Mature habitats associated with genetic divergence despite strong dispersal ability in an arthropod

Background  

Populations may be bound by contemporary gene flow, selective sweeps, and extinction-recolonization processes. Indeed, existing molecular estimates indicate that species with low levels of gene flow are rare. However, strong priority effects and local selective regimes may hinder gene flow (despite dispersal) sending populations on independent evolutionary trajectories. In this scenario (the monopolization hypothesis), population differentiation will increase with time and genealogical evidence should yield ample private haplotypes. Cyclical parthenogens (e.g. rotifers and cladocerans such as Daphnia) have an increased capacity for rapid local adaptation and priority effects because sexual reproduction is followed by multiple generations of clonal selection and massive egg bank formation. We aimed to better understand the history of population differentiation and ongoing gene flow in Daphnia rosea s.l., by comparing population and regional divergences in mature unglaciated areas and younger previously glaciated areas. We also examined the timing and paths of colonization of previously-glaciated areas to assess the dispersal limitations of D. rosea s.l. We used DNA sequence variation (84 populations and >400 individuals) at the mitochondrial ND2 and nuclear HSP90 loci from Holarctic populations for our genetic analyses.     

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.     

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.     

The effect of variable frequency of sexual reproduction on the genetic structure of natural populations of a cyclical parthenogen

Cyclical parthenogens are a valuable system in which to empirically test theoretical predictions as to the genetic consequences of sexual reproduction in natural populations, particularly if the frequency of sexual relative to asexual reproduction can be quantified. In this study, we used a series of lake populations of the cyclical parthenogen, Daphnia pulicaria, that vary consistently in their investment in sexual reproduction, to address the questions of whether the ecological variation in investment in sex is detectable at the genetic level, and if so, whether the genetic patterns seen are consistent with theoretical predictions. We show that there is variation in the genetic structure of these populations in a manner consistent with their investment in sexual reproduction. Populations engaging in a high frequency of sex were in Hardy-Weinberg and gametic phase equilibrium, and showed little genotypic differentiation across sampled years. In contrast, populations with a lower frequency of sex deviated widely from equilibrium, had reduced multilocus clonal diversity, and showed significant temporal genotypic deviation.     

Reproductive strategy, clonal structure and genetic diversity in populations of the aquatic macrophyte Sparganium emersum in river systems

Many aquatic and riparian plant species are characterized by the ability to reproduce both sexually and asexually. Yet, little is known about how spatial variation in sexual and asexual reproduction affects the genotypic diversity within populations of aquatic and riparian plants. We used six polymorphic microsatellites to examine the genetic diversity within and differentiation among 17 populations (606 individuals) of Sparganium emersum, in two Dutch-German rivers. Our study revealed a striking difference between rivers in the mode of reproduction (sexual vs. asexual) within S. emersum populations. The mode of reproduction was strongly related to locally reigning hydrodynamic conditions. Sexually reproducing populations exhibited a greater number of multilocus genotypes compared to asexual populations. The regional population structure suggested higher levels of gene flow among sexually reproducing populations compared to clonal populations. Gene flow was mainly mediated via hydrochoric dispersal of generative propagules (seeds), impeding genetic differentiation among populations even over river distances up to 50 km. Although evidence for hydrochoric dispersal of vegetative propagules (clonal plant fragments) was found, this mechanism appeared to be relatively less important. Bayesian-based assignment procedures revealed a number of immigrants, originating from outside our study area, suggesting intercatchment plant dispersal, possibly the result of waterfowl-mediated seed dispersal. This study demonstrates how variation in local environmental conditions in river systems, resulting in shifting balances of sexual vs. asexual reproduction within populations, will affect the genotypic diversity within populations. This study furthermore cautions against generalizations about dispersal of riparian plant species in river systems.     

Population genetic structure of the medicinal plant Vitex rotundifolia in China: implications for its use and conservation

Vitexrotundifolia L.is an important plant species used in traditional Chinese medicine.For its efficient use and conservation,genetic diversity and clonal variation of V.rotundifolia populations in China were investigated using inter-simple sequence repeat markers.Fourteen natural populations were included to estimate genetic diversity,and a large population with 135 individuals was used to analyze clonal variation and fine-scale spatial genetic structure.The overall genetic diversity (GD) of V.rotundifolia populations in China was moderate (GD=0.190),with about 40% within-population variation.Across all populations surveyed,the average within-population diversity was moderate (P = 22.6%; GD = 0.086).A relatively high genetic differentiation (Gst=0.587)among populations was detected based on the analysis of molecular variance data.Such characteristics of V.rotundifolia are likely attributed to its sexual/asexual reproduction and limited gene flow.The genotypic diversity (D=0.992) was greater than the average values of a clonal plant,indicating its significant reproduction through seedlings.Spatial autocorrelation analysis showed a clear within-population structure with gene clusters of approximately 20 m.Genetic diversity patterns of V.rotundifolia in China provide a useful guide for its efficient use and conservation by selecting particular populations displaying greater variation that may contain required medicinal compounds,and by sampling individuals in a population at >20 m spatial intervals to avoid collecting individuals with identical or similar genotypes.     

Neutral markers, ecologically relevant traits, and the structure of genetic variation in Daphnia

Zooplankton, Daphnia in particular, are increasingly used as model organisms to investigate general evolutionary biological questions. I here discuss some recent insights into the patterns and processes determining genetic diversity within and genetic differentiation among natural populations of cyclically parthenogenetic Daphnia. I focus on three aspects: (1) the interplay of phenotypic plasticity and genetic polymorphism in explaining variability in ecologically relevant traits, (2) the patterns of genetic variation revealed by neutral markers and ecologically relevant traits, and (3) the evolutionary ecological importance of hybridization events in Daphnia. The need for studies on the evolutionary ecology of sexual reproduction and dispersal via ephippial eggs in Daphnia is stressed.     

Fine-scale genetic analysis of Daphnia host populations infected by two virulent parasites - strong fluctuations in clonal structure at small temporal and spatial scales

Numerous theoretical studies suggest that parasites impose a strong selection pressure on their host, driving genetic changes within host populations. Yet evidence of this process in the wild is scarce. In the present study we surveyed, using high resolution microsatellite markers, the genetic structure of cyclically parthenogenetic Daphnia hosts within two different Daphnia communities belonging to the Daphnia longispina hybrid complex. One community, consisting of a single host species, was infected with the protozoan parasite Caullerya mesnili. The second community consisted of two parental Daphnia spp. and their hybrids, and was infected with the yeast parasite Metschnikowia. Significant differences in the clonal composition between random and infected sub-samples of Daphnia were detected on several occasions within both communities, indicating that host genotypes differ in resistance to both parasites. In addition, one parental species in the multi-taxon community was consistently under-infected, compared with the other taxa. Overall, our field data confirm that infection patterns are strongly affected by host genetic composition in various Daphnia-microparasite systems. Thus, parasite-driven selection operates in natural Daphnia populations and microparasites influence the clonal structure of host populations.     

Effects of clonality on the genetic variability of rare,insular species: the case of Ruta microcarpa from the Canary Islands

Many plant species combine sexual and clonal reproduction. Clonal propagation has ecological costs mainly related to inbreeding depression and pollen discounting; at the same time, species able to reproduce clonally have ecological and evolutionary advantages being able to persist when conditions are not favorable for sexual reproduction. The presence of clonality has profound consequences on the genetic structure of populations, especially when it represents the predominant reproductive strategy in a population. Theoretical studies suggest that high rate of clonal propagation should increase the effective number of alleles and heterozygosity in a population, while an opposite effect is expected on genetic differentiation among populations and on genotypic diversity. In this study, we ask how clonal propagation affects the genetic diversity of rare insular species, which are often characterized by low levels of genetic diversity, hence at risk of extinction. We used eight polymorphic microsatellite markers to study the genetic structure of the critically endangered insular endemic Ruta microcarpa. We found that clonality appears to positively affect the genetic diversity of R. microcarpa by increasing allelic diversity, polymorphism, and heterozygosity. Moreover, clonal propagation seems to be a more successful reproductive strategy in small, isolated population subjected to environmental stress. Our results suggest that clonal propagation may benefit rare species. However, the advantage of clonal growth may be only short‐lived for prolonged clonal growth could ultimately lead to monoclonal populations. Some degree of sexual reproduction may be needed in a predominantly clonal species to ensure long‐term viability.     

THE QUANTITATIVE AND MOLECULAR GENETIC ARCHITECTURE OF A SUBDIVIDED SPECIES

In an effort to elucidate the evolutionary mechanisms that determine the genetic architecture of a species, we have analyzed 17 populations of the microcrustacean Daphnia pulex for levels of genetic variation at the level of life-history characters and molecular markers in the nuclear and mitochondrial genomes. This species is highly subdivided, with approximately 30% of the variation for nuclear molecular markers and 50% of the variation for mitochondrial markers being distributed among populations. The average level of genetic subdivision for quantitative traits is essentially the same as that for nuclear markers, which superficially suggests that the life-history characters are diverging at the neutral rate. However, the existence of a strong correlation between the levels of population subdivision and broadsense heritabilities of individual traits argues against this interpretation, suggesting instead that the among-population divergence of some quantitative traits (most notably body size) is being driven by local adaptation to different environments. The fact that the mean phenotypes of the individual populations are also strongly correlated with local levels of homozygosity indicates that variation in local inbreeding plays a role in population differentiation. Rather than being a passive consequence of local founder effects, levels of homozygosity may be selected for directly for their effects on the phenotype (adaptive inbreeding depression). There is no relationship between the levels of variation within populations for molecular markers and quantitative characters, and this is explained by the fact that the average standing genetic variation for life-history characters in this species is equivalent to only 33 generations of variation generated by mutation.     

Partitioning of genetic variation in the weedy clonal herb Aegopodium podagraria (Apiaceae) in Sweden

Although sexual reproduction appears to be rare in many clonal plant species, the majority of clonal species show similar levels of genetic variation to non-clonal plant species. Aegopodium podagraria is a noxious garden weed and has become a successful invader in many natural habitats. Earlier studies have demonstrated population differentiation in life-history traits between different A. podagraria populations in Sweden. In this study, we used three methods to assess genetic variation in this species. Using analyses of molecular markers (chloroplast DNA PCR-RFLP and allozyme electrophoresis) we did not detect any variation between different A. podagraria clones. However, a multivariate analysis of leaflet shape in five populations from central Sweden revealed considerable variation both within and between populations. The variation found in leaflet shape is suggested to be genetically based because the leaves were collected from plants grown from seed under similar conditions in a common garden environment. These relatively high levels of variation within and between populations indicate that there is likely to be repeated seedling recruitment within established populations. ¹     

具混合繁殖策略的草本植物异果舞花姜的居群遗传结构

 居群遗传结构的形成受到各种因素的影响。其中, 繁殖方式可能对居群内遗传变异有极其重要的意义, 而距离隔离也是居群间变异产 生的主要原因之一。异果舞花姜(Globba racemosa)具有混合繁殖策略(以种子进行有性繁殖和以珠芽进行无性克隆繁殖)。调查分布于云南的7 个异果舞花姜居群间有性与无性克隆繁殖的差异。采用ISSR标记研究各个居群的遗传多样性与克隆多样性, 探讨繁殖方式和距离隔离对居群遗 传结构的影响。调查结果表明, 异果舞花姜各个居群存在一定的繁殖差异。ISSR结果显示, 该种在种水平上呈现较高水平的遗传变异 (PPB=71.19%), 大部分的变异来自于居群间(G_ST = 0.590 7)。同时, 异果舞花姜具有较高水平克隆多样性(G/N = 0.88)。遗传多样性和克隆多 样性与繁殖水平的变异间相关性不明显, 说明繁殖方式不是居群遗传结构形成的必要和决定性的因素。居群间的地理距离与遗传距离显著相关 (r = 0.68, p < 0.05), 表明距离隔离是居群间遗传变异形成的重要原因。其它因素(如少量新有性个体的补充、细胞突变、奠基效应等)也对 异果舞花姜居群遗传结构的形成和维持起到了重要作用。     

Genetic and clonal structures of the tree species Tilia cordata mill. in remnants of ancient forests in Denmark

The insect-pollinated forest tree Tilia cordata Mill. grows today in small fragmented populations in Denmark and other western European countries but was, in prehistoric times, a dominating species and is considered an indicator species for ancient forest. The species is known to propagate both sexually and vegetatively, forming clonal groups. Few studies have been made on the species' population genetics and on how clonality affects the population structure. The aim of this study is to evaluate the Danish gene pool by estimating genetic diversity and differentiation, as well as through exhaustive sampling describe clonal structures in some of the populations. Genetic analysis was carried out using nine nuclear microsatellite markers in nine populations, of which four were exhaustively or partly exhaustively sampled. The markers showed a high degree of genetic diversity but low differentiation between populations, with no geographic-related structure. Clonal structures were found in eight out of the nine populations. In the exhaustively sampled populations, recruitment strategies included both sexual and clonal reproduction with indications that clonality may be enhanced by management and other disturbances.     

Genetic Variation Within and Among Populations of Rhodiola alsia (Crassulaceae) Native to the Tibetan Plateau as Detected by ISSR Markers

Genetic variation of 10 Rhodiola alsia (Crassulaceae) populations from the Qinghai–Tibet Plateau of China was investigated using intersimple sequence repeat (ISSR) markers. R. alsia is an endemic species of the Qinghai–Tibet Plateau. Of the 100 primers screened, 13 were highly polymorphic. Using these primers, 140 discernible DNA fragments were generated with 112 (80%) being polymorphic, indicating pronounced genetic variation at the species level. Also there were high levels of polymorphism at the population level with the percentage of polymorphic bands (PPB) ranging from 63.4 to 88.6%. Analysis of molecular variance (AMOVA) showed that the genetic variation was mainly found among populations (70.3%) and variance within populations was 29.7%. The main factors responsible for the high level of differentiation among populations are probably the isolation from other populations and clonal propagation of this species. Occasional sexual reproduction might occur in order to maintain high levels of variation within populations. Environmental conditions could also influence population genetic structure as they occur in severe habitats. The strong genetic differentiation among populations in our study indicates that the conservation of genetic variability in R. alsia requires maintenance of as many populations as possible.     

Genetic variation and clonal structure of the rare,riparian shrub <Emphasis Type="Italic">Spiraea virginiana</Emphasis> (Rosaceae)

Genetic diversity is often considered important for species that inhabit highly disturbed environments to allow for adaptation. Many variables affect levels of genetic variation; however, the two most influential variables are population size and type of reproduction. When analyzed separately, both small population size and asexual reproduction can lead to reductions in genetic variation, although the exact nature of which can be contrasting. Genetic variables such as allelic richness, heterozygosity, inbreeding coefficient, and population differentiation have opposite predictions depending upon the trait (rarity or clonality) examined. The goal of this study was to quantify genetic variation and population differentiation in a species that resides in a highly stochastic environment and is both rare and highly clonal, Spiraea virginiana, and to determine if one trait is more influential genetically than the other. From populations sampled throughout the natural range of S. virginiana, we used microsatellite loci to estimate overall genetic variation. We also calculated clonal structure within populations, which included genotypic richness, evenness, and diversity. Gene flow was investigated by quantifying the relationship between genetic and geographic distances, and population differentiation (θ) among populations. Observed heterozygosity, genotypic richness, and inbreeding coefficients were found to be representative of high clonal reproduction (averaging 0.505, 0.1, and –0.356, respectively) and the number of alleles within populations was low (range = 2.0–3.6), being more indicative of rarity. Population differentiation (θ) among populations was high (average = 0.302) and there was no relationship between genetic and geographic distances. By examining a species that exhibits two traits that both can lead to reduced genetic variation, we may find an enhanced urgency for conservation. Accurate demographic counts of clonal species are rarely, if ever, possible and genetic exploration for every species is not feasible. Therefore, the conclusions in this study can be potentially extrapolated to other riparian, clonal shrubs that share similar biology as S. virginiana.     

Promiscuity in populations of the cushion plant Saxifraga oppositifolia in the Swiss Alps as inferred from random amplified polymorphic DNA (RAPD)

Overviews on patterns of genetic variation within and among plant populations show that widespread, outcrossing species should have a high proportion of the total genetic variation within populations and a low proportion among populations, which results in little population differentiation. However, in Alpine areas, large–scale distribution barriers as well as small-scale habitat heterogeneity could lead to geographical and temporal isolation, respectively. We investigated the genetic variation of Saxifraga oppositifolia from 10 populations of the Alps in southeastern Switzerland using random amplified polymorphic DNA (RAPD). Based on the banding patterns of four RAPD primers, 84 polymorphic markers identified all 189 sampled individuals as being genetically different. The genetic variation was mainly found within populations (95%), whereas less than 5% was found among populations and among regions. Analyses of molecular variance ( AMOVA ) suggested that population differentiation was highly significant. However, grouping populations differently into regions did not appear to result in a clear correspondence of genetic and geographical relatedness. Genetic variation did not significantly differ between populations of two elevational levels. This coincides with results of former pollination experiments that revealed a breeding system of S. oppositifolia which remains the same irrespective of the elevation. We assume that the high outcrossing rate, rare clonal reproduction, and some long-distance dispersal even among topographically separated populations are the crucial determinants for the pattern of genetic variation found in the investigated area.     

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.     

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.     

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.     

Genetic variation in an apomictic grass, heteropogon contortus, in the hawaiian islands

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic variation within and among Hawaiian populations of an apomictic grass, Heterogopon contortus (pili grass). From among 56 individuals sampled from six populations on O'Ahu and Hawai'i, 55 unique genotypes were detected using 33 polymorphic markers. This lack of uniformity among individuals may indicate frequent sexual reproduction in these populations. Analysis of molecular variance (AMOVA) revealed significant variation among populations (30.2%), but higher levels of variation within populations (68.1%). Cluster analysis revealed a high degree of clustering for most populations, but populations from different islands did not cluster together. The presence of among-population differentiation but lack of between-island differentiation may suggest that H. contortus was an early Polynesian introduction to the Hawaiian Islands.