The effect of genetic robustness on evolvability in digital organisms

Background  

Recent work has revealed that many biological systems keep functioning in the face of mutations and therefore can be considered genetically robust. However, several issues related to robustness remain poorly understood, such as its implications for evolvability (the ability to produce adaptive evolutionary innovations).     

The genetic architecture of immune defense and reproduction in male Bombus terrestris bumblebees

Understanding the architecture of genetic variation, that is the number, effect, location, and interaction, of genes responsible for phenotypic variability in nature is important for the understanding of microevolutionary processes. In this study, we have used a quantitative trait loci (QTL) approach to uncover the genetic architecture of fitness-relevant traits associated with reproduction and immune defense in male Bombus terrestris bumblebees. Three male reproductive investment traits, the number and length of the produced sperm and the size of the accessory glands, were studied. Two branches of the insect innate immune system, the activation of the Phenoloxidase-cascade and the hemolymph's antibacterial activity, were investigated. We found that variation in most of the studied traits is based on a network of minor QTLs and epistatic interactions. Unexpectedly, there was no evidence for phenotypic or genetic trade-offs between the presumably costly investment in immune defense and reproductive effort in this population for the measured traits. In fact, we found a positive correlation, both, in phenotype and genetic architecture for the number of produced sperm and antibacterial activity against an insect pathogen. A major finding for all traits analyzed was that the epistatic interactions accounted for a major proportion of the explained phenotypic variance. Especially for traits involved in immune defense, this pattern highlights the possible role of parasites in the evolution and maintenance of recombination and sexual reproduction.     

FtsA reshapes membrane architecture and remodels the Z‐ring in Escherichia coli

Cell division in prokaryotes initiates with assembly of the Z‐ring at midcell, which, in Escherichia coli, is tethered to the inner leaflet of the cytoplasmic membrane through a direct interaction with FtsA, a widely conserved actin homolog. The Z‐ring is comprised of polymers of tubulin‐like FtsZ and has been suggested to provide the force for constriction. Here, we demonstrate that FtsA exerts force on membranes causing redistribution of membrane architecture, robustly hydrolyzes ATP and directly engages FtsZ polymers in a reconstituted system. Phospholipid reorganization by FtsA occurs rapidly and is mediated by insertion of a C‐terminal membrane targeting sequence (MTS) into the bilayer and further promoted by a nucleotide‐dependent conformational change relayed to the MTS. FtsA also recruits FtsZ to phospholipid vesicles via a direct interaction with the FtsZ C‐terminus and regulates FtsZ assembly kinetics. These results implicate the actin homolog FtsA in establishment of a Z‐ring scaffold, while directly remodeling the membrane and provide mechanistic insight into localized cell wall remodeling, invagination and constriction at the onset of division.     

水螅的有性生殖

介绍了水螅的有性生殖,包括精卵发生,受精和胚胎发育,并讨论了杂交受精在水螅分类问题上的意义。     

风箱果有性繁殖研究

对风箱果（Physocarpus amurensis）适宜的采种时期、不同母树种子的成熟差异和幼苗的生长特征进行了研究。结果表明,风箱果种子的最适采种期在7月末,种子成熟后有休眠特性;方差分析表明,不同植株间种子的发芽率和千粒重都达到极显著水平（p<0.01）,并且发芽率与种子重量呈正相关,其相关程度最佳的为幂函数,确定系数是75.75%（p<0.01）;风箱果幼苗类型为子叶出土型,幼苗生物量对根的投资最大,其次是叶,茎的最少,在这3部分生物量投资中,对根和叶的投资比较稳定（其变异系数分别为6.8%和11.03%）,对茎的生物量投资具有较大的变异（其变异系数为21.81%）。基径是衡量风箱果幼苗空间大小的重要数量指标。风箱果构件生物量（根生物量、茎生物量、叶生物量及总生物量）各组分均随基径的增加,呈线性函数形式增长,这表明随着植株的空间扩展,各构件有着相同的物质生产与积累规律。     

Sexual reproduction in Hawaiian Acropora

Sexual reproductive maturity was evaluated in Acropora valida, Acropora cytherea and Acropora humilis at French Frigate Shoals, Northwest Hawaiian Islands during two consecutive summers. Acropora valida gonads matured at different rates in different habitats in both years. Spawning was inferred by the sudden disappearance of gonads of mature size. Histological sections of fertile polyps confirmed the maturity of gonads prior to spawning. An isolated colony of A. humilis spawned in early summer. Strong indications of sexually mature colonics of A. cytherea exist, but clear temporal patterns were not apparent. Lunar period of spawning in reef flat A. valida and A. humilis differed from that reported for these species from other regions. The three species did not overlap in time of spawning. Previous ideas concerning the allochthonous origin of larval recruits, as well as the absence of Acropora from high islands of the Hawaiian chain, are re-evaluated in light of new evidence for sexual reproductive capacity by native populations.     

Sexual reproduction and the evolution of microbial pathogens

Three common systemic human fungal pathogens--Cryptococcus neoformans, Candida albicans and Aspergillus fumigatus--have retained all the machinery to engage in sexual reproduction, and yet their populations are often clonal with limited evidence for recombination. Striking parallels have emerged with four protozoan parasites that infect humans: Toxoplasma gondii, Trypanosoma brucei, Trypanosoma cruzi and Plasmodium falciparum. Limiting sexual reproduction appears to be a common virulence strategy, enabling generation of clonal populations well adapted to host and environmental niches, yet retaining the ability to engage in sexual or parasexual reproduction and respond to selective pressure. Continued investigation of the sexual nature of microbial pathogens should facilitate both laboratory investigation and an understanding of the complex interplay between pathogens, hosts, vectors, and their environments.     

Sexual reproduction in the tropical corallimorpharian Rhodactis rhodostoma

Abstract. Polyps of the tropical corallimorpharian Rhodactis rhodostoma segregate sexes between center and edge positions within aggregations produced by clonal replication. On a reef flat at Eilat, northern Red Sea, infertile polyps and males occur mainly along the edges of clonal aggregations, while females mostly occupy central positions within each aggregation. In addition, on the inner to middle reef flat where polyps of this species are abundant, aggregations consist mostly of females. On the outer reef flat, where polyps are rare, a sampled aggregation consisted mostly of males and infertile polyps. Male polyps are significantly smaller than females, and the smallest polyps are infertile. Fecundity increases significantly with polyp size in females, but testis size and number do not vary with body size in males. Oocytes are present in polyps during most of the year and gradually increase in size until annual spawning in June-July during the period of maximum day length. Testes do not vary significantly in size during the year and remain a small proportion of body mass (>8%). In contrast, females invest up to 30% of their body mass into gonads during the months immediately before spawning. The annual spawning of gametes coincides with a temporary drop in the frequency of clonal replication by polyps. We estimate that each female polyp of R. rhodostoma may release up to 3000 large eggs (500 μm in maximum diameter) each summer. The high investment of this corallimorpharian in sexual production of planktonic propagules may allow rapid dispersal to reef habitats distant from parent populations.     

Sexual reproduction and dimorphism in the pathogenic basidiomycetes

Many fungi in the Basidiomycota have a dimorphic life cycle, where a monokaryotic yeast form alternates with a dikaryotic hyphal form. Most of the dimorphic basidiomycetes are pathogenic on plants, animals or other fungi. In these species, infection of a host appears to be closely linked to both dimorphism and the process of sexual reproduction. Sex in fungi is governed by a specialized region of the genome known as the mating type locus that confers cell-type identity and regulates progression through the sexual cycle. Here we investigate sexual reproduction and lifestyle in emerging human pathogenic yeasts and plant pathogenic smuts of the Basidiomycota and examine the relationship among sex, dimorphism and pathogenesis.     

Sexual reproduction in aflatoxin-producing Aspergillus nomius

Sexual reproduction was examined in the aflatoxin-producing fungus Aspergillus nomius. Crosses between sexually compatible strains resulted in the formation of multiple nonostiolate ascocarps within stromata, which places the teleomorph in genus Petromyces. Ascocarp and ascospore morphology in Petromyces nomius were similar to that in P. flavus and P. parasiticus, and differences between teleomorphs were insufficient for species separation. Formation of mature ascocarps was infrequent, with only 24% of the 83 crosses producing viable ascospores. The majority of P. nomius strains contained a single mating-type gene (MAT1-1 or MAT1-2), but several strains contained both genes. MAT1-1/MAT1-2 strains were self-sterile and capable of mating with both MAT1-1 and MAT1-2 strains; hence P. nomius appears to be functionally heterothallic.     

Diploidy and the selective advantage for sexual reproduction in unicellular organisms

This article develops mathematical models describing the evolutionary dynamics of both asexually and sexually reproducing populations of diploid unicellular organisms. The asexual and sexual life cycles are based on the asexual and sexual life cycles in Saccharomyces cerevisiae, Baker’s yeast, which normally reproduces by asexual budding, but switches to sexual reproduction when stressed. The mathematical models consider three reproduction pathways: (1) Asexual reproduction, (2) self-fertilization, and (3) sexual reproduction. We also consider two forms of genome organization. In the first case, we assume that the genome consists of two multi-gene chromosomes, whereas in the second case, we consider the opposite extreme and assume that each gene defines a separate chromosome, which we call the multi-chromosome genome. These two cases are considered to explore the role that recombination has on the mutation-selection balance and the selective advantage of the various reproduction strategies. We assume that the purpose of diploidy is to provide redundancy, so that damage to a gene may be repaired using the other, presumably undamaged copy (a process known as homologous recombination repair). As a result, we assume that the fitness of the organism only depends on the number of homologous gene pairs that contain at least one functional copy of a given gene. If the organism has at least one functional copy of every gene in the genome, we assume a fitness of 1. In general, if the organism has l homologous pairs that lack a functional copy of the given gene, then the fitness of the organism is κ _l . The κ _l are assumed to be monotonically decreasing, so that κ₀ = 1 > κ₁ > κ₂ > ⋯ > κ_∞ = 0. For nearly all of the reproduction strategies we consider, we find, in the limit of large N, that the mean fitness at mutation-selection balance is max{2 e^-m-1, 0} ,\hbox{max}\{2 e^{-\mu}-1, 0\} , where N is the number of genes in the haploid set of the genome, ε is the probability that a given DNA template strand of a given gene produces a mutated daughter during replication, and μ = Nε. The only exception is the sexual reproduction pathway for the multi-chromosomed genome. Assuming a multiplicative fitness landscape where κ _l  = α ^l for α ∈ (0, 1), this strategy is found to have a mean fitness that exceeds the mean fitness of all the other strategies. Furthermore, while other reproduction strategies experience a total loss of viability due to the steady accumulation of deleterious mutations once μ exceeds ln2 ,\ln 2 , no such transition occurs in the sexual pathway. Indeed, in the limit as α → 1 for the multiplicative landscape, we can show that the mean fitness for the sexual pathway with the multi-chromosomed genome converges to e ^−2μ, which is always positive. We explicitly allow for mitotic recombination in this study, which, in contrast to previous studies using different models, does not have any advantage over other asexual reproduction strategies. The results of this article provide a basis for understanding the selective advantage of the specific meiotic pathway that is employed by sexually reproducing organisms. The results of this article also suggest an explanation for why unicellular organisms such as Saccharomyces cerevisiae (Baker’s yeast) switch to a sexual mode of reproduction when stressed. While the results of this article are based on modeling mutation-propagation in unicellular organisms, they nevertheless suggest that, in more complex organisms with significantly larger genomes, sex is necessary to prevent the loss of viability of a population due to genetic drift. Finally, and perhaps most importantly, the results of this article demonstrate a selective advantage for sexual reproduction with fewer and much less restrictive assumptions than those of previous studies.     

Genetic variation in organisms with sexual and asexual reproduction

The genetic variation in a partially asexual organism is investigated by two models suited for different time scales. Only selectively neutral variation is considered. Model 1 shows, by the use of a coalescence argument, that three sexually derived individuals per generation are sufficient to give a population the same pattern of allelic variation as found in fully sexually reproducing organisms. With less than one sexual event every third generation, the characteristic pattern expected for asexual organisms appear, with strong allelic divergence between the gene copies in individuals. At intermediary levels of sexuality, a complex situation reigns. The pair-wise allelic divergence under partial sexuality exceeds, however, always the corresponding value under full sexuality. These results apply to large populations with stable reproductive systems. In a more general framework, Model 2 shows that a small number of sexual individuals per generation is sufficient to make an apparently asexual population highly genotypically variable. The time scale in terms of generations needed to produce this effect is given by the population size and the inverse of the rate of sexuality.     

The complex genetic architecture of the metabolome

Discovering links between the genotype of an organism and its metabolite levels can increase our understanding of metabolism, its controls, and the indirect effects of metabolism on other quantitative traits. Recent technological advances in both DNA sequencing and metabolite profiling allow the use of broad-spectrum, untargeted metabolite profiling to generate phenotypic data for genome-wide association studies that investigate quantitative genetic control of metabolism within species. We conducted a genome-wide association study of natural variation in plant metabolism using the results of untargeted metabolite analyses performed on a collection of wild Arabidopsis thaliana accessions. Testing 327 metabolites against >200,000 single nucleotide polymorphisms identified numerous genotype-metabolite associations distributed non-randomly within the genome. These clusters of genotype-metabolite associations (hotspots) included regions of the A. thaliana genome previously identified as subject to recent strong positive selection (selective sweeps) and regions showing trans-linkage to these putative sweeps, suggesting that these selective forces have impacted genome-wide control of A. thaliana metabolism. Comparing the metabolic variation detected within this collection of wild accessions to a laboratory-derived population of recombinant inbred lines (derived from two of the accessions used in this study) showed that the higher level of genetic variation present within the wild accessions did not correspond to higher variance in metabolic phenotypes, suggesting that evolutionary constraints limit metabolic variation. While a major goal of genome-wide association studies is to develop catalogues of intraspecific variation, the results of multiple independent experiments performed for this study showed that the genotype-metabolite associations identified are sensitive to environmental fluctuations. Thus, studies of intraspecific variation conducted via genome-wide association will require analyses of genotype by environment interaction. Interestingly, the network structure of metabolite linkages was also sensitive to environmental differences, suggesting that key aspects of network architecture are malleable.