Evidence for an even sex allocation in haplodiploid cyclical parthenogens

Recent theoretical work has shown that haplodiploid cyclical parthenogens, such as rotifers, are expected to have an equal frequency of male‐producing and resting‐egg producing females during their sexual phase. We tested this prediction by following sexual reproduction dynamics in two laboratory populations and one field population of the rotifer Brachionus plicatilis through two growing seasons. We recorded population density, proportion of sexual females, and sex allocation (the proportion of male‐producing sexual females as a fraction of total sexual females). We found this sex allocation ratio to vary from 0.3 to 1.0 in single sampling events. However, when we computed sex allocation by using the integrated densities of both male‐producing sexual females and resting‐egg producing sexual females over time, the two laboratory populations and one of the two field growing seasons showed sex allocation ratios that did not significantly differ from the expected value of 0.5.     

Optimal rates of bisexual reproduction in cyclical parthenogens with density-dependent growth

This work explores theoretical patterns of reproduction that maximize the production of resting eggs and the long-term fitness of genotypes in cyclical parthenogens. Our focus is on density-dependent reproduction as it influences the consequences of a trade-off between producing amictic daughters – which reproduce parthenogenetically and subitaneously – and producing mictic daughters – which undergo meiosis and bisexual reproduction. Amictic females increase competitive ability and allow the population to achieve a larger size; mictic females directly contribute to population survival through harsh periods by producing resting eggs. Although morphologically indistinguishable, the two types of females differ greatly in their ecological and reproductive roles. What factors underlie the differential allocation of resources to produce amictic and mictic females? Using a demographic model based on readily accessible parameters we demonstrate the existence of a frequency of mictic females that will maximize the population's long-term fitness. This frequency, termed the optimal mictic ratio, m_o, is 1 ? (q/b)^1/2, where q is the mortality rate and b is the maximum birth rate. Using computer simulation we compared the fitness of a population with this constant mictic ratio with populations having multiple switches from complete parthenogenetic growth to complete allocation in mixis (mictic ratio either 0 or 1). Two important conclusions for optimal mixis in density-dependent growth conditions are: (1) intermediate mictic ratios are optimal, and (2) optimal mictic ratios are higher when habitat conditions are better. Physiological cues responding to differences in birth and death rates are common so that it is possible that populations may adjust their relative rates of mictic and amictic female production in response to environmentally induced changes to the optimum mictic ratio. Our analysis demonstrates that different patterns of mixis are expected in different type of habitats. Since the optimal mictic ratio is sensitive to the effects of a variety of environmental challenges, our model makes possible a new means to evaluate life history evolution in cyclical parthenogens.     

The approach to equilibrium of multilocus genotype diversity under clonal selection and cyclical parthenogenesis

Sexual generations in cyclical parthenogens are typically separated by multiple generations of clonal reproduction. In contrast to sexual reproduction, during parthenogenesis the genome of the parent is passed on to the offspring as a unit. The absence of recombination during parthenogenesis leads to differences in the action of natural selection in the two reproductive phases. In addition, since recombination is a sampling process, random genetic drift is potentially more important in sexual reproduction than in parthenogenesis. A recent development in the study of rotifer population genetics is the use of microsatellites to characterize natural populations. Microsatellites are selectively neutral, show patterns of Mendelian inheritance and tend to be much more variable than allozymes. An advantage over allozymes is that microsatellite DNA can be cloned with PCR and thus multiple loci can be assayed from a single individual. We use a new computer model in this paper to investigate the response of selectively active and selectively neutral genes to evolutionary forces during cyclical parthenogenesis. Selectively active alleles may respond differently to selection in the parthenogenetic and sexual phases of cyclical parthenogenesis. Even when strong clonal selection is acting on loci associated with adaptation, the view that emerges with microsatellites may be one of Hardy-Weinberg and linkage equilibrium. Thus studies using selectively neutral loci may fail to detect clonal selection even when it is an important feature of the rotifer population's adaptive structure.     

群体遗传结构中的基因流

群体遗传结构上的差异是遗传多样性的一种重要体现,对群体遗传结构的研究已有较久的历史,而其中的基因流研究近些年来越来越受到重视。它对群体遗传学、进化生物学、保护生物学、生态学有着极其重要的作用。虽然传统的群体遗传学能估测基因流大小,但它的精确性还有很大局限性。随着生物技术的进步,对基因流的研究逐渐向分子水平过渡,应用蛋白质电泳技术、分子标记技术(RAPD、RFLP、VNTR、ISSR、DNA测序等)方法对群体间基因流的流动水平进行了深入细致的研究。通过综述群体遗传结构的几种模式:陆岛模式、海岛模式、阶石模式、距离隔离模式、层次模式,以及在群体遗传结构的几种模式基础上的基因流的研究方法、作用、地位和近些年来研究者的研究成果,并指出了这些方法的局限性。     

Clonal diversity,clonal persistence and rapid taxon replacement in natural populations of species and hybrids of the Daphnia longispina complex

Hybridization is common among cyclical parthenogens, especially in zooplankton species assemblages of the genus Daphnia. To explore hybridization dynamics and the extent of clonal diversity in the Daphnia longispina complex, we analysed population structure in eight permanent lakes. Based on 15 microsatellite loci, three major taxonomic units emerged: two species, D. galeata and D. longispina and their F1 hybrids, supported by factorial correspondence analysis and two Bayesian methods. At the same time, the detection of backcross classes differed between methods. Mean clonal diversity was lowest in the F1 hybrids, as expected from the high rate of asexual reproduction. Within taxa, replicated genotypes were of clonal origin, but clonal lineages persisted in subsequent years in only one of three resampled lakes. In another lake, the taxon composition changed from being dominated by hybrids to complete dominance by one parental taxon. Such a year‐to‐year taxon replacement has not been reported for the D. longispina complex before. Our data on this hybrid complex illustrate that high‐resolution genotyping is essential for the understanding of ecological and evolutionary outcomes of hybridization in partially clonal taxa.     

Functional gene networks based on the gene neighborhood in metagenomes

The gene neighborhood in prokaryotic genomes has been effectively utilized in inferring co-functional networks in various organisms. Previously, such genomic context information has been sought among completely assembled prokaryotic genomes. Here, we present a method to infer functional gene networks according to the gene neighborhood in metagenome contigs, which are incompletely assembled genomic fragments. Given that the amount of metagenome sequence data has now surpassed that of completely assembled prokaryotic genomes in the public domain, we expect benefits of inferring networks by the metagenome-based gene neighborhood. We generated co-functional networks for diverse taxonomical species using metagenomics contigs derived from the human microbiome and the ocean microbiome. We found that the networks based on the metagenome gene neighborhood outperformed those based on 1748 completely assembled prokaryotic genomes. We also demonstrated that the metagenome-based gene neighborhood could predict genes related to virulence-associated phenotypes in a bacterial pathogen, indicating that metagenome-based functional links could be sufficiently predictive for some phenotypes of medical importance. Owing to the exponential growth of metagenome sequence data in public repositories, metagenome-based inference of co-functional networks will facilitate understanding of gene functions and pathways in diverse species.     

The genetics of obligate parthenogenesis in an aphid species and its consequences for the maintenance of alternative reproductive modes

Although loss of sex is widespread among metazoans, the genetic mechanisms underlying the transition to asexuality are poorly understood. Aphids are good models to address this issue because they frequently show reproductive-mode variation at the species level, involving cyclical parthenogens (CP) that reproduce sexually once a year and obligate parthenogens (OP) that reproduce asexually all year round. Here, we explore the genetic basis of OP in the cereal aphid Sitobion avenae by crossing several genotypes with contrasting reproductive modes and then characterising the reproductive phenotypes of F1 and F2 offspring. The analysis of phenotypic variation in F1 and F2 progenies suggests that at least two autosomal loci control OP in S. avenae. First, the transition to asexuality seems to depend on a single recessive locus, because the offspring from self-crossed cyclical parthenogenetic genotypes contain either 0 or 25% OP. Second, as we observed OP in the F1 progenies from crosses between CP and OP, and some CP in the offspring from outcrossed OP, a dominant ‘suppressor'' gene may also be involved, being inactive when in a recessive homozygous state in CP; this is the most parsimonious explanation for these results. This oligogenic inheritance of OP in S. avenae appears to be an efficient genetic system to generate new OP genotypes continually. It also allows asexuality-inducing alleles to be protected locally during harsh winters when extreme frost kills most OP, and then to spread very quickly after winter.     

Adaptive molecular evolution of a defence gene in sexual but not functionally asexual evening primroses

Theory predicts that sexual reproduction provides evolutionary advantages over asexual reproduction by reducing mutational load and increasing adaptive potential. Here, we test the latter prediction in the context of plant defences against pathogens because pathogens frequently reduce plant fitness and drive the evolution of plant defences. Specifically, we ask whether sexual evening primrose plant lineages (Onagraceae) have faster rates of adaptive molecular evolution and altered gene expression of a class I chitinase, a gene implicated in defence against pathogens, than functionally asexual evening primrose lineages. We found that the ratio of amino acid to silent substitutions (K(a) /K(s) = 0.19 vs. 0.11 for sexual and asexual lineages, respectively), the number of sites identified to be under positive selection (four vs. zero for sexual and asexual lineages, respectively) and the expression of chitinase were all higher in sexual than in asexual lineages. Our results are congruent with the conclusion that a loss of sexual recombination and segregation in the Onagraceae negatively affects adaptive structural and potentially regulatory evolution of a plant defence protein.     

Fine‐scale asexual and sexual reproduction in Quercus crispula var. horikawae,a stunted shrub oak,on a mountain with deep snow in central Japan

Quercus crispula var. horikawae, a stunted shrub oak, occurs on mountains with deep snow on the Sea of Japan side of Japan. This oak generates patches of multiple creeping stems. It is unclear whether these patches are the result of asexual or sexual reproduction, or both. We therefore aimed to describe the clonal structure and gene flow in Q . crispula var. horikawae on Mount Nasu in central Japan by using nuclear microsatellites. Genotypes of 331 stems with no distinct connection with roots and creeping stems above the ground were determined using nine loci in two study plots, and 64 acorns from three mother genets in a plot were determined using eight loci. The results of the clonal identification indicated that the patches consisted of 51 genets; at least 85% of the stems may have been derived from asexual reproduction through sprouting and layering. The prominence of asexual reproduction may be a result of adaptation to the snowy environment. In contrast, 15% of the ramets in the study plots probably originate via sexual reproduction by seedling regeneration. Analyses of the spatial genetic structure and paternity showed that limited ability of the pollen and seeds to disperse might result in the spatial aggregations of closely related offspring at a relatively short distance (<10 m), and inbreeding, a factor that might reduce sexual reproduction, was not observed. Thus, sexual reproduction could be reduced by ecological rather than genetic factors, namely the hindrance of seedling regeneration by the dense coverage of dwarf bamboo (Sasa) on the forest floor.     

Climate effects on life cycle variation and population genetic architecture of the black bean aphid, Aphis fabae

Aphid species may exhibit different reproductive modes ranging from cyclical to obligate parthenogenesis. The distribution of life cycle variation in aphids is generally determined by ecological forces, mainly climate, because only sexually produced diapausing eggs can survive harsh winters or periods of absence of suitable host plants. Aphids are thus interesting models to investigate intrinsic and environmental factors shaping the competition among sexual and asexual lineages. We conducted a Europe-wide sampling of black bean aphids, Aphis fabae, and combined population genetic analyses based on microsatellite data with an experimental determination of life cycle strategies. Aphids were collected from broad beans (Vicia faba) as well as some Chenopodiaceae, but we detected no genetic differentiation between aphids from different host plants. Consistent with model predictions, life cycle variation was related to climate, with aphids from areas with cold winters investing more in sexual reproduction than aphids from areas with mild winters. Accordingly, only populations from mild areas exhibited a clear genetic signature of clonal reproduction. These differences arise despite substantial gene flow over large distances, which was evident from a very low geographic population structure and a lack of isolation-by-distance among 18 sites across distances of more than 1000 km. There was virtually no genetic differentiation between aphids with different reproductive modes, suggesting that new asexual lineages are formed continuously. Indeed, a surprising number of A. fabae genotypes even from colder climates produced some parthenogenetic offspring under simulated winter conditions. From this we predict that a shift to predominantly asexual reproduction could take place rapidly under climate warming.     

Gene flow between sexual and facultatively asexual lineages of an aphid species and the maintenance of reproductive mode variation

Many organisms considered as strictly clonal may in fact experience some rare events of sexual reproduction with their sexual relatives. However, the rate of sexual–asexual gene flow has rarely been assessed mainly because its evaluation is difficult to achieve in the field. In the cyclically parthenogenetic aphid Rhopalosiphum padi , two main sets of lineages, differing in their investment in sexual reproduction and in their genetic attributes, co-exist even at a very fine scale: the 'sexual' lineages which have a full commitment to the sexual reproduction, and the 'facultatively asexual' lineages, which allocate investment in the sexual and parthenogenetic reproduction. This system offers a unique opportunity to tackle the genetic interactions between two contrasting reproductive modes. Here, we provide evidence that gene flow occurred between sexual and facultatively asexual lineages of R. padi. We carefully examined the shuffling in phenotypic and genotypic variation following a sexual reproduction event that took place in the field. Combining genotypic data and phenotypic measurements showed that this gene mixing led to the production of a wide array of reproductive modes, including strictly asexual lineages. Finally, we discuss the central role played by facultatively asexual lineages on the maintenance of reproductive mode variation.     

Suppressive action of Samorin on the cyclical development of pathogenic trypanosomes in Glossina morsitans centralis

Male Glossina sexually sterilized by gamma-irradiation are as efficient vectors of trypanosomiasis as fertile males. An attempt was made, using isometamidium chloride (Samorin), to interfere with the cyclical development of trypanosomes in sterile males, destined for use in the sterile insect release (SIR) method of tsetse eradication. The infection rate with mature Trypanosoma congolense Broden was effectively reduced in sterile male Glossina morsitans centralis Machado, when the flies were fed on an infected goat 2 days after they were fed as tenerals on an in vitro bloodmeal containing 8 micrograms Samorin/ml blood. The infection rates with mature T.vivax Ziemann and T.brucei brucei Plimmer & Bradford were completely suppressed at this drug dose. Whensterile teneral males were fed on a bloodmeal containing 12 micrograms/ml Samorin and given the infected bloodmeal 10 days later, infections by mature T.vivax, T.congolense and T.b.brucei were completely suppressed. Hence in the management of a tsetse eradication programme utilizing the SIR method, it is recommended that the sterile teneral male tsetse should, prior to release, be given a bloodmeal containing Samorin at 12-15 micrograms/ml blood. This will effectively suppress future disease transmission.     

Population genetic structure of wild rice Oryza glumaepatula distributed in the Amazon flood area influenced by its life-history traits

Wild plant species develop their own way of living to adapt to the specific environment of their habitats. Their life-history traits strongly affect the genetic structure of the population. The wild species Oryza glumaepatula Steud. growing in the Amazon basin seems to have characteristic life-history traits suited for the flood condition. At the vegetative growth stage, the culms frequently break at internodes. With no roots anchoring on the ground, plant bodies floating in the water move downriver by water current and wind. To examine the association between the life-history traits and genetic population structure of Amazonian O. glumaepatula , we analysed allozyme variability at 29 loci of 16 enzymes using 37 populations from five regions. Allozymes were not so variable (total gene diversity H _E = 0.044) compared with Asian wild rice, O. rufipogon Griff. The bottleneck effect and rare opportunity of interspecies gene flow may prevent the development of allozyme variability. Population genotypes tended to be differentiated among geographically isolated regions. Observed heterozygosities were much lower than expected heterozygosities, or gene diversity ( H _O = 0.003 for whole population) and F _IS over polymorphic loci was 0.931, indicating that O. glumaepatula has developed an inbreeding system. But, the intrapopulation gene diversity ( H _S) was higher than interpopulation gene diversity ( D _ST), as generally observed in outbreeding populations. The migration ability of O. glumaepatula makes long-distance seed dispersal possible. This might have led to frequent gene flow among populations.     

Effects of forest plantations on the genetic composition of conspecific native Aleppo pine populations

Afforestation is a common and widespread management practice throughout the world, yet its implications for the genetic diversity of native populations are still poorly understood. We examined the effect of Aleppo pine (Pinus halepensis) plantations on the genetic composition of nearby conspecific native populations. We focused on two native populations in Israel with different levels of isolation from the surrounding plantations and compared the genetic diversity of naturally established young trees within the native populations with that of local native adults, using nine nuclear microsatellite markers. We found that the genetic composition of the recruits was significantly different from that of local adults in both populations, with allelic frequency changes between generations that could not be ascribed to random drift, but rather to substantial gene flow from the surrounding planted Aleppo pine populations. The more isolated population experienced a lower gene-flow level (22%) than the less isolated population (49%). The genetic divergence between native populations at the adult-tree stage (F(st) = 0.32) was more than twice as high as that of the young trees naturally established around native adults (F(st) = 0.15). Our findings provide evidence for a rapid genetic homogenization process of native populations following the massive planting efforts in the last decades. These findings have important implications for forest management and nature conservation and constitute a warning sign for the risk of translocation of biota for local biodiversity.     

Estimation of effective population size in continuously distributed populations: there goes the neighborhood

Use of genetic methods to estimate effective population size (N_e) is rapidly increasing, but all approaches make simplifying assumptions unlikely to be met in real populations. In particular, all assume a single, unstructured population, and none has been evaluated for use with continuously distributed species. We simulated continuous populations with local mating structure, as envisioned by Wright''s concept of neighborhood size (NS), and evaluated performance of a single-sample estimator based on linkage disequilibrium (LD), which provides an estimate of the effective number of parents that produced the sample (N_b). Results illustrate the interacting effects of two phenomena, drift and mixture, that contribute to LD. Samples from areas equal to or smaller than a breeding window produced estimates close to the NS. As the sampling window increased in size to encompass multiple genetic neighborhoods, mixture LD from a two-locus Wahlund effect overwhelmed the reduction in drift LD from incorporating offspring from more parents. As a consequence, never approached the global N_e, even when the geographic scale of sampling was large. Results indicate that caution is needed in applying standard methods for estimating effective size to continuously distributed populations.     

Effects of low dissolved oxygen on survival and asexual reproduction of scyphozoan polyps (Chrysaora quinquecirrha)

Hypoxic conditions are common in many coastal environments such as Chesapeake Bay. While medusae appear to be quite tolerant of low dissolved oxygen (DO) concentrations, the effects of hypoxia on the benthic polyp stages are unknown. Chrysaora quinquecirrha (DeSor) polyps, and were subjected to 5 DO treatments (air-saturated [control], 3.5, 2.5, 1.5 and 0.5 mg l^–1) in the laboratory. Polyp survival and development were documented over 24 d. Virtually no mortality occurred in any treatment during the first 5 d. Total polyp mortality after 24 d was 59.3% at the lowest DO concentration, whereas <3% mortality was observed in the air-saturated treatment. Formation of stolons and strobilae occurred in all treatments, however, the proportions of polyps undergoing stolonation and strobilation were significantly greater in all DO concentrations above 0.5 mg l^–1. Polyp encystment was not observed in any treatment over the course of the 24 d experiment. These results indicate that polyps can survive and asexually propagate even during prolonged exposure to hypoxic conditions.     

Impact of habitat fragmentation on the genetics of populations in dendritic landscapes

1. The effect of habitat fragmentation on freshwater species has been addressed using brown trout Salmo trutta L. as a model species with a dendritic population structure. 2. Microsatellite loci were employed as molecular markers. Levels of gene flow and population subdivision were determined in more than 1200 brown trout individuals inhabiting four south European rivers with contrasting patterns of fragmentation, defined by the presence of barriers. 3. The genetic units in the four rivers were restricted by artificial barriers, and gene flow among samples within each river was associated with the level of fragmentation of the river. 4. Loss of genetic diversity and dislocation of the dendritic model have been detected in fragmented rivers. These results emphasise the importance of mitigating the impact of dams by constructing passages to restore gene flow along the river, for fish and other migratory species, as well as the need for caution in relation to stocking in isolated areas to avoid problems of inbreeding.