Maciej Jan Ejsmond

New generation sequencers as a tool for genotyping of highly polymorphic multilocus MHC system

Accurate genotyping of complex systems, such as the major histocompatibility complex (MHC) often requires simultaneous analysis of multiple co‐amplifying loci. Here we explore the utility of the massively parallel 454 sequencing method as a universal tool for genotyping complex MHC systems in nonmodel vertebrates. The power of this approach stems from the use of tagged polymerase chain reaction (PCR) primers to identify individual amplicons which can be simultaneously sequenced to the arbitrarily chosen coverage. However, the error‐prone sequencing technology poses considerable challenges as it may be difficult to discriminate between sequencing errors and true rare alleles; due to complex nature of artefacts and errors, efficient quality control is required. Nevertheless, our study demonstrates the parallel 454 sequencing can be an efficient genotyping platform for MHC and provides an alternative to classical genotyping methods. We introduced procedures to identify the threshold that can be used to reduce number of genotyping errors by eliminating most of artefactual alleles (AA) representing PCR or sequencing errors. Our procedures are based on two expectations: first, that AA should be relatively rare, both overall and on per‐individual basis, and second, that most AA result from errors introduced to sequences of true alleles. In our data set, alleles with an average per‐individual frequency below 3% most likely represented artefacts. This threshold will vary in other applications according to the complexity of the genotyped system. We strongly suggest direct assessment of genotyping error in every experiment by running a fraction of duplicates: individuals amplified in independent PCRs.

MHC diversity in bottlenecked populations: a simulation model

The depletion of variation at MHC loci, which play a crucial role in pathogen recognition, has been postulated to be one of important extinction risk factors for endangered populations. Thus, it is important to understand how selection affects the level of polymorphism in these genes when populations undergo a reduction in size. We followed MHC diversity in computer simulations of population bottlenecks. The fates of MHC alleles in the simulations were determined either by drift, or by balancing selection resulting from host–parasite coevolution. We found that the impact of selection on MHC polymorphism in bottlenecked populations was dependent upon the timescales involved. Initially, selection maintained lower number of alleles than drift, but after ~40 generations of hosts selection maintained higher MHC diversity, as compared to drift. The adverse effects of decreased MHC polymorphism on population viability may be, to some extent, compensated for if selection helps to retain MHC alleles which show high functional diversity, which should allow protection against a broader range of pathogens. Our simulation shows, however, that the mean divergence of alleles retained under selection in bottlenecked populations is not, on average, significantly higher than the divergence due to drift.

MHC allele frequency distributions under parasite-driven selection: A simulation model.

BackgroundThe extreme polymorphism that is observed in major histocompatibility complex (MHC) genes, which code for proteins involved in recognition of non-self oligopeptides, is thought to result from a pressure exerted by parasites because parasite antigens are more likely to be recognized by MHC heterozygotes (heterozygote advantage) and/or by rare MHC alleles (negative frequency-dependent selection). The Ewens-Watterson test (EW) is often used to detect selection acting on MHC genes over the recent history of a population. EW is based on the expectation that allele frequencies under balancing selection should be more even than under neutrality. We used computer simulations to investigate whether this expectation holds for selection exerted by parasites on host MHC genes under conditions of heterozygote advantage and negative frequency-dependent selection acting either simultaneously or separately.ResultsIn agreement with simple models of symmetrical overdominance, we found that heterozygote advantage acting alone in populations does, indeed, result in more even allele frequency distributions than expected under neutrality, and this is easily detectable by EW. However, under negative frequency-dependent selection, or under the joint action of negative frequency-dependent selection and heterozygote advantage, distributions of allele frequencies were less predictable: the majority of distributions were indistinguishable from neutral expectations, while the remaining runs resulted in either more even or more skewed distributions than under neutrality.ConclusionsOur results indicate that, as long as negative frequency-dependent selection is an important force maintaining MHC variation, the EW test has limited utility in detecting selection acting on these genes.

Sexual selection and the evolutionary dynamics of the major histocompatibility complex

The genes of the major histocompatibility complex (MHC) are a key component of the adaptive immune system and among the most variable loci in the vertebrate genome. Pathogen-mediated natural selection and MHC-based disassortative mating are both thought to structure MHC polymorphism, but their effects have proven difficult to discriminate in natural systems. Using the first model of MHC dynamics incorporating both survival and reproduction, we demonstrate that natural and sexual selection produce distinctive signatures of MHC allelic diversity with critical implications for understanding host–pathogen dynamics. While natural selection produces the Red Queen dynamics characteristic of host–parasite interactions, disassortative mating stabilizes allele frequencies, damping major fluctuations in dominant alleles and protecting functional variants against drift. This subtle difference generates a complex interaction between MHC allelic diversity and population size. In small populations, the stabilizing effects of sexual selection moderate the effects of drift, whereas pathogen-mediated selection accelerates the loss of functionally important genetic diversity. Natural selection enhances MHC allelic variation in larger populations, with the highest levels of diversity generated by the combined action of pathogen-mediated selection and disassortative mating. MHC-based sexual selection may help to explain how functionally important genetic variation can be maintained in populations of conservation concern.

How to Time Growth and Reproduction during the Vegetative Season: An Evolutionary Choice for Indeterminate Growers in Seasonal Environments

Indeterminate growers such as plants, mollusks, fish, amphibians, and reptiles are highly diversified with respect to the seasonal timing of growth and reproduction. Current life‐history theory does not offer a consistent view on the origin of this diversity. We use dynamic optimization to examine resource allocation in seasonal environments, considering that offspring produced at different times of the season have unequal future prospects. Reduction of these prospects during the season produced indeterminate growers that grew mostly after maturation, achieving large final body sizes. It also changed the optimal timing of growth and reproduction during a season, from grow‐first‐reproduce‐later, as usually predicted by life‐history theory, to the reproduce‐first‐grow‐later tactic; other tactics were produced by the interactive effects of winter survival and unequal offspring prospects. The results suggest that devaluation of offspring production provides conditions for the evolution of capital breeding, even in fully predictable seasonal environments. Thus, the unequal fate of newborns from different parts of a season may explain the origin of diversity of reproductive phenologies, growth patterns, and capital breeding in nature.

Does climate affect pollen morphology? Optimal size and shape of pollen grains under various desiccation intensity

Seed production is likely constrained by pollen limitation and the viability of pollen grains decreases rapidly in time due to water evaporation. Any decrease in the surface-to-volume ratio, through increase in size or change in shape of a grain, reduces the rate of water loss. However, grain size trade-offs with the number of grains that can be produced by a plant. Here, we tested the hypothesis that under higher desiccation stress pollen grains become larger and more spherical. We analyzed data on the pollen morphology of eight Rosaceae species and the desiccation intensity based on temperature, potential evapotranspiration and altitude. To explain the mechanisms underlying our results, we present a model that optimizes the size and shape of pollen grains under different conditions. We report that pollen grains under more intense desiccation stress during flowering periods tend to be larger but do not change shape. This conclusion is consistent with the results of a theoretical model presented here. Our report fills a gap in our knowledge about a fundamental process in plant reproduction. We also discuss the significance of our results in light of current palynological and ecological problems (e.g., global climate change).

Seasonality in Offspring Value and Trade-Offs with Growth Explain Capital Breeding

The degree to which reproduction is based on reserves (capital breeding) and/or current acquisition (income breeding) drives extensive variation in organism life histories. In nature, pure income and capital breeding are endpoints of a continuum of diversity whose ultimate drivers are poorly understood. To study the adaptive value of capital and income breeding, we present an annual routine model of the life history of a perennial organism where reproductive value at birth varies seasonally. The model organisms allocate time and resources to growth, reproduction, and storage. Our model predicts that capital breeding is adaptive when timing of birth affects offspring reproductive value. The stronger the seasonality, the more time is dedicated to capital breeding and growth after maturation (indeterminate growth) instead of income breeding. This is because storage and growth are investments in future (residual) reproduction taken at times when offspring value is low. Storage is a short-term investment in offspring through capital breeding; growth is a long-term investment in reproductive potential. Because the modeled production rate increases less than linearly with body size, growth brings diminishing returns for larger organisms, favoring capital breeding. Building storage requires time, which limits growth opportunities, and we show for the first time that in seasonal environments, the degree of capital breeding is tightly linked to body size of indeterminate growers through allocation trade-offs.

Red Queen Processes Drive Positive Selection on Major Histocompatibility Complex (MHC) Genes.

Major Histocompatibility Complex (MHC) genes code for proteins involved in the incitation of the adaptive immune response in vertebrates, which is achieved through binding oligopeptides (antigens) of pathogenic origin. Across vertebrate species, substitutions of amino acids at sites responsible for the specificity of antigen binding (ABS) are positively selected. This is attributed to pathogen-driven balancing selection, which is also thought to maintain the high polymorphism of MHC genes, and to cause the sharing of allelic lineages between species. However, the nature of this selection remains controversial. We used individual-based computer simulations to investigate the roles of two phenomena capable of maintaining MHC polymorphism: heterozygote advantage and host-pathogen arms race (Red Queen process). Our simulations revealed that levels of MHC polymorphism were high and driven mostly by the Red Queen process at a high pathogen mutation rate, but were low and driven mostly by heterozygote advantage when the pathogen mutation rate was low. We found that novel mutations at ABSs are strongly favored by the Red Queen process, but not by heterozygote advantage, regardless of the pathogen mutation rate. However, while the strong advantage of novel alleles increased the allele turnover rate, under a high pathogen mutation rate, allelic lineages persisted for a comparable length of time under Red Queen and under heterozygote advantage. Thus, when pathogens evolve quickly, the Red Queen is capable of explaining both positive selection and long coalescence times, but the tension between the novel allele advantage and persistence of alleles deserves further investigation.

Large pollen at high temperature: an adaptation to increased competition on the stigma?

Pollen availability is a major constraint of plant reproductive success. Because pollen size trades-off with the quantity of produced grains, the link between climate characteristics and the determination of pollen size is of fundamental importance. To minimize the rate of water loss due to desiccation, a plant should produce larger grains that also have a lower surface-to-volume ratio. We used a comparative analysis to examine the hypothesis predicting increase in pollen size as a response to desiccation intensity. To test the hypothesis, we correlated the data on pollen size with the climate characteristics, temperature and desiccation intensity of the flowering period, for 232 plant species of 11 taxonomic groups. The analysis showed a positive relationship between the pollen size and temperature, but not with the desiccation intensity. We discuss the potential mechanisms by which increased temperature is an indicator of high competition among pollen grains on the stigma, which in turn is expected to promote large pollen. Our work provides insight into the temperature dependence of pollen production in plants and reveals a link between environmental temperature and the intensity of limitation of plant reproductive success by pollen availability. The result is relevant in the context of global climate change. We also discuss why environmental temperature has to be controlled in studies dealing with pollen production, particularly in investigations of size-number trade-off.

The role of MHC supertypes in promoting trans-species polymorphism remains an open question

The role of MHC supertypes in promoting trans-species polymorphism remains an open question