Natural selection on a polymorphic disease-resistance locus in Ipomoea purpurea

Although disease-resistance polymorphisms are common in natural plant populations, the mechanisms responsible for this variation are not well understood. Theoretical models predict that balancing selection can maintain polymorphism within a population if the fitness effects of a resistance allele vary from a net cost to a net benefit, depending upon the extent of pathogen damage. However, there have been a few attempts to determine how commonly this mechanism operates in natural plant-pathogen interactions. Ipomoea purpurea populations are often polymorphic for resistance and susceptibility alleles at a locus that influences resistance to the fungal pathogen, Coleosporium ipomoeae. We measured the fitness effects of resistance over three consecutive years at natural and manipulated levels of damage to characterize the type of selection acting on this locus. Costs of resistance varied in magnitude from undetectable to 15.5%, whereas benefits of resistance sometimes equaled, but never exceeded, these costs. In the absence of net benefits of resistance at natural or elevated levels of disease, we conclude that selection within individual populations of I. purpurea probably does not account completely for maintenance of this polymorphism. Rather, the persistence of this polymorphism is probably best explained by a combination of variable selection and meta-population processes.     

The Genetic Basis of Sex Ratio in Silene Alba (= S. Latifolia)

A survey of maternal families collected from natural populations showed that the sex ratio in Silene alba was slightly female biased. Sex ratio varied among populations and among families within a female biased population. Crosses among plants from the most female biased population and the most male biased population showed that the sex ratio polymorphism was inherited through or expressed in the male parent. Males from one family in particular exhibited a severe female bias, characterized by less than 20% male progeny. The inheritance of sex ratio was investigated using a reciprocal crossing design. Sex ratios from reciprocal crosses were significantly different, indicating either sex-linkage or cytoplasmic inheritance of sex ratio. The sex ratios produced by males generally resembled the sex ratios produced by their male parents, indicating that the sex ratio modifier was Y linked. The maternal parent also significantly influenced sex ratio through an interaction with the genotype of the paternal parent. Sex ratio, therefore, is apparently controlled by several loci. Although sex ratio bias in this species may be due to deleterious alleles on the Y chromosome, it is more likely to involve an interaction between loci that cause the female bias and a Y-linked locus that enhances the proportion of males in the progeny.     

SELECTION ON A FLORAL COLOR POLYMORPHISM IN THE TALL MORNING GLORY (IPOMOEA PURPUREA): TRANSMISSION SUCCESS OF THE ALLELES THROUGH POLLEN

The W locus, a codominant locus influencing floral pigment intensity in the tall morning glory, Ipomoea purpurea, is polymorphic throughout the southeastern United States. Previous studies suggest that this polymorphism is actively maintained by balancing selection, and that increased selfing accompanied by lack of pollen discounting (“Fisher effect”) may act to protect the white allele when it is rare. Processes that act to protect the dark allele and thus stabilize the polymorphism in conjunction with the Fisher effect have not been previously detected. The goal of this study was to determine whether any of three such processes might operate in I. purpurea. Estimates of breeding system parameters in a large experimental population in which the white allele was in higher than normal frequency (0.5) provided little evidence that either dark- or light-flowered plants were more successful as pollen parents than white-flowered plants. In addition, no evidence was found for a transmission bias favoring the dark allele in the ovules produced by light heterozygotes. In contrast, a strong transmission bias favoring the dark allele in pollen of heterozygotes was observed. A simple model using parameter estimates derived from this and previous studies indicates that a balance between the Fisher effect and biased transmission in heterozygote pollen could account for many properties of the polymorphism.     

Heterozygote advantage and the maintenance of polymorphism for multilocus traits

Explaining how polymorphism is maintained in the face of selection remains a puzzle since selection tends to erode genetic variation. Provided an infinitely large unsubdivided population and no frequency-dependance of selective values, heterozygote advantage is the text book explanation for the maintenance of polymorphism when selection acts at a diallelic locus. Here, we investigate whether this remains true when selection acts at multiple diallelic loci. We use five different definitions of heterozygote advantage that largely cover this concept for multiple loci. Using extensive numerical simulations, we found no clear associations between the presence of any of the five definitions of heterozygote advantage and the maintenance of polymorphism at all loci. The strength of the association decreases as the number of loci increases or as recombination decreases. We conclude that heterozygote advantage cannot be a general mechanism for the maintenance of genetic polymorphism at multiple loci. These findings suggest that a correlation between the number of heterozygote loci and fitness is not warranted on theoretical ground.     

The generation and maintenance of genetic variation by frequency-dependent selection: constructing polymorphisms under the pairwise interaction model

Frequency-dependent selection remains the most commonly invoked heuristic explanation for the maintenance of genetic variation. For polymorphism to exist, new alleles must be both generated and maintained in the population. Here we use a construction approach to model frequency-dependent selection with mutation under the pairwise interaction model. The pairwise interaction model is a general model of frequency-dependent selection at the genotypic level. We find that frequency-dependent selection is able to generate a large number of alleles at a single locus. The construction process generates multiallelic polymorphisms with a wide range of allele-frequency distributions and genotypic fitness relationships. Levels of polymorphism and mean fitness are uncoupled, so constructed polymorphisms remain permanently invasible to new mutants; thus the model never settles down to an equilibrium state. Analysis of constructed fitness sets reveals signatures of heterozygote advantage and positive frequency dependence.     

A cyclophilin gene marker confirming geographical differentiation of Norway spruce populations and indicating viability response on excess soil-born salinity

A newly identified cyclophilin-encoding cDNA clone was used to design a codominant inherited EST-PCR marker in Norway spruce. The study of the current minor polymorphism revealed a geographically structured differentiation pattern across 17 test populations, showing a slight clinal variation south-north through Europe. Based on the frequency of alleles, isolation-by-distance analysis and the Ewens-Watterson test, we conclude that a selectively neutral random-drift mutation recently occurred within the Alpine population group, thus being responsible for the genetic variation detected. Analysis of tolerant and susceptible subsets of two adjacent Bavarian spruce populations affected by soil-born NaCl pollution, revealed that the cyclophilin marker locus also confirms biased genotype frequencies. Considering an unlinked PCR marker of a ribosomal protein-encoding EST clone, deviations between pooled tolerant subsets and pooled sensitive subsets were proven to be more significant for two-locus homozygous genotypes than for each locus alone. We suggest that both loci are linked to adaptive genomic regions. Their potential to test the feasibility of marker-assisted selection of both NaCl-tolerant and drought resistant tree populations is discussed.     

Frequency-dependent selection and the maintenance of genetic variation: exploring the parameter space of the multiallelic pairwise interaction model

When individuals' fitnesses depend on the genetic composition of the population in which they are found, selection is then frequency dependent. Frequency-dependent selection (FDS) is often invoked as a heuristic explanation for the maintenance of large numbers of alleles at a locus. The pairwise interaction model is a general model of FDS via intraspecific competition at the genotypic level. Here we use a parameter-space approach to investigate the full potential for the maintenance of multiallelic equilibria under the pairwise interaction model. We find that FDS maintains full polymorphism more often than classic constant-selection models and produces more skewed equilibrium allele frequencies. Fitness sets with some degree of rare advantage maintained full polymorphism most often, but a wide variety of nonobvious fitness patterns were also found to have positive potential for polymorphism. An example is put forth suggesting possible explanations for multiallelic polymorphisms maintained despite positive FDS on individual alleles.     

Polymorphisms at newly identified lipid-associated loci are associated with blood lipids and cardiovascular disease in an Asian Malay population

We conducted a cross-sectional study of Malay participants aged 40-80 years (n = 2,932) to examine the associations between polymorphisms at newly identified, lipid-associated loci with blood lipid levels and prevalent cardiovascular disease (CVD) in a Malay population in Asia. A polymorphism adjacent to the TRIB1 locus (rs17321515) was associated with elevated total cholesterol and LDL-cholesterol (LDL-C) after adjustment for age and sex (both P values <0.007) and with increased risk of coronary heart disease and CVD [odds ratio (OR) 1.23, 95% confidence interval (95% CI) 1.03-1.46; and OR 1.2, 95% CI 1.02-1.42, respectively] under an additive model of inheritance. In addition, using recessive models of inheritance, polymorphisms on chromosome 19 adjacent to the CILP2 and PBX4 loci (rs16996148) and on chromosome 1 at the GALNT2 locus (rs4846914) were associated with elevated HDL-C (P = 0.005) and lower LDL-C (P = 0.048), respectively. Although novel, the former is consistent with the association between this polymorphism and lower blood triglycerides observed in the initial studies conducted in populations of European ancestry. Neither showed statistically significant association with CVD. These observations should form the basis of further investigation to identify the causative polymorphisms at this locus, and also to understand the mechanistic roles that this protein may play in lipoprotein metabolism in Asians and other populations.     

A General Model of Negative Frequency Dependent Selection Explains Global Patterns of Human ABO Polymorphism

The ABO locus in humans is characterized by elevated heterozygosity and very similar allele frequencies among populations scattered across the globe. Using knowledge of ABO protein function, we generated a simple model of asymmetric negative frequency dependent selection and genetic drift to explain the maintenance of ABO polymorphism and its loss in human populations. In our models, regardless of the strength of selection, models with large effective population sizes result in ABO allele frequencies that closely match those observed in most continental populations. Populations must be moderately small to fall out of equilibrium and lose either the A or B allele (N_e ≤ 50) and much smaller (N_e ≤ 25) for the complete loss of diversity, which nearly always involved the fixation of the O allele. A pattern of low heterozygosity at the ABO locus where loss of polymorphism occurs in our model is consistent with small populations, such as Native American populations. This study provides a general evolutionary model to explain the observed global patterns of polymorphism at the ABO locus and the pattern of allele loss in small populations. Moreover, these results inform the range of population sizes associated with the recent human colonization of the Americas.     

Opposing natural selection from herbivores and pathogens may maintain floral-color variation in Claytonia virginica (Portulacaceae)

The maintenance of floral-color variation within natural populations is enigmatic because directional selection through pollinator preferences combined with random genetic drift should lead to the rapid loss of such variation. Fluctuating, balancing, and negative frequency-dependent selection mediated through pollinators have been identified as factors that may contribute to the maintenance of floral-color variation, and recently it has been suggested that indirect responses to selection on correlated characters through agents of selection other than pollinators may substantially shape the evolution of floral traits. Here, I provide empirical support for this latter view in Claytonia virginica (Portulacaceae) through a multiseason field study, a pollen supplementation study, and an artificial herbivory experiment. These studies show that most individuals fall into one of four discrete color classes, and suggest pollinator-mediated selection for increased floral redness in concurrent years. Floral color is also an indirect target of opposing directional selection via herbivores and pathogens that fluctuates through time. Taken together, these data suggest a novel mechanism by which floral-color variation may be maintained, and illustrate the importance of an inclusive, pluralistic view of selection when investigating the evolution of complex phenotypes.     

An analysis of selection on a colour polymorphism in the northern leopard frog

In this study, we investigated the role of selection in the maintenance of a dorsal colour polymorphism in natural populations of the northern leopard frog, Rana pipiens. We determined genetic structure both spatially and temporally from a suite of putatively neutral molecular markers and tested whether or not the colour locus exhibited patterns of genetic variation that differed from those of the neutral loci. Spatial genetic structure at the colour locus was indistinguishable from structure at neutral loci [95% confidence intervals of F(ST) (neutral) = (0.07, 0.35), F(ST) (colour locus) = 0.114]. In the temporal analysis, we found that the variance among populations in the change in allele frequency at the colour locus (equal to 0.004) lies within the 95% confidence intervals for the variance among populations in changes in allele frequencies at neutral loci. In light of our inability to show evidence for the selective maintenance of the colour polymorphism, we used computer simulations to infer the power of our spatial and temporal techniques to detect selection. The computer simulations showed that although the strength of selection (s) would need to be relatively strong to have been detected by the temporal approach (s = 0.1-0.4, depending on the model tested), the spatial analysis would have detected all but weak selection (s = 0.01-0.04, depending on the model tested). This study illustrates the importance of using a locus comparison approach to detect evidence for selective maintenance before conducting studies to measure the selective mechanisms maintaining a polymorphism.     

MAINTENANCE OR LOSS OF GENETIC VARIATION UNDER SEXUAL AND PARENTAL ANTAGONISM AT A SEX-LINKED LOCUS

An intralocus genetic conflict occurs when a locus is selected in opposing directions in different subsets of a population. Populations with two sexes have the potential to host a pair of distinct intralocus conflicts: sexual antagonism and parental antagonism. In this article, we examine the population genetic consequences of these conflicts for X-linked genes. Both conflicts are capable of maintaining genetic variation in a population, but to different degrees. For weak sexual antagonism, the X chromosome has a higher opportunity for polymorphism than the autosomes. For parental antagonism, there is a very limited opportunity for polymorphism on the X chromosome relative to autosomes or to sexual antagonism. X-linkage introduces an asymmetry in the inheritance and expression of sexually and parentally antagonistic genes that leads to a biased fixation of alleles with certain effects. We find little support for the commonly held intuition that the X chromosome should be biased toward fixing female-beneficial alleles. Contrary to this intuition, we find that the X chromosome is biased toward fixation of male-beneficial alleles for much of the range of dominance. Additionally, we find that the X chromosome is more favorable to the fixation of alleles that are beneficial when maternally derived.     

Effects of a Locus Affecting Floral Pigmentation in Ipomoea Purpurea on Female Fitness Components

A locus influencing floral pigment intensity in the morning glory, Ipomoea purpurea, is polymorphic throughout the southeastern United States. Previous work has suggested that the white allele at this locus has a transmission advantage during mating because of the effect of flower color on pollinator behavior. The experiment described here was designed to determine whether other effects of the W locus may contribute an opposing selective advantage to the dark allele. Dark homozygotes were vegetatively smaller and produced fewer flowers, seed capsules and seeds than either light heterozygotes or white homozygotes. In addition, dark homozygotes produced smaller seeds than heterozygotes, and there is some indication that white homozygotes also produced smaller seeds than heterozygotes. Pleiotropic effects on seed number thus do not seem to contribute to selection opposing the mating advantage associated with the white allele. However, pleiotropic effects on seed size might contribute to overdominance that could stabilize the W locus polymorphism.     

Two Modes of Balancing Selection in Drosophila Melanogaster: Overcompensation and Overdominance

Overdominance is often invoked to account for the extensive polymorphisms found in natural populations of organisms; overcompensation, however, may be equally or more important. Overcompensation occurs when limiting resources are better exploited by a genetically mixed than by a uniform population, and is often causally related to frequency-dependent selection. We have designed experiments to test whether overcompensation occurs in Drosophila melanogaster, using the Sod locus as a marker. Tests are made at each of two densities and two temperatures for cultures with desired genetic compositions. Both temperature and density have statistically significant effects on the per-female productivity of the cultures. More important, there are strong effects due to overcompensation. Cultures that are more polymorphic are also more productive than less polymorphic ones even when the level of individual heterozygosity is the same in all. There is also overdominance for the Sod locus: the heterozygotes are more productive than either homozygote at every temperature and density, and the differences are statistically significant in several cases. These results corroborate previous studies showing that overdominance may contribute to the maintenance of the Sod polymorphisms. Moreover, our results indicate that the significance of overcompensation as a mechanism to account for polymorphism in natural populations deserves further investigation.     

Balancing selection on a floral polymorphism

Abstract.— The common morning glory, Ipomoea purpurea , exhibits a flower color polymorphism at the W locus throughout the southeastern North America. The W locus controls whether flowers will be darkly pigmented ( WW ), lightly pigmented ( Ww ), or white with pigmented rays ( ww ). In this report, we describe results of a perturbation, or convergence, experiment using five plots designed to determine whether balancing selection operates on the W locus. The pattern of gene frequency changes obtained are indicative of balancing selection operating at the W locus, providing direct evidence that both the alleles are actively maintained by selection.     

短串联重复序列D7S2201基因座的群体遗传学研究

用扩增片段长度多态性技术分析短串联重复序列D7S2201基因座的遗传多态性,在262个中国成都地区汉族无关个体及119个泰国曼谷地区泰人无关个体中分别发现7个和5个等位基因,首次获得该基因座在两群体中的频率分布,其等位基因片段大小范围为100～124bp。两群体的基因型频率分布均符合Hardy Weinberg平衡。该基因座在两群体中的个人识别能力（PD）、杂合度（H）、多态性信息含量（CPI）及非父排除率（PE）分别为0.7038、0.5992、0.4789、0.2900和0.7351、0.5882、0.5012、0.2770。家系调查证实了等位基因的传递遵循孟德尔遗传规律。χ2检验表明两群体间等位基因频率分布无显著性差异。 Abstract：The polymorphism of a new short tandem repeat (STR) locus D7S2201 was analyzed by using AmpFLP. Seven alleles were observed in 262 unrelated Chinese individuals living in Chengdu and five alleles in 119 unrelated Thai individuals living in Bangkok, the ranges of fragment size were 100～124bp. The genotypes distributions of D7S2201 locus in the two populations were in accordance with Hardy Weinberg equilibrium. The discriminating power (PD), observed heterozygosity (H), polymorphism information content (CPI) and power of exclusion (PE) were 0.7038, 05992, 04789, 02900 in Chinese population and 0.7351, 0.5882, 0.5012, 0.2770 in Thai population respectively. Family studies confirmed Mendelian inheritance of alleles. No significant difference was observed between the two populations.     

A cost of disease resistance: paradigm or peculiarity?

Disease is one of the main driving forces of biological evolution. Parasites cause natural selection for disease resistance in populations of their hosts. Why then are all organisms susceptible to some parasites? One explanation is that resistance to disease is costly, reducing the fitness of the host in the absence of disease. A recent article shows that such costs might have helped to maintain polymorphism at a resistance locus. Other work, however, has questioned whether the costs of resistance are indeed necessary to account for polymorphism in host–parasite interactions.     

Theoretical value of estimates of general combining ability in the autotetraploid crop

Summary The means of half-sib progenies have been indicated as selection criteria for intra-population improvement while the average of the means of full-sib progenies in diallel analyses have been proposed as predictors, in part, of the means of untested synthetic varieties. When these measures based on progeny means are expressed as deviations from a defined greater population of crosses, they are often termed the general combining ability (GCA). In this study the GCA estimates or a facsimile were theoretically investigated for the one locus, digene, autotetraploid model to verify the genetic basis and its value for selection and prediction in the presence of a naturally occurring phenomena of autopolyploids called gametic disequilibrium with three types of non-additive inheritance. Two breeding objectives were envisioned, the selection of best parents with recurrent selection based on GCA in the continued development of elite populations and the prediction of advanced generation synthetic variety performance. The first generation means of progenies with a potential bias due to gametic disequilibrium were compared to GCA estimation of same progenies in the absence of gametic disequilibrium. The results indicated that testcrossing plants to a population without gametic disequilibrium could be used for selection of best parents. The gametic disequilibrium in the cross may increase or depress selection response dependent on the array of genotypes which happen to be evaluated, on the type of genic action at the locus, and on the frequency of the desirable allele in the testor population. The GCA estimates for prediction of synthetic performance were potentially biased by gametic disequilibrium. An assumption of pollination by the same array of gametes was made for all plants, but obviously was unrealistic for GCA estimation with partial diallels, or with no selfing, and in other situations. The GCA estimate was shown to be an unreliable predictor of synthetic variety performance. When it was assumed that different plants were pollinated by different arrays of gametes, a more realistic situation, no genetic interpretation of GCA values was possible even with purely additive gene action at the locus.Cooperative investigation of the Alfalfa Production Research Unit, United States Department of Agriculture, Agricultural Research Service, and the Nevada Agricultural Experiment Station, Reno, Nevada     

Allelic diversity at the Mhc-DQA locus of woodmouse populations (Apodemus sylvaticus) present in the islands and mainland of the northern Mediterranean

Aim Polymorphism at neutral markers and at MHC loci in rodent populations living on islands is generally low. The main genetic factors that may contribute to a reduced level of genetic variability are genetic drift, reduced gene flow and founder events. We investigated the pattern of polymorphism at the second exon of the Mhc‐DQA gene in island populations of Apodemus sylvaticus and in their mainland counterparts to investigate the pattern of MHC polymorphism in a phylogeographical context and to assess the impact of insularity on diversity at this locus. Location Eight north Mediterranean populations of Apodemus sylvaticus were studied, including five island populations (Majorca, Minorca, Porquerolles, Port‐Cros and Sicily) and three mainland populations. Methods cDNA sequencing and nucleotide sequences analyses. Synonymous and non‐synonymous substitutions were examined at the PBR and non‐PBR sites. The DQA allelic distribution in populations was compared with the woodmouse phylogeography. Results This study presents novel DQA alleles. High polymorphism of the DQA locus is recorded in natural populations of A. sylvaticus with 13 alleles being widely distributed irrespective of the geographical origin and palaeoclimatic history of populations. The DQA locus does not show the expected pattern for non‐synonymous substitutions at the PBR sites. However, island populations show a weak loss of polymorphism in comparison with their mainland counterparts. Main conclusions The DQA locus in the woodmouse seems to be subject to weak selection and does not allow resolution of phylogeographical relationships among European woodmouse populations. The presence of at least three alleles in island populations and the maintenance of five alleles between the two European lineages over 1.5 Myr suggest that balancing selection may act within populations, and more precisely within island populations, to maintain genetic variability. This study shows that phylogeographical studies are a prerequisite for any genetic investigation of selected genes in natural populations.