The use of genetic markers in the analysis of competitive interactions in Drosophila melanogaster

A range of long established inbred lines derived from the TEXAS population of Drosophila melanogaster have been used to elucidate the nature of the competitive interactions which occur in genetically heterogeneous mixtures. A prerequisite for this type of investigation is the ability to distinguish the genotypes which compete in mixed culture. Specific marker alleles are generally used to achieve this distinction although in the past little attention has been given to the possibility of competitive bias introduced by the marker alleles themselves. For the experiments reported in this paper two specific marker alleles (y ² and w ^a) have been introduced independently into the TEXAS inbred lines. In this way the original wild type inbred lines could be compared with similar series of genotypes marked with either y ² or w ^a and the effects of the marker alleles determined.The results indicated that the body colour mutation (y ²) was neutral in its effect on the competitive interaction of recipient strains. The introduction of the white apricot eye colour mutation (w ^a) however, had a pronounced and deleterious effect on competitive ability. This effect was to render genotypes less able to compete effectively in mixed culture by depressing inter-genotypic competitive ability. These effects were found to be consistent over a range of genotypes and for each of two characters measuring competitive success.     

Maintenance of androdioecy in the freshwater shrimp, Eulimnadia texana: estimates of inbreeding depression in two populations

Androdioecy is an uncommon form of reproduction in which males coexist with hermaphrodites. Androdioecy is thought to be difficult to evolve in species that regularly inbreed. The freshwater shrimp Eulimnadia texana has recently been described as both androdioecious and highly selfing and is thus anomalous. Inbreeding depression is one factor that may maintain males in these populations. Here we examine the extent of "late" inbreeding depression (after sexual maturity) in these clam shrimp using two tests: (1) comparing the fitness of shrimp varying in their levels of individual heterozygosity from two natural populations that differ in overall genetic diversity; and (2) specifically outcrossing and selfing shrimp from these same populations and comparing fitness of the resulting offspring. The effects of inbreeding differed within each population. In the more genetically diverse population, fecundity, size, and mortality were significantly reduced in inbred shrimp. In the less genetically diverse population, none of the fitness measures was significantly lowered in selfed shrimp. Combining estimates of early inbreeding depression from a previous study with current estimates of late inbreeding depression suggests that inbreeding depression is substantial (delta = 0.68) in the more diverse population and somewhat lower (delta = 0.50) in the less diverse population. However, given that males have higher mortality rates than hermaphrodites, neither estimate of inbreeding depression is large enough to account for the maintenance of males in either population by inbreeding depression alone. Thus, the stability of androdioecy in this system is likely only if hermaphrodites are unable to self-fertilize many of their own eggs when not mated to a male or if male mating success is generally high (or at least high when males are rare). Patterns of fitness responses in the two populations were consistent with the hypothesis that inbreeding depression is caused by partially recessive deleterious alleles, although a formal test of this hypothesis still needs to be conducted.     

Competitive effects in monocultures and mixtures of spring barley (Hordeum vulgare)

Summary The presence of significant levels of intergenotypic competition amongst barley (Hordeum vulgare) genotypes has profound consequences for barley breeding programmes. Breeding programmes based on the pedigree system attempt to identify genotypes in genetically heterogeneous populations but the elite genotypes are grown in monoculture. Thus, to attain varietal status genotypes produced by this breeding strategy must perform well in mixtures as well as in pure stands. The effectiveness of early generation selection may be hampered by intergenotypic competition. To examine this problem in spring barley, a modified substitution experiment (Mather and Caligari 1981, 1983) was used and included genotypes sampled from a random set of inbred lines generated without conscious selection. This approach to the investigation of competitive effects in barley indicated the presence of significant levels of intergenotypic competition for a range of agronomic characters. The analyses allowed a distinction to be made between aggression (a) and response (r) with the component r displaying greater variation than a. The lack of correlation in the distribution of a and r suggested that they were under separate genetic control and hence adjustable by selection. The implications of these results for barley improvement, the use of varietal mixtures and mixed cropping are discussed.     

Inbreeding and kinship in the ant Plagiolepis pygmaea

In ants the presence of multiple reproductive queens (polygyny) decreases the relatedness among workers and the brood they rear, and subsequently dilutes their inclusive fitness benefits from helping. However, adoption of colony daughters, low male dispersal in conjunction with intranidal (within nest) mating and colony reproduction by budding may preserve local genetic differences, and slow down the erosion of relatedness. Reduced dispersal and intranidal mating may, however, also lead to detrimental effects owing to competition and inbreeding. We studied mating and dispersal patterns, and colony kinship in three populations of the polygynous ant Plagiolepis pygmaea using microsatellite markers. We found that the populations were genetically differentiated, but also a considerable degree of genetic structuring within populations. The genetic viscosity within populations can be attributed to few genetically homogeneous colony networks, which presumably have arisen through colony reproduction by budding. Hence, selection may act at different levels, the individuals, the colonies and colony networks. All populations were also significantly inbred (F=0.265) suggesting high frequencies of intranidal mating and low male dispersal. Consequently the mean regression relatedness among workers was significantly higher (r = 0.529-0.546) than would be expected under the typically reported number (5-35) of queens in nests of the species. Furthermore, new queens were mainly recruited from their natal or a neighbouring related colony. Finally, the effective number of queens coincided with that found upon excavation, suggesting low reproductive skew.     

A general mixture model approach for mapping quantitative trait loci from diverse cross designs involving multiple inbred lines

Most current statistical methods developed for mapping quantitative trait loci (QTL) based on inbred line designs apply to crosses from two inbred lines. Analysis of QTL in these crosses is restricted by the parental genetic differences between lines. Crosses from multiple inbred lines or multiple families are common in plant and animal breeding programmes, and can be used to increase the efficiency of a QTL mapping study. A general statistical method using mixture model procedures and the EM algorithm is developed for mapping QTL from various cross designs of multiple inbred lines. The general procedure features three cross design matrices, W, that define the contribution of parental lines to a particular cross and a genetic design matrix, D, that specifies the genetic model used in multiple line crosses. By appropriately specifying W matrices, the statistical method can be applied to various cross designs, such as diallel, factorial, cyclic, parallel or arbitrary-pattern cross designs with two or multiple parental lines. Also, with appropriate specification for the D matrix, the method can be used to analyse different kinds of cross populations, such as F2 backcross, four-way cross and mixed crosses (e.g. combining backcross and F2). Simulation studies were conducted to explore the properties of the method, and confirmed its applicability to diverse experimental designs.     

Diversity Among a Heterodera glycines Field Isolate and Derived Inbreds Based on RAPD Analysis and Reproduction on Soybean Genotypes

A field population of Heterodera glycines was inbred by a combination of controlled male-female matings and inoculation of soybean with second-stage juveniles (J2) from single cysts. The initial and four F₆ inbred populations were subjected to random amplified polymorphic DNA analysis and were also tested for their ability to reproduce on race differentials. The RAPD patterns of the inbred populations had a lower number of total bands and a lower percentage of polymorphic bands among individual cysts than the initial population. The estimated number of polymorphic loci detected by RAPD analysis was about 25% for the initial population and 4% to 7% for the inbred lines. Reproduction of H. glycines decreased for 6 of 24 inbred-soybean combinations. In particular, reproduction of three inbred populations on PI 90763 was greatly reduced. Inbreeding did not decrease variance of cyst number on soybean genotypes. The inbreeding coefficient calculated from RAPD data was greater than that derived from the known inbreeding pedigree.     

Outcomes of reciprocal invasions between genetically diverse and genetically uniform populations of <Emphasis Type="Italic">Daphnia obtusa</Emphasis> (Kurz)

Ecological theory predicts that genetic variation produced by sexual reproduction results in niche diversification and provides a competitive advantage both to facilitate invasion into genetically uniform asexual populations and to withstand invasion by asexual competitors. We tested the hypothesis that a large group of diverse clones of Daphnia obtusa has greater competitive advantage when invading into genetically uniform populations of this species than a smaller group with inherently less genetic diversity. We compared competitive outcomes to those of genetically uniform groups of small and large size invading into genetically diverse populations. Genetically diverse invaders of initially large group size increased their representation by more than those of initially small size; in contrast, genetically uniform invaders of initially large group size diminished on average by more than those of initially small size. These results demonstrate an advantage to the genetic variation produced by sexual reproduction, both in invasion and resisting invasion, which we attribute to competitive release experienced by individuals in genetically diverse populations.     

Hatching phenology,life history and egg bank size of fairy shrimp Branchipodopsis spp. (Branchiopoda,Crustacea) in relation to the ephemerality of their rock pool habitat

In temporary aquatic habitats, permanence and the severe disturbance associated with desiccation are strong selective agents expected to lead to differentiation in life history strategies in populations experiencing different disturbance regimes. Besides optimal timing of hatching of dormant life stages, maturation and reproduction, pool inhabitants also benefit from the acquisition of reliable cues for the quality of the ambient environment. We investigated whether hatching patterns, life history characteristics and egg bank size of Branchipodopsis fairy shrimp (Branchiopoda, Anostraca) inhabiting a cluster of temporary rock pools in South Africa reflect variation in habitat stability and hatching cues. Long-term hydrological variation was used to select pools along a gradient of habitat stability. Initial conductivity was a good indicator for the length of inundations. No hatching occurred under elevated conductivities, which may present a mechanism to avoid abortive hatching. Egg bank size was unaffected by habitat size or habitat stability but instead was related to cover by a protective sheet of dry aquatic vegetation, which presumably counteracts egg bank erosion by wind when pools are dry. Life history but not hatching phenology reflected some aspects of habitat stability. Fairy shrimp populations in ephemeral pools started reproduction earlier than populations in more stable habitats. Additional common garden or transplant experiments, however, will be required to assess the relative importance of environmental and genetic components in explaining the observed variation and acquire more insight into the trade-offs that lie at the base of the evolution of life history strategies along the pond permanence gradient.     

Boechera, a model system for ecological genomics

The selection and development of a study system for evolutionary and ecological functional genomics (EEFG) depend on a variety of factors. Here, we present the genus Boechera as an exemplary system with which to address ecological and evolutionary questions. Our focus on Boechera is based on several characteristics as follows: (i) native populations in undisturbed habitats where current environments reflect historical conditions over several thousand years; (ii) functional genomics benefitting from its close relationship to Arabidopsis thaliana; (iii) inbreeding tolerance enabling development of recombinant inbred lines, near-isogenic lines and positional cloning; (iv) interspecific crosses permitting mapping for genetic analysis of speciation; (v) apomixis (asexual reproduction by seeds) in a genetically tractable diploid; and (vi) broad geographic distribution in North America, permitting ecological genetics for a large research community. These characteristics, along with the current sequencing of three Boechera species by the Joint Genome Institute, position Boechera as a rapidly advancing system for EEFG studies.     

Genetic variation and the performance of a mass‐reared parasitoid,Trichogramma pretiosum (Hymenoptera: Trichogrammatidae), in laboratory trials

During mass rearing, adaptation of biological control agents to the rearing environment is a potential problem. Using the parasitoid wasp Trichogramma pretiosum, the performance of 26 highly inbred lines, five composite ‘populations’ (created from the inbred lines) and one insectary‐reared population was compared using fertility life tables. Of the composite populations, three were created with maximal and identical genetic variation as a mixture of all 26 inbred lines, but these were then reared for a different number of generations (2, 6 or 17) before their performance was measured. The remaining two composite populations were created based on the performance of the individual inbred lines: one was a combination of two inbred lines with a high intrinsic rate of natural increase (rm), ‘high rm’; and the other was a combination of two lines with a ‘low rm’. High and low rm populations were reared for two generations prior to testing. Parameters measured were fertility, longevity and sex ratio. We found no difference between the maximally variable population reared for two generations and the ‘high rm’ population (rm = 0.285 and 0.282, respectively). ‘Low rm’ was the population with the lower performance (rm = 0.255). Genetically variable population reared for two generations for 48 h produced significantly more offspring than the populations reared for 6 and 17 generations. Hybrid population derived from the high‐rm lines did significantly better than that derived from the low‐rm lines. Low‐performance populations become more male based than high performance at 48 h. The potential benefits to improve population's performance using inbred lines for mass rearing are discussed.     

Oscillatory dynamics in evolutionary games are suppressed by heterogeneous adaptation rates of players

Game dynamics in which three or more strategies are cyclically competitive, as represented by the rock-scissors-paper game, have attracted practical and theoretical interests. In evolutionary dynamics, cyclic competition results in oscillatory dynamics of densities of individual strategists. In finite-size populations, it is known that oscillations blow up until all but one strategies are eradicated if without mutation. In the present paper, we formalize replicator dynamics with players who have different adaptation rates. We show analytically and numerically that the heterogeneous adaptation rate suppresses the oscillation amplitude. In social dilemma games with cyclically competing strategies and homogeneous adaptation rates, altruistic strategies are often relatively weak and cannot survive in finite-size populations. In such situations, heterogeneous adaptation rates save coexistence of different strategies and hence promote altruism. When one strategy dominates the others without cyclic competition, fast adaptors earn more than slow adaptors. When not, mixture of fast and slow adaptors stabilizes population dynamics, and slow adaptation does not imply inefficiency for a player.     

Quantitative trait locus analysis of male mating success and sperm competition in Drosophila melanogaster

Much of sexual selection theory depends on assumptions about the genetic basis of variation in male mating success and sperm competitive ability. Despite intense interest in this topic, few genes have been identified that contribute to variation in these traits. Here we report the results of quantitative trait locus (QTL) analyses of mating success of male Drosophila melanogaster when exposed to virgin females, remating success of males with previously mated females, and both defense and offense components of sperm competition. We found two to four significant QTLs for remating success, but no QTLs for mating success, even though mating success was more genetically variable than remating success in the recombinant inbred lines used in this study. By combining these results with data from previous gene-expression experiments, we were able to identify three X-linked candidate genes for variation in remating ability. For two of these genes, QTL and expression data were completely concordant with respect to directionality of effects: high mating success was associated with high levels of gene expression and with beneficial QTL effects on the trait. We found equivocal evidence for genetic variation in sperm offense and defense in the recombinant inbred lines, and we did not find any significant QTLs for either sperm competition trait.     

The evolution of parasite host range in heterogeneous host populations

Theory on the evolution of niche width argues that resource heterogeneity selects for niche breadth. For parasites, this theory predicts that parasite populations will evolve, or maintain, broader host ranges when selected in genetically diverse host populations relative to homogeneous host populations. To test this prediction, we selected the bacterial parasite Serratia marcescens to kill Caenorhabditis elegans in populations that were genetically heterogeneous (50% mix of two experimental genotypes) or homogeneous (100% of either genotype). After 20 rounds of selection, we compared the host range of selected parasites by measuring parasite fitness (i.e. virulence, the selected fitness trait) on the two focal host genotypes and on a novel host genotype. As predicted, heterogeneous host populations selected for parasites with a broader host range: these parasite populations gained or maintained virulence on all host genotypes. This result contrasted with selection in homogeneous populations of one host genotype. Here, host range contracted, with parasite populations gaining virulence on the focal host genotype and losing virulence on the novel host genotype. This pattern was not, however, repeated with selection in homogeneous populations of the second host genotype: these parasite populations did not gain virulence on the focal host genotype, nor did they lose virulence on the novel host genotype. Our results indicate that host heterogeneity can maintain broader host ranges in parasite populations. Individual host genotypes, however, vary in the degree to which they select for specialization in parasite populations.     

Testing for stress-dependent inbreeding depression in Impatiens capensis (Balsaminaceae)

The relevance of inbreeding depression to the persistence of plant populations can depend upon whether stress magnifies inbreeding depression for fitness-related traits. To examine whether drought stress exacerbates inbreeding depression in gas exchange traits and biomass, we grew selfed and outcrossed progeny of inbred lines from two populations of Impatiens capensis in a greenhouse experiment under water-limited and moist soil conditions. Drought stress did not magnify the degree of inbreeding depression for any of the traits measured. In fact, in one population there was a trend for stronger inbreeding depression under well-watered, benign conditions. Furthermore, significant inbreeding depression for carbon assimilation rate and stomatal conductance was only detected in the lines from one population. In contrast, inbreeding depression for biomass was detected within both populations and differed among lines. Drought stress exerted significant selection on physiological traits, favoring increased carbon assimilation rates and decreased stomatal conductance in drought-stressed plants. Patterns of selection did not differ between inbred and outcrossed plants but did differ marginally between populations. Thus, estimates of selection were not biased by the mixed mating system per se, but may be biased by combining individuals from populations with different histories of selection and inbreeding.     

Histocompatible chicken inbred lines: homogeneities in the major histocompatibility complex antigens of the GSP, GSN/1, PNP/DO and BM-C inbred lines assessed by hemagglutination, mixed lymphocyte reaction and skin transplantation.

Chicken inbred lines of the GSP, GSN/1, PNP/DO and BM-C have been established by selection of a specific allele at the B blood group locus (MHC B-G region) and other polymorphic loci through pedigree mating. To extend the potential of these inbred lines as experimental animals in Aves, we assessed the antigenic homogeneities of the MHC antigens by three immunological methods. Antigenic variations of red blood cells (RBCs) were surveyed in the inbred lines and a random-bred line (NG) derived from the Nagoya breed by using ten kinds of intact antisera produced in the inbred line of chickens against RBCs of a red junglefowl and hybrids. In the hemagglutination test, no individual variations were found within the inbred line at all, while all the ten antisera detected highly heterogeneous reactions in individuals of the NG. The reciprocal one-way mixed lymphocyte reactions gave constantly higher stimulation responses (P<0.01) between individual pairs from the inbred lines having different B alleles compared to pairs within the inbred line, while lower stimulation was observed between pairs of the GSP and GSN/1 inbred lines both having the B(21) allele. In reciprocal skin transplantation, the transplanted skingrafts within the inbred line and between individuals from the GSP and GSN/1 inbred lines survived more than 100 days, while all the skingrafts showed signs of rejection within 7 days among the inbred lines having different B alleles. The results obtained by the three practical methods coincidentally indicated that the individuals in the respective four inbred lines were histocompatible, and further, that the GSP and GSN/1 individuals were histocompatible.     

Compositional differences between near‐isogenic GM and conventional maize hybrids are associated with backcrossing practices in conventional breeding

Here, we show that differences between genetically modified (GM) and non‐GM comparators cannot be attributed unequivocally to the GM trait, but arise because of minor genomic differences in near‐isogenic lines. Specifically, this study contrasted the effect of three GM traits (drought tolerance, MON 87460; herbicide resistance, NK603; insect protection, MON 89034) on maize grain composition relative to the effects of residual genetic variation from backcrossing. Important features of the study included (i) marker‐assisted backcrossing to generate genetically similar inbred variants for each GM line, (ii) high‐resolution genotyping to evaluate the genetic similarity of GM lines to the corresponding recurrent parents and (iii) introgression of the different GM traits separately into a wide range of genetically distinct conventional inbred lines. The F1 hybrids of all lines were grown concurrently at three replicated field sites in the United States during the 2012 growing season, and harvested grain was subjected to compositional analysis. Proximates (protein, starch and oil), amino acids, fatty acids, tocopherols and minerals were measured. The number of statistically significant differences (α = 0.05), as well as magnitudes of difference, in mean levels of these components between corresponding GM variants was essentially identical to that between GM and non‐GM controls. The largest sources of compositional variation were the genetic background of the different conventional inbred lines (males and females) used to generate the maize hybrids and location. The lack of any compositional effect attributable to GM suggests the development of modern agricultural biotechnology has been accompanied by a lack of any safety or nutritional concerns.     

Inbreeding and reintroduction: Progeny success in rare Silene populations of varied density

Genetic factors influence the populationviability of rare species, yet the fitnessconsequences of inbred and outbred progeny areseldom tested empirically in reintroductionstrategies designed for species recovery orhabitat restoration. Rare and endangeredplants of Silene (Caryophyllaceae) occuron four continents, including North America. In Oregon, inbred and outbred progeny weremonitored for three years after experimentalreintroduction of a narrow endemic, S.douglasii var. oraria, into formerlygrazed habitat within its presumed historicalrange. Survival and reproduction were comparedfor progeny that were derived from the seeds ofself- versus cross-pollinated flowersproduced in situ at Cascade Head, aUNESCO Biosphere Reserve where the largest ofthree extant populations occurs. Progeny ofcross-pollinated flowers had significantlygreater field survival in all years than didoffspring of selfed or open-pollinated flowers(P < 0.01). Outbred progeny alsosignificantly exceeded other treatment cohortsin canopy area, and produced more reproductivestems and flowers than other progeny types ofthe same maternity. For plots varying in plantdensity, mortality was greatest in thehigh-density competitive regime but thesurvivors reached significantly larger sizesand reproductive capacities than in low densityplots (P < 0.05). In all, successfulconservation plans involving reintroduction mayrequire genetically diverse progeny to offsetinbreeding depression as well as suitableplanting densities and source populations.     

基于醇溶蛋白的20份小麦种质遗传完整性分析

采用醇溶蛋白电泳技术对同一品种不同繁殖年份的20份小麦种质进行遗传完整性分析。结果表明：供试种质中有10份具有一种醇溶蛋白谱带带型的同质性种质;另外10份具有2～4种醇溶蛋白谱带带型的异质性种质,其中6份为地方品种。表明地方品种具有较高的遗传多样性。在10份异质性种质中,两个繁殖年份种质之间的醇溶蛋白带型频率变化差异不显著的有5份,其第一繁殖年份的种质发芽率均高于75％,而另外5份存在显著差异的种质,第一年份的发芽率都低于66％。进一步分析表明,这10份异质性种质在两个繁殖年份之间,其发芽率差值与带型频率差值之间呈极显著正相关,相关系数为0．8665。上速结果表明,小麦更新时较高的发芽率是维持异质性种质遗传完整性的关键因素。     

Genetic distance and species formation in evolving populations

Summary We compare the behavior of the genetic distance between individuals in evolving populations for three stochastic models.In the first model reproduction is asexual and the distribution of genetic distances reflects the genealogical tree of the population. This distribution fluctuates greatly in time, even for very large populations.In the second model reproduction is sexual with random mating allowed between any pair of individuals. In this case, the population becomes homogeneous and the genetic distance between pairs of individuals has small fluctuations which vanish in the limit of an infinitely large population.In the third model reproduction is still sexual but instead of random mating, mating only occurs between individuals which are genetically similar to each other. In that case, the population splits spontaneously into species which are in reproductive isolation from one another and one observes a steady state with a continual appearance and extinction of species in the population. We discuss this model in relation to the biological theory of speciation and isolating mechanisms.We also point out similarities between these three models of evolving populations and the theory of disordered systems in physics. Offprint requests to: P.G. Higgs