Models of experimental evolution: the role of genetic chance and selective necessity

We present a theoretical framework within which to analyze the results of experimental evolution. Rapidly evolving organisms such as viruses, bacteria, and protozoa can be induced to adapt to laboratory conditions on very short human time scales. Artificial adaptive radiation is characterized by a list of common observations; we offer a framework in which many of these repeated questions and patterns can be characterized analytically. We allow for stochasticity by including rare mutations and bottleneck effects, demonstrating how these increase variability in the evolutionary trajectory. When the product Np, the population size times the per locus error rate, is small, the rate of evolution is limited by the chance occurrence of beneficial mutations; when Np is large and selective pressure is strong, the rate-limiting step is the waiting time while existing beneficial mutations sweep through the population. We derive the rate of divergence (substitution rate) and rate of fitness increase for the case when Np is large and illustrate our approach with an application to an experimental data set. A minimal assumption of independent additive fitness contributions provides a good fit to the experimental evolution of the bacteriophage phiX174.     

Evaluating the fitness consequences of plasticity in tolerance to pesticides

In a rapidly changing world, phenotypic plasticity may be a critical mechanism allowing populations to rapidly acclimate when faced with novel anthropogenic stressors. Theory predicts that if exposure to anthropogenic stress is heterogeneous, plasticity should be maintained as it allows organisms to avoid unnecessary expression of costly traits (i.e., phenotypic costs) when stressors are absent. Conversely, if exposure to stressors becomes constant, costs or limits of plasticity may lead to evolutionary trait canalization (i.e., genetic assimilation). While these concepts are well‐established in theory, few studies have examined whether these factors explain patterns of plasticity in natural populations facing anthropogenic stress. Using wild populations of wood frogs that vary in plasticity in tolerance to pesticides, the goal of this study was to evaluate the environmental conditions under which plasticity is expected to be advantageous or detrimental. We found that when pesticides were absent, more plastic populations exhibited lower pesticide tolerance and were more fit than less plastic populations, likely avoiding the cost of expressing high tolerance when it was not necessary. Contrary to our predictions, when pesticides were present, more plastic populations were as fit as less plastic populations, showing no signs of costs or limits of plasticity. Amidst unprecedented global change, understanding the factors shaping the evolution of plasticity will become increasingly important.     

Ecological consequences of genetic diversity

Understanding the ecological consequences of biodiversity is a fundamental challenge. Research on a key component of biodiversity, genetic diversity, has traditionally focused on its importance in evolutionary processes, but classical studies in evolutionary biology, agronomy and conservation biology indicate that genetic diversity might also have important ecological effects. Our review of the literature reveals significant effects of genetic diversity on ecological processes such as primary productivity, population recovery from disturbance, interspecific competition, community structure, and fluxes of energy and nutrients. Thus, genetic diversity can have important ecological consequences at the population, community and ecosystem levels, and in some cases the effects are comparable in magnitude to the effects of species diversity. However, it is not clear how widely these results apply in nature, as studies to date have been biased towards manipulations of plant clonal diversity, and little is known about the relative importance of genetic diversity vs. other factors that influence ecological processes of interest. Future studies should focus not only on documenting the presence of genetic diversity effects but also on identifying underlying mechanisms and predicting when such effects are likely to occur in nature.     

Pollinating fig wasps: genetic consequences of island recolonization

The levels of genetic diversity and gene flow may influence the long-term persistence of populations. Using microsatellite markers, we investigated genetic diversity and genetic differentiation in island (Krakatau archipelago, Indonesia) and mainland (Java and Sumatra, Indonesia) populations of Liporrhopalum tentacularis and Ceratosolen bisulcatus, the fig wasp pollinators of two dioecious Ficus (fig tree) species. Genetic diversity in Krakatau archipelago populations was similar to that found on the mainland. Population differentiation between mainland coastal sites and the Krakatau islands was weak in both wasp species, indicating that the intervening 40 km across open sea may not be a barrier for wasp gene flow (dispersal) and colonization of the islands. Surprisingly, mainland populations of the fig waSPS may be more genetically isolated than the islands, as gene flow between populations on the Javan mainland differed between the two wasp species. Contrasting growth forms and relative 'immunity' to the effects of deforestation in their host fig trees may account for these differences.     

Evaluation of the genetic activity profiles of 65 pesticides

We have previously reported the qualitative results of a major study on 65 pesticides (Waters et al., 1982). Dose information from this investigation (either lowest effective or highest ineffective dose tested) has now been incorporated into a computerized data management system. This report focuses on the qualitative profiles of genetic activity produced by these pesticides and our efforts to classify them according to their genotoxic effects and chemical structures. Three main categories may be distinguished based on the qualitative results: Category 1 pesticides were active in most of the in vitro and in vivo assays employed. These 9 compounds include the structurally similar organophosphate insecticides, acephate, demeton, monocrotophos and trichlorfon; the phthalimide fungicide analogues, captan and folpet; and the thiocarbamate herbicide analogues, diallate, sulfallate and triallate. The 26 Category 2 compounds demonstrated fewer positive results and may be subdivided into two parts, one of which contains 12 halogenated aromatic or heterocyclic ring compounds, including the phenoxy herbicides, 2,4-D, 2,4-DB and 2,4,5-T. The remaining part of Category 2 (14 compounds) consists of structurally similar organophosphate insecticides, azinphos-methyl, crotoxyphos, disulfoton, methyl parathion; three similar ethylenebisdithiocarbamate fungicides, maneb, mancozeb, and zineb; three similar pyrethroid insecticides, allethrin, chrysanthemic acid, and ethyl chrysanthemate; and four structurally diverse compounds, cacodylic acid, dinoseb, sec.-butylamine and benomyl. The third category of 30 pesticides gave negative results in all tests and represents structurally diverse compounds. Using the computerized profile matching methodology, from 2080 possible pairwise chemical combinations of the 65 pesticides, 20 statistically significant pairs were selected, 6 groups of pesticides were identified which were substantially similar to groups of pesticides we had formed previously (Waters et al., 1982) based on genetic activity and chemical structure. The matches showed excellent qualitative and, in most cases, excellent quantitative agreement. Hence it appears that specific patterns of test results present in the genetic activity profiles are related directly to chemical structure. Conversely, the data suggests that certain groups of compounds may be recognized by a well defined series of concordant tests results. As additional data is added, comparison of test results for new chemicals with existing data for known genotoxicants should aid in the evaluation of potential genetic health hazards.     

Approaches to genetic control for the use of pesticides

Analysis of data available in literature has shown that 65% of 400 pesticides studied for their mutagenicity exert a mutagenic effect on any test-object. The number of revealed mutagens approaches 100% when four or more test-objects are used. Recommendations for quantitative estimation of genetic risk worked out under conditions of model experiments with standard mutagens are not available for pesticides since they are slight mutagens. The necessity for genetic stage-by-stage monitoring of pesticide use is substantiated. This monitoring should be carried out at the stage of experimental studies by means of classifications by the degree of potential mutagenic danger (the method is described) and at the stage of ecological and genetic investigations--by means of the regulation for application with due regard for the summary mutagenic background.     

The nature and reality of the aphid clone: genetic variation, adaptation and evolution

1 When aphid clones and clonality are discussed, it is still often said that they are ‘genetically identical’, a statement for which there is no direct evidence, and certainly not for the entire genome. By contrast, there is a growing body of empirical data from the application of high resolution molecular (DNA) markers that aphid asexual lineages rapidly mutate and that, in some documented cases, this variation is selectable, either positively or negatively. 2 Although it is true that, in enclosed conditions (e.g. laboratory or field cage), a so‐called clone as defined as the asexual progeny of a single foundress may be traceable, this is rarely if ever possible in the field without the use of genetic markers, and even then, usually only at a relatively few loci (multilocus genotypes, ‘MLGs’). 3 The continued use of the term clone without qualification of its true nature and the reality of its interesting biology is likely to hamper a proper understanding of the ecology and evolution of these insects (which are interesting in their own right because of their complex life histories, but also because they are important as major pests globally, both by causing direct feeding damage and by transmitting pathogenic plant viruses and thereby leading to huge economic losses in the agricultural, horticultural and forestry industries). 4 In this short review, I provide evidence of what is now known about aphid clonality after the widespread use of molecular markers, comprising information mainly gained within the last 15 years or so. 5 The data demonstrate widespread adaptation and evolution, sometimes involving introgression and hybridization. Because of this new knowledge, our ideas of what constitutes a clone are in need of serious re‐evaluation.     

Evolutionary consequences of indirect genetic effects

Indirect genetic effects (IGEs) are environmental influences on the phenotype of one individual that are due to the expression of genes in a different, conspecific, individual. Historically, work has focused on the influence of parents on offspring but recent advances have extended this perspective to interactions among other relatives and even unrelated individuals. IGEs lead to complicated pathways of inheritance, where environmental sources of variation can be transmitted across generations and therefore contribute to evolutionary change. The existence of IGEs alters the genotype-phenotype relationship, changing the evolutionary process in some dramatic and non-intuitive ways.     

杂交产生的遗传危害--以植物为例

杂交是自然界的普遍现象,并在农林业生产中发挥着重要作用,但如不注意亦会带来遗传危害。当把两个遗传差异较大的物种（种群）混植在一起时,我们要考虑远交衰退的危害,即杂交破坏了亲代具有的共适应等位基因组合,导致杂交后代适应性的降低;当杂交发生在两亲本个体（或花粉）数量悬殊时,我们就要考虑遗传同化的危害,即小种群一方由于产生自己“纯”后代数量的减少而被前者“稀释”掉,导致小种群遗传特异性丧失或灭绝。另外,当杂交体具有杂种优势时,它可取代亲本,威胁到亲本的生存;如果有害物种（种群）由渐渗杂交获得某种优良性状（抗病、抗药、抗逆性等）时,可能失去控制,造成生态危害。针对杂交在这几个方面潜在的遗传危害,本文在濒危物种的迁地和就地保护、生态恢复中的种源选择等方面提出相应的建议和措施。     

The alluring simplicity and complex reality of genetic rescue

A series of important new theoretical, experimental and observational studies demonstrate that just a few immigrants can have positive immediate impacts on the evolutionary trajectory of local populations. In many cases, a low level of immigration into small populations has produced fitness benefits that are greater than those predicted by theoretical models, resulting in what has been termed 'genetic rescue'. However, the opposite result (reduced fitness) can also be associated with immigration of genetically divergent individuals. Central to our understanding of genetic rescue are complex interactions among fundamental concepts in evolutionary and population biology, including both genetic and non-genetic (environmental, behavioral and demographic) factors. Developing testable models to predict when genetic rescue is likely to occur is a daunting challenge that will require carefully controlled, multi-generation experiments as well as creative use of information from natural 'experiments'.     

Loss of genetic variability in social spiders: genetic and phylogenetic consequences of population subdivision and inbreeding

The consequences of population subdivision and inbreeding have been studied in many organisms, particularly in plants. However, most studies focus on the short‐term consequences, such as inbreeding depression. To investigate the consequences of both population fragmentation and inbreeding for genetic variability in the longer term, we here make use of a natural inbreeding experiment in spiders, where sociality and accompanying population subdivision and inbreeding have evolved repeatedly. We use mitochondrial and nuclear data to infer phylogenetic relationships among 170 individuals of Anelosimus spiders representing 23 species. We then compare relative mitochondrial and nuclear genetic variability of the inbred social species and their outbred relatives. We focus on four independently derived social species and four subsocial species, including two outbred–inbred sister species pairs. We find that social species have 50% reduced mitochondrial sequence divergence. As inbreeding is not expected to reduce genetic variability in the maternally inherited mitochondrial genome, this suggests the loss of variation due to strong population subdivision, founder effects, small effective population sizes (colonies as individuals) and lineage turnover. Social species have < 10% of the nuclear genetic variability of the outbred species, also suggesting the loss of genetic variability through founder effects and/or inbreeding. Inbred sociality hence may result in reduction in variability through various processes. Sociality in most Anelosimus species probably arose relatively recently (0.1–2 mya), with even the oldest social lineages having failed to diversify. This is consistent with the hypothesis that inbred spider sociality represents an evolutionary dead end. Heterosis underlies a species potential to respond to environmental change and/or disease. Inbreeding and loss of genetic variability may thus limit diversification in social Anelosimus lineages and similarly pose a threat to many wild populations subject to habitat fragmentation or reduced population sizes.     

Evolutionary genetic consequences of facultative sex and outcrossing

Explaining the selective forces that underlie different reproductive modes forms a major part of evolution research. Many organisms are facultative sexuals, with the ability to reproduce both sexually and asexually. Reduced sequencing costs means it is now possible to start investigating genome sequences of a wider number of these organisms in depth, but teasing apart the genetic forces underlying the maintenance of facultative sexual reproduction remains a challenge. An analogous problem exists when determining the genetic consequences of a degree of outcrossing (and recombination) in otherwise self‐fertilizing organisms. Here, I provide an overview of existing research on the evolutionary basis behind different reproductive modes, with a focus on explaining the population genetic effects favouring low outcrossing rates in either partially selfing or asexual species. I review the outcomes that both self‐fertilization and asexuality have on either purging deleterious mutations or fixing beneficial alleles, and what empirical data exist to support these theories. In particular, a greater application of mathematical models to genomic data has provided insight into the numerous effects that transitions to self‐fertilization from outcrossing have on genetic architecture. Similar modelling approaches could be used to determine the forces shaping genetic diversity of facultative sexual species. Hence, a further unification of mathematical models with next‐generation sequence data will prove important in exploring the genetic influences on reproductive system evolution.     

Assessing the genetic consequences of flower-harvesting in Rhododendron decorum Franchet (Ericaceae) using microsatellite markers

Rhododendron decorum is widely distributed shrub in southwest China, and its flower is a favorite food of the local people. To investigate the impacts of harvesting, we genotyped 8 nuclear microsatellite loci in a total of 247 individuals from 10 natural populations and 4 flower-harvesting populations. No significant differences in allelic richness, effective number of alleles, private allelic richness, heterozygosity and effective population size were found among the natural and flower-harvesting populations. Differentiation between the 14 populations is relatively low (F_ST = 0.107). R. decorum showed high levels of intra-population genetic diversity. AMOVA analysis indicated that over 89% of the variation was contained within the populations, and that only 0.47% of the variation was attributed by human harvesting practices. Cluster analysis revealed two basic clusters related to the plants' geographical locations. Our results indicate that historical flower-harvesting practices do not lead to loss of genetic variation in R. decorum.     

High genetic diversity in the remnant island population of hihi and the genetic consequences of re-introduction

The maintenance of genetic diversity is thought to be fundamental for the conservation of threatened species. It is therefore important to understand how genetic diversity is affected by the re-introduction of threatened species. We use establishment history and genetic data from the remnant and re-introduced populations of a New Zealand endemic bird, the hihi Notiomystis cincta, to understand genetic diversity loss and quantify the genetic effects of re-introduction. Our data do not support any recent bottleneck events in the remnant population. Furthermore, all genetic diversity measures indicate the remnant hihi population has retained high levels of genetic diversity relative to other New Zealand avifauna with similar histories of decline. Genetic diversity (N(A) , alleles per locus, allelic richness, F(IS) and H(S) ) did not significantly decrease in new hihi populations founded through re-introduction when compared to their source populations, except in the Kapiti Island population (allelic richness and H(S) ) which had very slow post-re-introduction population growth. The N(e) /N(c) ratio in the remnant population was high, but decreased in first-level re-introductions, which together with significant genetic differentiation between populations (F(ST) & Fisher's exact tests) suggest that extant populations are diverging as a result of founder effects and drift. Importantly, simulations of future allele loss predict that the number of alleles lost will be higher in populations with a slow population growth, fewer founding individuals and with nonrandom mating. Interestingly, this species has very high levels of extra-pair paternity which may reduce reproductive variance by allowing social and floater males to reproduce a life history trait that together with a large remnant population size may help maintain higher levels of genetic diversity than expected.     

Hybrid wheat: quantitative genetic parameters and consequences for the design of breeding programs

Key message

Commercial heterosis for grain yield is present in hybrid wheat but long-term competiveness of hybrid versus line breeding depends on the development of heterotic groups to improve hybrid prediction.

Abstract

Detailed knowledge of the amount of heterosis and quantitative genetic parameters are of paramount importance to assess the potential of hybrid breeding. Our objectives were to (1) examine the extent of midparent, better-parent and commercial heterosis in a vast population of 1,604 wheat (Triticum aestivum L.) hybrids and their parental elite inbred lines and (2) discuss the consequences of relevant quantitative parameters for the design of hybrid wheat breeding programs. Fifteen male lines were crossed in a factorial mating design with 120 female lines, resulting in 1,604 of the 1,800 potential single-cross hybrid combinations. The hybrids, their parents, and ten commercial wheat varieties were evaluated in multi-location field experiments for grain yield, plant height, heading time and susceptibility to frost, lodging, septoria tritici blotch, yellow rust, leaf rust, and powdery mildew at up to five locations. We observed that hybrids were superior to the mean of their parents for grain yield (10.7 %) and susceptibility to frost (?7.2 %), leaf rust (?8.4 %) and septoria tritici blotch (?9.3 %). Moreover, 69 hybrids significantly (P < 0.05) outyielded the best commercial inbred line variety underlining the potential of hybrid wheat breeding. The estimated quantitative genetic parameters suggest that the establishment of reciprocal recurrent selection programs is pivotal for a successful long-term hybrid wheat breeding.     

Development and evolution of insect pigmentation: genetic mechanisms and the potential consequences of pleiotropy

Insect pigmentation is a premier model system in evolutionary and developmental biology. It has been at the heart of classical studies as well as recent breakthroughs. In insects, pigments are produced by epidermal cells through a developmental process that includes pigment patterning and synthesis. Many aspects of this process also impact other phenotypes, including behavior and immunity. This review discusses recent work on the development and evolution of insect pigmentation, with a focus on pleiotropy and its effects on color pattern diversification.     

Bistable responses in bacterial genetic networks: designs and dynamical consequences

A key property of living cells is their ability to react to stimuli with specific biochemical responses. These responses can be understood through the dynamics of underlying biochemical and genetic networks. Evolutionary design principles have been well studied in networks that display graded responses, with a continuous relationship between input signal and system output. Alternatively, biochemical networks can exhibit bistable responses so that over a range of signals the network possesses two stable steady states. In this review, we discuss several conceptual examples illustrating network designs that can result in a bistable response of the biochemical network. Next, we examine manifestations of these designs in bacterial master-regulatory genetic circuits. In particular, we discuss mechanisms and dynamic consequences of bistability in three circuits: two-component systems, sigma-factor networks, and a multistep phosphorelay. Analyzing these examples allows us to expand our knowledge of evolutionary design principles networks with bistable responses.     

Genomic conflict in scale insects: the causes and consequences of bizarre genetic systems

It is now clear that mechanisms of sex determination are extraordinarily labile, with considerable variation across all taxonomic levels. This variation is often expressed through differences in the genetic system (XX‐XY, XX‐XO, haplodiploidy, and so on). Why there is so much variation in such a seemingly fundamental process has attracted much attention, with recent ideas concentrating on the possible role of genomic conflicts of interest. Here we consider the role of inter‐ and intra‐genomic conflicts in one large insect taxon: the scale insects. Scale insects exhibit a dizzying array of genetic systems, and their biology promotes conflicts of interest over transmission and sex ratio between male‐ and female‐expressed genes, parental‐ and offspring‐expressed genes (both examples of intra‐genomic conflict) and between scale insects and their endosymbionts (inter‐genomic conflict). We first review the wide range of genetic systems found in scale insects and the possible evolutionary transitions between them. We then outline the theoretical opportunities for genomic conflicts in this group and how these might influence sex determination and sex ratio. We then consider the evidence for these conflicts in the evolution of sex determination in scale insects. Importantly, the evolution of novel genetic systems in scale insects has itself helped create new conflicts of interest, for instance over sex ratio. As a result, a major obstacle to our understanding of the role of conflict in the evolution of sex‐determination and genetic systems will be the difficulty in identifying the direction of causal relationships. We conclude by outlining possible experimental and comparative approaches to test more effectively how important genomic conflicts have been.     

Intratetrad mating and its genetic and evolutionary consequences

Genetic characteristics of intratetrad mating, i.e., fusion of haploid products of one meiotic division, are considered. Upon intratetrad mating, the probability of homozygotization is lower than that upon self-fertilization, while heterozygosity at genes linked to the mating-type locus, which determines the possibility of cell fusion, is preserved. If the mating-type locus is linked to the centromere, the genome regions adjoining the centromeres of all chromosomes remain heterozygous. Intratetrad mating is characteristic of a number of fungi (Saccharomyces cerevisiae, Saccharomycodes ludwigii, Neurospora tetrasperma, Agaricus bisporus, Microbotrium violaceum, and others). Parthenogenetic reproduction in some insects also involves this type of fusion of nuclei. Intratetrad mating leads to the accumulation of haplolethals (i.e., lethals manifesting in haploid cells but not hindering their mating) in pericentric chromosome regions. Since heterozygosity increases viability of an organism, recombination has been suppressed during evolution in fungi characterized by intratetrad mating, which ensures heterozygosity of the most part of the genome.     

Intratetrad mating and its genetic and evolutionary consequences

Genetic characteristics of intratetrad mating, i.e., fusion of haploid products of one meiotic division, are considered. Upon intratetrad mating, the probability of homozygotization is lower than that upon self-fertilization, while heterozygosity at genes linked to the mating-type locus, which determines the possibility of cell fusion, is preserved. If the mating-type locus is linked to the centromere, the genome regions adjoining the centromeres of all chromosomes remain heterozygous. Intratetrad mating is characteristic of a number of fungi (Saccharomyces cerevisiae, Saccharomycodes ludwigii, Neurospora tetrasperma, Agaricus bisporus, Microbotryum violaceum, and others). Parthenogenetic reproduction in some insects also involves this type of fusion of nuclei. Intratetrad mating leads to the accumulation of haplolethals (i.e., lethals manifesting in haploid cells but not hindering their mating) in pericentric chromosome regions. Since heterozygosity increases viability of an organism, recombination has been suppressed during evolution in fungi characterized by intratetrad mating, which ensures heterozygosity of the most part of the genome.__________Translated from Genetika, Vol. 41, No. 4, 2005, pp. 508–519.Original Russian Text Copyright © 2005 by Zakharov.