. It did not affect fibre type, colour, haem pigment and lipid contents, collagen solubility or drip loss. 6. In conclusion, the effects of Muscovy duck selection on meat quality were relatively moderate.

Aging↗
PubMed1999

Life-History Consequences of Divergent Selection on Egg Size in Drosophila melanogaster.

Life histories are generally assumed to evolve via antagonistic pleiotropy (negative genetic correlations) among traits, and trade-offs between life-history traits are typically studied using either phenotypic manipulations or selection experiments. We investigated the trade-off between egg size and fecundity in Drosophila melanogaster by examining both the phenotypic and genetic relationships between these traits after artificial selection for large and small eggs, relative to female body size. Egg size responded strongly to selection in both directions, increasing in the large-egg selected lines and decreasing in the small-egg selected lines. Phenotypic correlations between egg size and fecundity in the large-egg selected lines were negative, but no relationship between these traits occurred in either the control or small-egg selected lines. There was no negative genetic correlation between egg size and fecundity. Total reproductive allocation decreased in the small-egg selected lines but did not increase in the large-egg lines. Our results have three implications. First, our selection procedure may have forced females selected for large eggs into a physiological trade-off not reflected in a negative genetic correlation between these traits. Second, the lack of a negative genetic correlation between egg size and number suggests that the phenotypic trade-off frequently observed between egg size and number in other organisms may not evolve over the short term via a direct genetic trade-off whereby increases in egg size are automatically accompanied by decreased fecundity. Finally, total reproductive allocation may not evolve independently of egg size as commonly assumed.

Drosophila melanogaster↗
PubMed2000

Spatial Variation in the Selective Scenarios of Hormathophylla spinosa (Cruciferae).

The effects of multispecific systems containing both mutualistic and antagonistic interacting organisms on the evolution of plant traits have seldom been analyzed. We studied the selection exerted by several species of herbivores and pollinators in three populations of Hormathophylla spinosa (Cruciferae) in the Sierra Nevada (Spain) over 4 yr by using path analyses and structural equation modeling (SEM). The main selective pressures in our study sites were ungulates and pollinators. However, the importance of each kind of interacting organism differed among populations. Our results indicate a selection mosaic among populations of H. spinosa in the Sierra Nevada caused by the spatial variation in the relative importance of different interactions as selective pressures. We found two main selective scenarios, depending on the presence or absence of ungulates. In the populations with low ungulate pressure, there was positive phenotypic selection in flower number per plant and in flower density (mediated by nectarivorous pollinators). In the two populations with high ungulate pressure, there was a strong positive, ungulate-mediated selection in thorn density. Our results suggest that the application of SEM to several populations simultaneously monitored might help to isolate the major selection pressures on local populations and identify potential differences in selection among populations, becoming a useful exploratory approach to study the geographical variation of selection in complex systems.

evolutionary ecology↗
PubMed2001

The power to detect linkage disequilibrium with quantitative traits in selected samples.

Results from power studies for linkage detection have led to many ongoing and planned collections of phenotypically extreme nuclear families. Given the great expense of collecting these families and the imminent availability of a dense diallelic marker map, the families are likely to be used in allelic-association as well as linkage studies. However, optimal selection strategies for linkage may not be equally powerful for association. We examine the power to detect linkage disequilibrium for quantitative traits after phenotypic selection. The results encompass six selection strategies that are in widespread use, including single selection (two designs), affected sib pairs, concordant and discordant pairs, and the extreme-concordant and -discordant design. Selection of sibships on the basis of one extreme proband with high or low trait scores provides as much power as discordant sib pairs but requires the screening and phenotyping of substantially fewer initial families from which to select. Analysis of the role of allele frequencies within each selection design indicates that common trait alleles generally offer the most power, but similarities between the marker- and trait-allele frequencies are much more important than the trait-locus frequency alone. Some of the most widespread selection designs, such as single selection, yield power gains only when both the marker and quantitative trait loci (QTL) are relatively rare in the population. In contrast, discordant pairs and the extreme-proband design provide power for the broadest range of QTL-marker-allele frequency differences. Overall, proband selection from either tail provides the best balance of power, robustness, and simplicity of ascertainment for family-based association analysis.

Alleles↗
PubMed2003

The influence of neighbor relatedness on multilevel selection in the Great Lakes sea rocket.

Natural selection can operate at the individual and group level in natural populations. This study investigates the ecological factors that determine the relative importance of individual versus group selection. In particular, it determines how the relatedness of interacting neighbors influences multilevel natural selection in a population of the Great Lakes sea rocket. Focal plants were grown in groups of siblings, groups of plants that were themselves siblings but unrelated to the focal plants, and groups of plants with mixed genotypes. Significant group selection on plant size was observed only when the neighbors were siblings but not when they were unrelated. In sibling groups, individuals with heavier stems had higher fitness, and individuals growing with heavier but shorter neighbors also had higher fitness. Thus, individual and group selection on stem weight operated in the same direction. The detection of group selection in sibling groups can be attributed in part to an increased opportunity for group selection in these groups since sibling groups differed more from one another than the other group types. In addition, the quality of the selective environment in sibling groups may have differed from that for the other group types. Group selection was therefore more prevalent in the most genetically structured sample, in which responses to group selection are also most likely to occur.

Analysis of Variance↗