Genetic variation in sexual and clonal lineages of a freshwater snail

Sexual reproduction within natural populations of most plants and animals continues to remain an enigma in evolutionary biology. That the enigma persists is not for lack of testable hypotheses but rather because of the lack of suitable study systems in which sexual and asexual females coexist. Here we review our studies on one such organism, the freshwater snail Potamopyrgus antipodarum (Gray). We also present new data that bear on hypotheses for the maintenance of sex and its relationship to clonal diversity. We have found that sexual populations of the snail are composed of diploid females and males, while clonal populations are composed of a high diversity of triploid apomictic females. Sexual and asexual individuals coexist in stable frequencies in many ‘mixed’ populations; genetic data indicate that clones from these mixed populations originated from the local population of sexual individuals without interspecific hybridization. Field data show that clonal and sexual snails have completely overlapping life histories, but individual clonal genotypes are less variable than individuals from the sympatric sexual population. Field data also show segregation of clones among depth‐specific habitat zones within a lake, but clonal diversity remains high even within habitats. A new laboratory experiment revealed extensive clonal variation in reproductive rate, a result which suggests that clonal diversity would be low in nature without some form of frequency‐dependent selection. New results from a long‐term field study of a natural, asexual population reveal that clonal diversity remained nearly constant over a 10‐year period. Nonetheless, clonal turnover occurs, and it occurs in a manner that is consistent with parasite‐mediated, frequency‐dependent selection. Reciprocal cross‐infection experiments have further shown that parasites are more infective to sympatric host snails than to allopatric snails, and that they are also more infective to common clones than rare clones within asexual host populations. Hence we suggest that sexual reproduction in these snails may be maintained, at least in part, by locally adapted parasites. Parasite‐mediated selection possibly also contributes to the maintenance of local clonal diversity within habitats, while clonal selection may be responsible for the distribution of clones among habitats. © 2003 The Linnean Society of London. Biological Journal of the Linnean Society 2003, 79 , 165–181.     

Parasites, sex, and clonal diversity in natural snail populations

Under the Red Queen hypothesis, host-parasite coevolution selects against common host genotypes. Although this mechanism might underlie the persistence of sexual reproduction, it might also maintain high clonal diversity. Alternatively, clonal diversity might be maintained by multiple origins of parthenogens from conspecific sexuals, a feature in many animal groups. Herein, we addressed the maintenance of overall genetic diversity by coevolving parasites, as predicted by the Red Queen hypothesis. We specifically examined the contribution of parasites to host clonal diversity and the frequency of sexually reproducing individuals in natural stream populations of Potamopyrgus antipodarum snails. We also tested the alternative hypothesis that clonal diversity is maintained by the input of clones by mutation from sympatric sexuals. Clonal diversity and the frequency of sexual individuals were both positively related to infection frequency. Surprisingly, although clones are derived by mutation from sexual snails, parasites explained more of the genotypic variation among parthenogenetic subpopulations. Our findings thus highlight the importance of parasites as drivers of clonal diversity, as well as sex.     

PATTERNS OF GENOTYPIC DIVERSITY IN CLONAL PLANT SPECIES

We compile and analyze data on the population genetic structure of broad-sense clonal plant populations where sexual recruitment is rare or absent. The data from 27 studies show a common theme: multiclonal populations of intermediate diversity and evenness tend to be the rule, most clones are restricted to one or a few populations, and widespread clones are exceptional. While a few studies have demonstrated that ecological differences among sympatric clones do occur, more experimental and theoretical studies are necessary to determine the role of selection and other evolutionary forces in maintaining clonal polymorphism.     

Speciation through competition: a critical review

We examined causes of speciation in asexual populations in both sympatry and parapatry, providing an alternative explanation for the speciation patterns reported by Dieckmann and Doebeli (1999) and Doebeli and Dieckmann (2003). Both in sympatry and parapatry, they find that speciation occurs relatively easily. We reveal that in the sympatric clonal model, the equilibrium distribution is continuous and the disruptive selection driving evolution of discrete clusters is only transient. Hence, if discrete phenotypes are to remain stable in the sympatric sexual model, there should be some source of nontransient disruptive selection that will drive evolution of assortment. We analyze sexually reproducing populations using the Bulmer's infinitesimal model and show that cost-free assortment alone leads to speciation and disruptive selection only arises when the optimal distribution cannot be matched--in this example, because the phenotypic range is limited. In addition, Doebeli and Dieckmann's analyses assumed a high genetic variance and a high mutation rate. Thus, these theoretical models do not support the conclusion that sympatric speciation is a likely outcome of competition for resources. In their parapatric model (Doebeli and Dieckmann 2003), clustering into distinct phenotypes is driven by edge effects, rather than by frequency-dependent competition.     

Clonal diversity in the rare Calamagrostis porteri ssp. insperata (Poaceae): comparative results for allozymes and random amplified polymorphic DNA (RAPD) and intersimple sequence repeat (ISSR) markers

Four populations of the rare, highly clonal grass Calamagrostis porteri ssp. insperata were examined using allozymes and the two polymerase chain reaction (PCR)-based markers, random amplified polymorphic DNA (RAPD) and intersimple sequence repeat (ISSR) bands. Only one of the 15 allozyme loci was variable and two alleles were detected, both of which were found in two populations, while only one genotype was detected in the other two populations. ISSR and RAPD markers detected more genotypes within populations than did allozymes. ISSR markers detected more diversity than RAPD markers in three of the four populations examined. In one population, no RAPD diversity was found whereas eight different genotypes were found among the 10 plants with ISSR markers. This diversity is present despite rare flowering, no documented occurrence of seed set in natural populations and very low seed set with experimental pollinations, all of which suggest that sexual reproduction rarely occurs. The subspecies is self-compatible, but seed initiation is lower in selfed ovules; also, there is high embryo abortion regardless of pollen source. Variation detected by RAPD and ISSR primers may reflect higher levels of sexual reproduction in the past, very rare sexual reproduction in extant populations, somatic mutations, or a combination of the three. Although the PCR-based markers identify several multilocus genotypes within populations, it is not known whether these all represent distinct genets generated by sexual reproduction or result from somatic mutations in the old, perennial and highly clonal plants.     

Clonal erosion and genetic drift in cyclical parthenogens – the interplay between neutral and selective processes

The occurrence of alternating phases of clonal and sexual reproduction may strongly impact the interplay between neutral and selective genetic variation in populations. Using a physiologically structured model of the life history of Daphnia, we investigated to what extent clonal erosion associated with selection during the clonal phase affects the genetic structure as observed by neutral markers. Incorporating conservative levels of quantitative genetic variation at 11 physiological and life history traits induces strong clonal erosion, reducing clonal diversity (CD) near the end of the simulations (1000 days) to a level between 1 and 5, even in habitats with high initial CD (10⁸ clones). This strong clonal erosion caused by selection can result in reduced genetic diversity, significant excess of heterozygotes and significant genetic differentiation between populations as observed by neutral markers. Our results indicate that, especially in relatively small habitats, clonal selection may strongly impact the genetic structure and may contribute to the often observed high level of neutral genetic differentiation among natural populations of cyclical parthenogens.     

Faster clonal turnover in high‐infection habitats provides evidence for parasite‐mediated selection

According to the Red Queen hypothesis for sex, parasite‐mediated selection against common clones counterbalances the reproductive advantage of asexual lineages, which would otherwise outcompete sexual conspecifics. Such selection on the clonal population is expected to lead to a faster clonal turnover in habitats where selection by parasites is stronger. We tested this prediction by comparing the genetic structure of clonal and sexual populations of freshwater snail Potamopyrgus antipodarum between years 2003 and 2007 in three depth‐specific habitats in Lake Alexandrina (South Island, New Zealand). These habitats differ in the risk of infection by castrating trematodes and in the relative proportion of sexual individuals. As predicted, we found that the clonal structure changed significantly in shallow and mid‐water habitats, where prevalence of infection was high, but not in the deep habitat, where parasite prevalence was low. Additionally, we found that both clonal diversity and evenness of the asexual population declined in the shallow habitat. In contrast, the genetic structure (based on F–statistics) of the coexisting sexual population did not change, which suggests that the change in the clonal structure cannot be related to genetic changes in the sexual population. Finally, the frequency of sexuals had no effect on the diversity of the sympatric clonal population. Taken together, our results show a more rapid clonal turnover in high‐infection habitats, which gives support for the Red Queen hypothesis for sex.     

Clonality and recombination in the arctic plant Saxifraga cernua

The circumarctic clonal plant Saxifraga cernua reproduces efficiently via bulbils, largely depends on insects for pollination and appears to set seed very rarely. However, high levels of genotypic variation observed at small spatial scales in the arctic archipelago of Svalbard have been taken as evidence of occasional sexual reproduction. Here we assess the relative contributions of mutation and recombination to random amplified polymorphic DNA variation in four populations in East Greenland and re-analyse the Svalbard data. Greater variation due to recombination was predicted in Greenland than in Svalbard, because the higher summer temperatures and longer growing season likely increase the chances for sexual reproduction. Although we observed higher levels of genotypic diversity in Greenland than in Svalbard, matrix incompatibility and linkage disequilibrium measures provided no evidence of more sexuality, suggesting differences in glacial/postglacial history. The genetic structure and spatial distribution of clones suggest that clonal migration may increase variability in local populations, which is consistent with frequent large-scale migration in this species inferred from a circumarctic analysis of chloroplast DNA haplotypes. We conclude that a combination of somatic mutations and sexual reproduction has contributed to the observed patterns of genotypic diversity in the Greenland and Svalbard populations of S. cernua , and that sexual reproduction is important in maintaining genotypic diversity, despite the rarity of observations of seed setting.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 152 , 209–217.     

Environmental gradients structure Daphnia pulex × pulicaria clonal distribution

The rarity of eukaryotic asexual reproduction is frequently attributed to the disadvantage of reduced genetic variation relative to sexual reproduction. However, parthenogenetic lineages that evolved repeatedly from sexual ancestors can generate regional pools of phenotypically diverse clones. Various theories to explain the maintenance of this genetic diversity as a result of environmental and spatial heterogeneity [frozen niche variation (FNV), general-purpose genotype] are conceptually similar to community ecological explanations for the maintenance of regional species diversity. We employed multivariate statistics common in community ecological research to study population genetic structure in the freshwater crustacean, Daphnia pulex × pulicaria. This parthenogenetic hybrid arose repeatedly from sexual ancestors. Daphnia pulex × pulicaria populations harboured substantial genetic variation among populations and the clonal composition at each pond corresponded to nutrient levels and invertebrate predator densities. The interclonal selection process described by the FNV hypothesis likely structured our D. pulex × pulicaria populations.     

Ecological Implications of Clonal Diversity in Parthenogenetic Morphospecies

Most parthenogenetic animal taxa which have been investigatedelectrophoretically, cytologically, or with tissue graftingtechniques are clonally diverse. I have examined data on multiclonalparthenogenetic populations using ecological diversity measuresto elucidate patterns of clonal coexistence. Analysis of a discretepopulation cage experiment on clones of Drosophila mercatorumrevealed monotonic decay of clonal diversity and evenness; however,in a continuous generation cage, clonal diversity appeared tostabilize. Clonal diversity and evenness fluctuated widely overtime in several multiclonal populations of Daphnia magna althoughno clonal extinction was observed. There were few spatial trendsin clonal diversity and evenness within parthenogenetic taxa.It is suggested that the degree of clonal differentiation, determinedby the mode of clonal origin, is important in determining whetheror not selection occurs among sympatric clones     

Clonal diversity driven by parasitism in a freshwater snail

One explanation for the widespread abundance of sexual reproduction is the advantage that genetically diverse sexual lineages have under strong pressure from virulent coevolving parasites. Such parasites are believed to track common asexual host genotypes, resulting in negative frequency‐dependent selection that counterbalances the population growth‐rate advantage of asexuals in comparison with sexuals. In the face of genetically diverse asexual lineages, this advantage of sexual reproduction might be eroded, and instead sexual populations would be replaced by diverse assemblages of clonal lineages. We investigated whether parasite‐mediated selection promotes clonal diversity in 22 natural populations of the freshwater snail Melanoides tuberculata. We found that infection prevalence explains the observed variation in the clonal diversity of M. tuberculata populations, whereas no such relationship was found between infection prevalence and male frequency. Clonal diversity and male frequency were independent of snail population density. Incorporating ecological factors such as presence/absence of fish, habitat geography and habitat type did not improve the predictive power of regression models. Approximately 11% of the clonal snail genotypes were shared among 2–4 populations, creating a web of 17 interconnected populations. Taken together, our study suggests that parasite‐mediated selection coupled with host dispersal ecology promotes clonal diversity. This, in return, may erode the advantage of sexual reproduction in M. tuberculata populations.     

Factors Affecting Clonal Diversity and Coexistence

Recent genetic studies of asexually reproducing fishes in thegenus Poeciliopsis (Poeciliidae) revealed abundant variationin the form of multiple sympatric clones. Recurrent hybridizationsbetween sexual species provides the principal source of clonalvariation. The hybrids are spontaneously endowed with a clonalreproductive mechanism that perpetuates a high level of heterozygosity.Migration within and between river systems, and mutations, alsocontribute to clonal diversity in these fish. Coexistence amongdifferent clones and with the sexual ancestors depends in partupon specializations characteristic of individual clones. Clonalreproduction is an efficient mechanism for freezing a portionof the niche-width variation contained in the gene pool of themore broadly adapted, sexual ancestors. Multiclonal populationsachieve significantly higher densities relative to the sexualforms than do monoclonal populations. This relationship is afunction of the clonal variability upon which natural selectioncan act and upon the capacity of a multiclonal population tobetter exploit a heterogeneous environment through niche diversification.In all-female organisms such as Poeciliopsis, which are dependentupon sexual species for insemination, competitive abilitiesprobably are at a premium in the densely populated pools andarroyos of the Sonoran Desert. Competitive abilities are probablyless important for truly parthenogenetic clones which rely oncolonization abilities to escape from their sexual ancestorsand from other clones.     

Predictable patterns of disruptive selection in stickleback in postglacial lakes

Disruptive selection is often assumed to be relatively rare, because it is dynamically unstable and hence should be transient. However, frequency-dependent interactions such as intraspecific competition may stabilize fitness minima and make disruptive selection more common. Such selection helps explain the maintenance of genetic variation and may even contribute to sympatric speciation. There is thus great interest in determining when and where disruptive selection is most likely. Here, we show that there is a general trend toward weak disruptive selection on trophic morphology in three-spine stickleback (Gasterosteus aculeatus) in 14 lakes on Vancouver Island. Selection is inferred from the observation that, within a lake, fish with intermediate gill raker morphology exhibited slower growth than phenotypically extreme individuals. Such selection has previously been shown to arise from intraspecific competition for alternate resources. However, not all environments are equally conducive to disruptive selection, which was strongest in intermediate-sized lakes where both littoral and pelagic prey are roughly balanced. Also, consistent with theory, we find that sexual dimorphism in trophic traits tends to mitigate disruptive selection. These results suggest that it may be possible to anticipate the kinds of environments and populations most likely to experience disruptive selection.     

Clonal diversity of populations of Calamagrostis epigejos in relation to environmental stress and habitat heterogeneity

The clonal diversity of four populations of the vegetatively propagating grass Calamagrostis epigejos was studied with isozyme markers From each population, 100 individuals were sampled within a 10 × 10 m gnd In two populations of unpolluted sites 5 and 10 clones were distinguished, respectively Higher levels of clonal diversity were found m the populations at an abandoned sewage farm (59 clones) and around a copper smelter (92 clones) The level of clonal diversity observed suggests that sexual recruitment is important for the genetic structure in this species On the unpolluted, presumably more suitable habitats, the clonal diversity was lower than on the habitats polluted with heavy metals The results are discussed in relation to environmental stress and habitat heterogeneity, with the conclusion that in the unpolluted habitats intraspecific competition results in low clonal diversity On the other hand, stressful conditions decrease the importance of competition and facilitate the coexistence of a great number of clones     

INTENSE SELECTION OF MITE CLONES IN A HETEROGENEOUS ENVIRONMENT

Genetic diversity within obligatorily parthenogenic species can be high, contrary to common views of the evolutionary consequences of this reproductive system. How this clonal diversity is maintained within populations is not clearly understood. Previous studies showing high clonal diversity have used parthenogenic organisms with known sexual forms or relatives. Here we report significant spatial and temporal clonal diversity within two populations of an obligatorily parthenogenic mite, Penthaleus major, which has no known sexual form or close sexual relative. Fitness estimates from temporal sampling at two sites and manipulated field plots reveal intense natural selection acting on ecologically different clones. We propose that environmental heterogeneity contributes to the maintenance of clonal diversity within populations of P. major and that selection is strong enough to overcome the problems of relative niche size.     

Parasitism and breeding system variation in North American populations of Daphnia pulex

The Red Queen hypothesis proposes that frequency-dependent selection by parasites may be responsible for the evolutionary maintenance of sexual reproduction. We sought to determine whether parasites could be responsible for variation in the occurrence of sexual reproduction in 21 populations of Daphnia pulex (Crustacea; Cladocera) that previous studies have shown to consist of either cyclical parthenogens, obligate parthenogens, or a mixture of both. We measured parasite prevalence over a four-week period (which essentially encompasses an entire season for the temporary snow-melt habitats we sampled) and regressed three different measures of sexuality against mean levels of parasite prevalence. Levels of parasitism were low and we found no relationship between levels of sexuality and mean parasite prevalence. Genetic variation with infection level was detected in 2 of the 21 populations, with several different clones showing signs of overparasitism or underparasitism. Overall, however, our results suggest that parasites are not a major source of selection in these populations and it thus seems unlikely they are responsible for maintaining breeding system variation across the study region.     

Genetic structure of natural populations of black locust (Robinia pseudoacacia L.) at Coweeta, North Carolina

Natural population of black locust maintains very high levels of genetic diversity within populations without any noticeable geographic patterns. In order to assess the species' potential for manipulation through breeding programs, more detailed spatial pattern analyses of fine-scale population structure was attempted in the two study sites (watershed 2 and 21) in the Coweeta River Basin of southern Appalachian mountains using allozyme markers. Of the 200 and 420 plants examined in watershed 21 and 2 respectively, 13 and 15 major genotypes of clone were distinguished. Within watersheds 2 and 21, 60% of the pairwise clone combinations had three or four loci differences out of the 8 loci investigated. No correlation between distance between clones and the number of allele difference was found. The similarity values (16 highest and 0 lowest value) among clones for watershed 2 and 21 were 12.82 and 10.19 respectively. Typical distances between clones on both watershed 2 and 21 were from 90 and 190 m, but the range varied from several meters up to 300 m. An average distance among clones were 140.9±66.0 m and 239.4±108.6 m in watershed 2 and 21 respectively, whereas an average distance within clone was 38.7±36.2 m and 145.0±123.6 m in watershed 2 and 21. Genotype diversity indices (DG) for watershed 2 and 21 were 0.89 and 0.86 respectively. The largest clones on both watersheds covered more than 100 m×100 m. On the other hand, some clones on watershed 2, which had a few fallen trees with many young sprouts (up to 200 individuals), were 45 m×30 m in size under the open habitat. Although clonal substructure and limited seed dispersal may cause near neighbor mating interaction, significant genetic patchiness among clones of black locust was not evident. Although the first establishment of a black locust population would have relied on an off-site seed source, it is more likely that asexual reproduction has occurred for many generations in these black locust populations because of the presence of many different sizes of trees (or ages) in one clone despite widespread opportunities for sexual reproduction. Presence of three or four different sizes of trees within a clone implies that the trees has developed from a clone at each different time. The current study suggested that the amount of sexual reproduction and dispersal rate (especially seed dispersal) should be determined. It would be useful to examine whether or not clonal strategies and patterns of clonal growth of black locust are influenced by density dependent regulation of ramet recruitment and death.     

The population genetics of clonal and partially clonal diploids

The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation approaches. High rates of clonal reproduction will positively affect heterozygosity. As a consequence, nearly twice as many alleles per locus can be maintained and population differentiation estimated as F(ST) value is strongly decreased in purely clonal populations as compared to purely sexual ones. With increasing clonal reproduction, effective population size first slowly increases and then points toward extreme values when the reproductive system tends toward strict clonality. This reflects the fact that polymorphism is protected within individuals due to fixed heterozygosity. Contrarily, genotypic diversity smoothly decreases with increasing rates of clonal reproduction. Asexual populations thus maintain higher genetic diversity at each single locus but a lower number of different genotypes. Mixed clonal/sexual reproduction is nearly indistinguishable from strict sexual reproduction as long as the proportion of clonal reproduction is not strongly predominant for all quantities investigated, except for genotypic diversities (both at individual loci and over multiple loci).     

珠芽蓼种群克隆多样性及克隆结构的初步研究

珠芽蓼(Polygonum viviparum)是青藏高原东缘广泛分布的克隆植物,具有有性和无性(根状茎和珠芽)两种生殖方式。该研究采用RAPD技术对分布于不同海拔的珠芽蓼7个自然种群进行了克隆结构和克隆多样性(是单克隆种群还是多克隆种群)以及克隆多样性与海拔因子之间的相关性研究,为了解高山克隆植物对环境的适应性策略及揭示克隆植物的繁殖和分布特点提供科学依据。研究结果表明:1)采用13条RAPD引物对珠芽蓼7个种群共140个样本进行扩增分析,共扩增到117个位点,其中多态性位点84个,多态位点百分率PPL达到71.79%,检测到43个基因型,且全部为局限型基因型;2)与Ellstrand和Roose(1987)总结的克隆植物的克隆多样性平均值相比(PD=0.17,D=0.62),珠芽蓼种群克隆多样性水平稍高,Simpson指数平均为0.639,基因型比率PD平均为0.307;3)克隆结构分析表明,珠芽蓼种群内克隆之间的镶嵌明显,这可能与珠芽蓼过渡型的克隆构型有关。研究中珠芽蓼种群的构型有游击型、密集型以及这两者之间的过渡类型;4)采用SPSS软件对珠芽蓼种群的克隆多样性与海拔高度进行相关性分析,结果显示它们之间并无明显的相关性。     

Ecological and evolutionary opportunities of apomixis: insights from Taraxacum and Chondrilla

The ecological and evolutionary opportunities of apomixis in the short and the long term are considered, based on two closely related apomictic genera: Taraxacum (dandelion) and Chondrilla (skeleton weed). In both genera apomicts have a wider geographical distribution than sexuals, illustrating the short-term ecological success of apomixis. Allozymes and DNA markers indicate that apomictic populations are highly polyclonal. In Taraxacum, clonal diversity can be generated by rare hybridization between sexuals and apomicts, the latter acting as pollen donors. Less extensive clonal diversity is generated by mutations within clonal lineages. Clonal diversity may be maintained by frequency-dependent selection, caused by biological interactions (e.g. competitors and pathogens). Some clones are geographically widespread and probably represent phenotypically plastic 'general-purpose genotypes'. The long-term evolutionary success of apomictic clones may be limited by lack of adaptive potential and the accumulation of deleterious mutations. Although apomictic clones may be considered as 'evolutionary dead ends', the genes controlling apomixis can escape from degeneration and extinction via pollen in crosses between sexuals and apomicts. In this way, apomixis genes are transferred to a new genetic background, potentially adaptive and cleansed from linked deleterious mutations. Consequently, apomixis genes can be much older than the clones they are currently contained in. The close phylogenetic relationship between Taraxacum and Chondrilla and the similarity of their apomixis mechanisms suggest that apomixis in these two genera could be of common ancestry.