Intracolonial genetic variation in the scleractinian coral Seriatopora hystrix

In recent years, increasing numbers of studies revealed intraorganismal genetic variation, primarily in modular organisms like plants or colonial marine invertebrates. Two underlying mechanisms are distinguished: Mosaicism is caused by somatic mutation, whereas chimerism originates from allogeneic fusion. We investigated the occurrence of intracolonial genetic variation at microsatellite loci in five natural populations of the scleractinian coral Seriatopora hystrix on the Great Barrier Reef. This coral is a widely distributed, brooding species that is at present a target of intensive population genetic research on reproduction and dispersal patterns. From each of 155 S. hystrix colonies, either two or three samples were genotyped at five or six loci. Twenty-seven (~17%) genetically heterogeneous colonies were found. Statistical analyses indicated the occurrence of both mosaicism and chimerism. In most cases, intracolonial variation was found only at a single allele. Our analyses suggest that somatic mutations present a major source of genetic heterogeneity within a single colony. Moreover, we observed large, apparently stable chimeric colonies that harbored clearly distinct genotypes and contrast these findings with the patterns typically observed in laboratory-based experiments. We discuss the error that mosaicism and chimerism introduce into population genetic analyses.     

Genetic mosaics of ecosystem functioning across aspen-dominated landscapes

Genetic diversity is the foundation of all biodiversity, and the genetic variation within species is increasingly recognized as being important to ecosystem level processes. Recent research demonstrates that plant genotype influences above- and belowground communities as well as basic ecosystem functions. However, the extent to which plant genotypes create spatial mosaics of genetically mediated ecosystem processes in natural forests is uncertain. We use Populus tremuloides as a model system to demonstrate the importance of plant genotype on carbon and nitrogen cycling in natural systems. We identified 24 distinct P. tremuloides clones with multiple ramets across 25 km² in southern Wisconsin, United States, using microsatellite makers. We then sampled clone leaf chemistry and belowground nutrient content and microbial extracellular enzyme activity. Aspen-induced variation in belowground carbon and nitrogen content, and microbial activity, varied widely among clones. Variation in green leaf chemistry and belowground microbial activity were correlated with genetic distance among clones, such that more genetically distant clones created more divergent patches of ecosystem processes. These data suggest that aspen genotypes create spatial mosaics of genetically mediated ecosystem functioning across natural landscapes and can therefore have evolutionary consequences for co-occurring species.     

Fine-scale genetic structure of grape phylloxera from the roots and leaves of Vitis

Patterns of variation at microsatellite loci suggest that root populations of the pest grape phylloxera (Daktulosphaira vitifoliae) are largely parthenogenetic in Australian vineyards. To investigate reproduction in leaf galling phylloxera and the association between these individuals and phylloxera on roots, we examined in detail genetic variation in phylloxera from a vineyard block. Some genotypes found on leaf galls within this block were not present on roots, whereas others spanned both zones. There was no evidence that genotypes on roots were the product of sexual reproduction in leaf galls. mtDNA variation was not associated with the location of the phylloxera clones. The spatial distribution of genotypes within a root population was further investigated by intensively sampling phylloxera from another vineyard block. Join-count spatial autocorrelation statistics were used to explore fine-scale spatial structure. Clones were nonrandomly distributed within the block and there was evidence that the distribution of clones followed rows. These findings suggest firstly that there is limited dispersal of root and leaf feeding phylloxera, and secondly that factors, other than vine host, are likely to be important and contribute to clonal structure within populations.     

Life cycle of Chattonella marina (Raphidophyceae) inferred from analysis of microsatellite marker genotypes

Red tides of Chattonella spp. have caused continuous damage to Japanese aquaculture, however, the life cycle of this organism remains incompletely understood. To further investigate this matter, we assessed genotypes at 14 microsatellite markers in three varieties of Chattonella marina, viz., C. marina var. antiqua, C. marina var. marina, and C. marina var. ovata, to establish whether Chattonella undergoes asexual diploidization or sexual reproduction. After genotyping 287 strains of C. marina, all but one of these strains was shown to be heterozygous for at least some loci, and thus, in the diploid state, suggesting that Chattonella strains undergo sexual reproduction. In addition, we performed single‐cell amplification on ‘small cells’ that are derived from vegetative cells under dark and low‐nutrient conditions. The results indicated the existence of two types of small cells. The ‘Small cell Type 1’ was found to be heterozygous, genotypically equivalent to the vegetative cells, and is therefore diploid. These small cells may change to resting cells (cysts) directly. The ‘Small cell Type 2’ was homozygous at all analyzed loci, suggesting that these small cells are haploid and may be derived by meiosis. As fusion between small cells has previously been observed, the ‘Small cell Type 2’ may be the gamete of Chattonella. We present a construct of the full life cycle of Chattonella marina based on our own and previous results.     

Genotyping the clonal structure of a gorgonian coral, Junceella juncea (Anthozoa: Octocorallia), using microsatellite loci

The identification of different clones is fundamental to the study of population structure among organisms with mixed reproductive modes such as cnidarians. However, due to the low genetic variation of coral mtDNA and contamination by zooxanthellate DNA, very few molecular markers are available for studying the clonal structure of cnidarians. Herein we used four polymorphic loci of microsatellite DNA isolated from a zooxanthellae-free octocoral, Junceella juncea, to study its clonal structure in seven populations collected from three localities in Taiwan. In total, 40 multilocus genotypes were found among 152 colonies, and the number of genotypes (clones) identified in the seven populations ranged from 2 to 16. Each of the 40 multilocus genotypes was restricted to a single population, even where adjacent populations were only 100 m distant. The ratio of observed to expected genotypic diversity (G_o:G_e) ranged from 0.217 to 0.650, and G_o showed a significant departure from G_e (p<0.05) at each site indicating that asexual fragmentation may play a major role in the maintenance of established populations. Mean relatedness (R) values showed that genotypes within reefs were more closely related than those between regions. The results indicate that microsatellites are useful for discerning the clonal structures among and within populations at different spatial scales. Electronic supplement: Unique multilocus genotypes (clones) revealed by 4 polymorphic loci for Junceella juncea colonies collected from Xiashuijui (Reefs A, B, C, Transplant, Transect), Nanwan and Shicheng     

The components of life-history traits variation in Daphnia magna population

The variation of six growth and reproduction traits in the parthenogenetic clones of Daphnia magna and its relationships with the genotypes at 5 isozyme loci were studied under controlled conditions at three food concentrations. A significant genetic component of age at maturity, growth rate and fecundity variation was detected. Nested ANOVA revealed the influences of the genotypes of the isozyme loci, that are more pronounced at the high food concentration. In some cases the genotype-environment interactions were found.The variation of body length at 6 days and total number of offspring includes a significant heterozygosity — environment interaction. The most heterozygous clones show the least differences in life history traits between food conditions.Life-history traits heritability, genotype-environment interactions and different reproductive strategies of the clones are discussed.     

ALLOZYMIC VARIATION IN LOCAL APOMICTIC POPULATIONS OF LEMNA MINOR (LEMNACEAE)

Flowering occurrence and allozymic variation were studied in eight local populations of Lemna minor in eastern Ontario, Canada. After 2 years of survey, not a single flower was observed. This absence of flowering suggests the possibility of loss of sexual reproduction. This may have had no net adverse effect on fitness given the simple life history and prolific vegetative propagation in L. minor. However, the absence of sexual reproduction may limit genotypic diversity. The allozymic analysis detected 18 loci from 13 enzyme systems. Large deviations from Hardy-Weinberg equilibrium were common because of an excess of homozygotes for several enzyme systems. The genotypic diversity within these eight populations had a mean D value of 0.973 with an average number of genotypes per population of 19.6. These results suggest that genotypic diversity within these populations is not severely limited by the rarity of sexual reproduction. The mean genotypic distance index (D₁₄ = 0.801) suggests a high degree of differentiation between populations. The mean number of populations per genotype was 1.78. Using a Mantel test, the genotypic distance matrix was not significantly related to the population-to-population distance matrix (t = -0.161, P = 0.413). Although rare events of sexual reproduction may help maintain genetic variation, somatic mutations and multiple origins of clones may be important factors maintaining genetic diversity both within and between populations of L. minor.     

Patterns, sources and ecological implications of clonal diversity in apomictic Ranunculus carpaticola (Ranunculus auricomus complex, Ranunculaceae)

Sources and implications of genetic diversity in agamic complexes are still under debate. Population studies (amplified fragment length polymorphisms, microsatellites) and karyological methods (Feulgen DNA image densitometry and flow cytometry) were employed for characterization of genetic diversity and ploidy levels of 10 populations of Ranunculus carpaticola in central Slovakia. Whereas two diploid populations showed high levels of genetic diversity, as expected for sexual reproduction, eight populations are hexaploid and harbour lower degrees of genotypic variation, but maintain high levels of heterozygosity at many loci, as is typical for apomicts. Polyploid populations consist either of a single AFLP genotype or of one dominant and a few deviating genotypes. genotype/genodive and character incompatibility analyses suggest that genotypic variation within apomictic populations is caused by mutations, but in one population probably also by recombination. This local facultative sexuality may have a great impact on regional genotypic diversity. Two microsatellite loci discriminated genotypes separated by the accumulation of few mutations ('clone mates') within each AFLP clone. Genetic diversity is partitioned mainly among apomictic populations and is not geographically structured, which may be due to facultative sexuality and/or multiple colonizations of sites by different clones. Habitat differentiation and a tendency to inhabit artificial meadows is more pronounced in apomictic than in sexual populations. We hypothesize that maintenance of genetic diversity and superior colonizing abilities of apomicts in temporally and spatially heterogeneous environments are important for their distributional success.     

Characterization of dinucleotide microsatellite markers in the parthenogenetic mourning gecko (Lepidodactylus lugubris)

We present 16 variable dinucleotide microsatellite markers to quantify genetic variation in the parthenogenetic gecko, Lepidodactylus lugubris. Genetic diversity at these loci was unusually high for an asexual species. Subsets of individuals produced identical genotypes across all loci. Individual loci revealed evidence of polyploidy and marked differences between observed and expected heterozygosity, indicating the presence of null alleles. These patterns conform to prior expectations based on the distant genetic relationships between the presumed sexual progenitors of L. lugubris. Comparisons with sexual relatives will be required to determine the sources of the observed genetic variation.     

Genetic distance predicts trait differentiation at the subpopulation but not the individual level in eelgrass,Zostera marina

Ecological studies often assume that genetically similar individuals will be more similar in phenotypic traits, such that genetic diversity can serve as a proxy for trait diversity. Here, we explicitly test the relationship between genetic relatedness and trait distance using 40 eelgrass (Zostera marina) genotypes from five sites within Bodega Harbor, CA. We measured traits related to nutrient uptake, morphology, biomass and growth, photosynthesis, and chemical deterrents for all genotypes. We used these trait measurements to calculate a multivariate pairwise trait distance for all possible genotype combinations. We then estimated pairwise relatedness from 11 microsatellite markers. We found significant trait variation among genotypes for nearly every measured trait; however, there was no evidence of a significant correlation between pairwise genetic relatedness and multivariate trait distance among individuals. However, at the subpopulation level (sites within a harbor), genetic (F_ST) and trait differentiation were positively correlated. Our work suggests that pairwise relatedness estimated from neutral marker loci is a poor proxy for trait differentiation between individual genotypes. It remains to be seen whether genomewide measures of genetic differentiation or easily measured “master” traits (like body size) might provide good predictions of overall trait differentiation.     

Microsatellite and morphological analysis of population structure in the parthenogenetic freshwater snail Melanoides tuberculata: insights into the creation of clonal variability

The distribution of variability was studied at various geographical scales in the tropical freshwater snail Melanoides tuberculata, in order to analyse the role of factors shaping this distribution, including the mating system and population dynamics. This parthenogenetic polyploid species reproduces mainly asexually, with males occurring at low frequency. About 800 individuals (38 sites) were sampled from Africa and the Middle East, where the species originated, and from recently colonized habitats in South and Central America, and especially the island of Martinique. We first described variation of general aspects and ornamentation of the shells. This analysis confirms the existence of discrete morphs. Second, individuals were studied at three microsatellite loci, showing that each morph is a genetic clone with some minor variation compatible with models of microsatellite evolution. The genetic analysis also showed much more variation within than between clones. However, two populations from Africa exhibited a large amount of variability, and a mixture of sexual and asexual reproduction might explain these genetic patterns. The worldwide distribution of variability is, therefore, compatible with the African origin of the species, and the introduction of a few clones in other parts of the world. These results also suggest that the distribution of variability in Martinique is influenced by flooding events, and that two morphs from Martinique can be interpreted as hybrids between two pre-existing morphs, based on morphological, genetic and geographical arguments.     

Genetic structure of Polytrichum formosum in relation to the breeding system as revealed by microsatellites

Microsatellite variation was determined for three Danish and three Dutch populations of the haploid moss species Polytrichum formosum to gain insight into the relative importance of sexual vs. asexual reproduction for the amount and structure of genetic variation. In general, low levels of microsatellite variation were observed within this species. Even when estimated for polymorphic loci only, the levels of microsatellite variability (P=90.6, A=4.3 and H_S=0.468) within populations were on average lower than those reported for most other plant species. In contrast, genotypic diversity was high within each of the examined populations, indicating that sexual reproduction is a very important determinant of the genetic structure of P. formosum within populations. In agreement with previous findings for allozyme data, no significant genetic differentiation (F_ST=0.028, R_ST=0.015) was observed neither between populations nor between regions approximately 450 km apart (Denmark vs. the Netherlands). These low levels of population differentiation observed for both types of genetic markers are probably best explained by a high level of effective spore dispersal (gene flow) between populations. Therefore, also on a large geographical scale sexual reproduction is the most important determinant of the genetic structure of P. formosum, despite the high potential to reproduce clonally.     

Genetic Analysis of <Emphasis Type="Italic">Porphyra yezoensis</Emphasis> Using Microsatellite Markers

Microsatellites are repetitive genomic elements that show high levels of variation and therefore are useful tools for studying genetic polymorphism and constructing genetic linkage maps of eukaryotic organisms. Porphyra yezoensis Ueda is an economically important seaweed that is being targeted for genetic improvement using marker-assisted breeding. Hence, in an attempt to develop microsatellite markers for P. yezoensis, a microsatellite (or simple sequence repeat)-enriched library was constructed to identify (GA)n and (CA)n motifs. A total of 71 perfect microsatellite clones were identified, of which 30 simple sequence repeat primer pairs were developed. Of these, 24 (80%) amplified polymerase chain reaction products of expected sizes. Twelve primer pairs amplified two to four bands, whereas another 12 primer pairs produced monomorphic banding patterns. Data for 12 loci were analyzed using POPGENE software version 1.32. A total of 29 alleles were produced at 12 loci, with an average of 2.42 alleles (Na) and 1.81 effective alleles (Ne) per locus. These markers were used to analyze the genetic diversity within 11 geographically different lines of P. yezoensis. Overall, these lines were clustered into two divisions with those from close geographic locations clustering together. Further cloning and sequencing of size variant alleles at two microsatellite loci revealed that the variable numbers of motif repeats in different alleles were major sources of polymorphisms.     

Contrasting abundance and contribution of clonal proliferation to the population structure of the corkscrew sea anemone Bartholomea annulata in the tropical Western Atlantic

Clonal propagation is an important life history trait for many sessile organisms, and often leads to the formation of monoclonal aggregations. In the marine environment, sea anemones have been model species for testing theory regarding the evolution of sex and understanding the contribution of sexual versus asexual reproduction to the population structure in facultatively clonal animals. However, little attention has been paid to tropical actiniarians. The corkscrew anemone Bartholomea annulata is common in tropical marine habitats in the western Atlantic and Caribbean; it forms small aggregations (2–4 anemones) on coral reefs and larger aggregations (>10 anemones) in mangrove habitats. We used field surveys and molecular analyses to investigate patterns of distribution, abundance, and genetic structure of aggregations formed by B. annulata on a reef in the US Virgin Islands and in a unique mangrove habitat in the Florida Keys. Abundance was greatest at the abandoned rock quarry mangrove habitat in the Florida Keys, where anemones formed continuously distributed aggregations carpeting the exposed limestone walls. Genetic diversity assessed via intersimple sequence repeats (ISSRs) and six microsatellite loci revealed that asexual reproduction plays only a minor role in the formation of both small and large anemone aggregations. Specifically, ISSR analyses showed that only ~10% of anemone aggregations were clonal in the US Virgin Islands, while microsatellite genotyping identified clonality in only 1 of 35 aggregations. In the Florida Keys, only four clonal genotypes were recovered within aggregations, but eight clones, representing 33% of the total surveyed population, had individuals in multiple aggregations. Thus, population structure of B. annulata appears to rely primarily on sexual reproduction, although asexual reproduction may play a nontrivial role in some environments. Mechanisms that drive the formation of genotypically diverse aggregations remain unknown, but may include attraction toward conspecifics, shared use of preferred habitats, or the local retention of larvae in partially enclosed habitats.     

THE ORIGIN AND DISTRIBUTION OF CLONAL DIVERSITY IN ALSOPHILA POMETARIA (LEPIDOPTERA: GEOMETRIDAE)

A survey of spatial and temporal variation in the frequency of electrophoretically defined genotypes in the geometrid moth Alsophila pometaria revealed a high diversity of uncommon or rare asexual genotypes and clinal distributions of two of the more common clones. There was substantial year-to-year variation in genotype frequencies in seven of eleven sites. Progeny tests have revealed that sexual reproduction is uncommon in two populations and that new asexual genotypes arise from the sexual population. The recurrent origin of asexual genotypes is likely to account for the high genetic and ecological diversity of the asexual contingent of this species' populations, in contrast to the lower genetic diversity in some obligately asexual species in which such recruitment does not occur.     

THE GENETIC STRUCTURE OF LARGE-LAKE DAPHNIA POPULATIONS

Cyclical parthenogenesis allows study of the genetic and evolutionary characteristics of groups exhibiting both asexual and sexual reproduction. The cladoceran genus Daphnia contains species which vary with respect to the relative incidence of sexual reproduction; pond species tend to undergo sexual reproduction more regularly than species found in large lakes. Previous genetic studies have focused on pond populations, generating expectations about large-lake populations that have not been fully met by recent studies. The present study of the Palearctic species Daphnia galeata further examines the genetic structure of large-lake populations. Nine local populations, from lakes in northern Germany, are examined for genetic variation at seven enzyme loci. Populations exhibit similar allelic arrays and often similar allele frequencies at the five polymorphic loci; values of Nei's genetic distance (D) ranged from 0.002 to 0.239, with a mean of 0.084. F_ST values range from 0.012 to 0.257, and spatial autocorrelation coefficients range from -0.533 to 0.551, for the eight alleles analyzed. With few exceptions, within-population genotypic frequencies were in Hardy-Weinberg equilibrium. There was, however, significant heterogeneity in genotypic frequencies among populations. The number of coexisting clonal groups, as determined by three locus genotypes, is high within populations. Clonal groups are widely distributed among localities. The amount of genetic divergence observed among these large-lake populations is smaller than that previously observed among pond populations and suggests that different processes may be important in determining the genetic structure and subsequent phenotypic divergence of lake versus pond populations.     

Microevolution, low clonal diversity and genetic affinities of parthenogenetic sitobion aphids in new zealand

In sharp contrast to their southeast Asian and European counterparts, Sitobion miscanthi and S. near fragariae aphids in Australia exhibit a complete absence of sexual reproduction. This demands an explanation within the context of the evolution and maintenance of sex and parthenogenesis. Accordingly, we executed a genetic analysis of the two species in neighbouring New Zealand. Microsatellites and single-stranded conformation polymorphism/sequence analysis of the nuclear gene elongation factor 1alpha were used to identify aphid clones and confirm species identification, respectively. Karyotypic variation was also investigated. The New Zealand fauna showed few (nonrecombining) genotypes and appears to have received migrants from both Australia and Asia. Other genotypes have apparently arisen in situ in New Zealand, exhibiting stepwise mutation of microsatellite alleles and also karyotypic change. Thus, these data represent rare evidence of evolution within wild-living parthenogenetic lineages. Karyotypic changes appear to occur at a rate even greater than that of microsatellite evolution. Strong geographical partitioning of genotypes/karyotypes was found, with certain ones predominating over large areas. These data suggest that clonal selection could be important in the distribution and patterning of genetic variation. We present a model to explain the genetic patterns, with particular reference to the absence of sexual reproduction in Sitobion aphids in New Zealand and Australia.     

Evidence for predominant clones in a cyclically parthenogenetic organism provided by combined demographic and genetic analyses

Aphids are particularly interesting models in the study of genetic and demographic components of plant adaptation because of their breeding system which combines parthenogenesis and sexual reproduction (i.e. cyclical parthenogenesis), and the frequent emergence of host-adapted races reported in this group. In this paper, patterns of host adaptation were assessed on local populations of the aphid Sitobion avenae by following their demographic and genetic structure in a maize field for two consecutive years. The existence of putative generalist (polyphagous) or specialized (host-adapted) genotypes was also investigated by comparing the genotypic distribution of this aphid on maize and other cultivated host plants, using five microsatellite loci. Although population dynamics revealed strong variation in aphid abundance during the colonization period on maize, two genotypes identified at seven additional microsatellite loci were predominant and exhibited stable frequencies over cropping season and between years. Based on present and earlier studies, these two prevalent genotypes were shown to survive on different host plants other than maize, to colonize large geographical zones and to persist parthenogenetically for several years. All these data strongly suggest that these two genotypes are asexual generalist clones that could have been favoured by agricultural practices encountered in western Europe. Besides these two clones, a continual replacement of rare genotypes was observed on maize in both years. Hypotheses involving selection via aphid-plant interactions and natural enemies were proposed for explaining the disappearance of these genotypes on maize.     

Polyploidy and microsatellite variation in the relict tree Prunus lusitanica L.: how effective are refugia in preserving genotypic diversity of clonal taxa?

Refugia are expected to preserve genetic variation of relict taxa, especially in polyploids, because high gene dosages could prevent genetic erosion in small isolated populations. However, other attributes linked to polyploidy, such as asexual reproduction, may strongly limit the levels of genetic variability in relict populations. Here, ploidy levels and patterns of genetic variation at nuclear microsatellite loci were analysed in Prunus lusitanica, a polyploid species with clonal reproduction that is considered a paradigmatic example of a Tertiary relict. Sampling in this study considered a total of 20 populations of three subspecies: mainland lusitanica (Iberian Peninsula and Morocco), and island azorica (Azores) and hixa (Canary Islands and Madeira). Flow cytometry results supported an octoploid genome for lusitanica and hixa, whereas a 16‐ploid level was inferred for azorica. Fixed heterozygosity of a few allele variants at most microsatellite loci resulted in levels of allelic diversity much lower than those expected for a high‐order polyploid. Islands as a whole did not contain higher levels of genetic variation (allelic or genotypic) than mainland refuges, but island populations displayed more private alleles and higher genotypic diversity in old volcanic areas. Patterns of microsatellite variation were compatible with the occurrence of clonal individuals in all but two island populations, and the incidence of clonality within populations negatively correlated with the estimated timing of colonization. Our results also suggest that gene flow has been very rare among populations, and thus population growth following founder events was apparently mediated by clonality rather than seed recruitment, especially in mainland areas. This study extends to clonal taxa the idea of oceanic islands as important refugia for biodiversity, since the conditions for generation and maintenance of clonal diversity (i.e. occasional events of sexual reproduction, mutation and/or seed immigration) appear to have been more frequent in these enclaves than in mainland areas.     

Predominance of clonal reproduction, but recombinant origins of new genotypes in the free-floating aquatic bladderwort Utricularia australis f. tenuicaulis (Lentibulariaceae)

Aquatic plants are a biological group sharing several adaptations to aquatic conditions. The most striking evolutionary convergence in this group is the extensive reliance on clonal reproduction, which largely determines the patterns and process of evolution in aquatic plants. Utricularia australis f. tenuicaulis is a free-floating aquatic bladderwort that reproduces both sexually via seeds and clonally via turions and shoot fragments. Amplified fragment length polymorphism analysis was conducted on 267 ramets collected from 30 populations in Japan. The genotypic diversity within populations was extremely low, regardless of the geographical distribution range: the mean number of genotypes per population (G) was 1.4 and the mean genotypic diversity (D), including monoclonal populations, was 0.17. In contrast to the predominance of a few clones within populations, many of the populations investigated had different genotypes; a large portion of the genetic variation was explained by variation among populations. Character compatibility analysis clearly revealed that somatic mutations did not contribute to the origin of genotypic diversity in this aquatic bladderwort; instead, rare-to-sporadic sexual reproduction probably generated new genotypes. Thus, future studies should examine the role of sexual reproduction in this species from the viewpoint of long-term evolutionary benefits.