Vitality composition and its role in subpopulation loci of <Emphasis Type="Italic">Soldanella hungarica</Emphasis> Simonk. (Primulaceae) in the Carpathians

A long-term monitoring (1974–2009) of the regularities of subpopulation organization of Soldanella hungarica Simonk. (Primulaceae) has been conducted in the plant community of Mugetum luzulosum in the Carpathians. The basic principles of formation and dynamics of the subpopulation loci have been revealed. The conclusion is made that the heterogeneity of luminance in the mountain-pine crooked forests creates a matrix of microhabitats, which serves as a basis for formation of subpopulation loci with their specific composition and dynamics. The arguments are given that the heterogeneity of vitality of the loci is the most important condition for the preservation of homeostasis and vitality of the natural historic populations of plants.     

Genetic Architecture of Natural Variation of Telomere Length in Arabidopsis thaliana

Telomeres represent the repetitive sequences that cap chromosome ends and are essential for their protection. Telomere length is known to be highly heritable and is derived from a homeostatic balance between telomeric lengthening and shortening activities. Specific loci that form the genetic framework underlying telomere length homeostasis, however, are not well understood. To investigate the extent of natural variation of telomere length in Arabidopsis thaliana, we examined 229 worldwide accessions by terminal restriction fragment analysis. The results showed a wide range of telomere lengths that are specific to individual accessions. To identify loci that are responsible for this variation, we adopted a quantitative trait loci (QTL) mapping approach with multiple recombinant inbred line (RIL) populations. A doubled haploid RIL population was first produced using centromere-mediated genome elimination between accessions with long (Pro-0) and intermediate (Col-0) telomere lengths. Composite interval mapping analysis of this population along with two established RIL populations (Ler-2/Cvi-0 and Est-1/Col-0) revealed a number of shared and unique QTL. QTL detected in the Ler-2/Cvi-0 population were examined using near isogenic lines that confirmed causative regions on chromosomes 1 and 2. In conclusion, this work describes the extent of natural variation of telomere length in A. thaliana, identifies a network of QTL that influence telomere length homeostasis, examines telomere length dynamics in plants with hybrid backgrounds, and shows the effects of two identified regions on telomere length regulation.     

Population Dynamics of the Segregation Distorter Polymorphism of DROSOPHILA MELANOGASTER

Two two-locus models of the population dynamics of the segregation distortion (SD) polymorphism of Drosophila melanogaster are described. One model is appropriate for understanding the population genetics of SD in nature, whereas the other is a special case appropriate for understanding an artificial population that has been extensively analysed. The models incorporate the general features of the Sd and Rsp loci which form the core of the SD system. It is shown that the SD polymorphism can be established only when there is sufficiently tight linkage between Sd and Rsp. An approximate treatment, valid for tight linkage, is given of all the equilibria of the system and their stabilities. It is shown that the observed composition of natural and artificial populations with respect to the Sd and Rsp loci is predicted well by the model, provided that restrictions are imposed on the fertilities of certain genotypes. Highly oscillatory paths towards equilibrium are usually to be expected on the basis of this model. The selection pressures on inversions introduced into this system are also investigated.     

Gene Flow in Natural Populations of DROSOPHILA MELANOGASTER with Special Reference to Lethal Allelism Rates and Protein Variation

A simultaneous survey of 14 protein loci, together with frequencies and within- and between-population allelism rates of lethal chromosomes, was carried out in five (four Japanese and one Korean) natural populations and one cage population of Drosophila melanogaster. It was found that lethal allelism rates decrease rapidly as geographic distance between two populations increases, while variation at protein loci shows a remarkable similarity over all populations examined. These findings suggest that there are very high levels of gene flow in these natural populations and that selection at protein loci which can maintain substantial geographic variation, if present, is overshadowed by gene flow. There is no indication that invasion of D. melanogaster to the Far East occurred so recently that the frequencies of lethal chromosomes are still in nonequilibrium.     

<Emphasis Type="Italic">Parnassius apollo nevadensis</Emphasis>: identification of recent population structure and source–sink dynamics

Population persistence depends in many cases on gene flow between local populations. Parnassius apollo nevadensis is an endemic subspecies of Apollo butterfly in the Sierra Nevada (southern Spain), whose populations are distributed in discrete patches at altitudes between 1850 and 2700 m. In this paper, we use 13 microsatellite loci to examine the genetic structure of this P. apollo subspecies. We revealed both a strong pattern of isolation by distance (which was stronger when calculated with realistic travel distances that accounted for topography) and source–sink dynamics. The observed population genetic structure is consistent with strongly asymmetrical gene flow, leading to constant directional migration and differential connectivity among the populations. The apparently contradictory results from the clustering algorithms (Structure and Geneland) are also consistent with a recent (<100 ya) reduction in the distribution range. The results point to global warming as a possible cause of this reduction, as in other populations of this species. We identify some natural and anthropogenic barriers to gene flow that may be the cause of the recent population structure and source–sink dynamics.     

用分子标记揭示植物随机大居群中亚居群的遗传结构——茅栗自然居群空间遗传结构的SSR分析

采用微卫星标记对茅栗(Castanea sequinii)随机大居群以及其中各亚居群的遗传结构进行了空间自相关分析,以探讨植物自然居群内遗传变异的分布特征及其形成机制。通过9对微卫星引物所产生的119个多态位点,测定了大别山区域内茅栗居群以及各亚居群的空间自相关系数Moran's I值。结果表明:大别山分布的野生茅栗为一个缺乏空间结构的随机大居群,茅栗亚居群之间频繁的花粉流削弱了地理隔离导致的遗传漂变或分化作用在维系居群随机遗传结构中具有的重要作用。但是,在接近亚居群大小的地域范围内(0.228 km)具有一定的空间结构,即小地域尺度中的亚居群存在着空间遗传结构。取样的3个亚居群在小格局范围内都存在一定的空间结构,遗传变异基本上呈非随机分布,在短距离内(61 m)3个亚居群一致表现出不同程度的显著正相关,而随着距离的增加,Moran's I值虽然在不同亚居群间存在一定差异变化,但是总体而言趋向预期值,即不存在空间结构,说明其遗传变异在亚居群内只是在短距离内形成一定的空间结构。研究认为有限的种子散播以及微生境选择等因素可能是产生这种小格局的遗传结构的主要原因。上述研究结果有助于进一步了解植物随机大居群的进化历史和生态过程,同时也为栗属植物中国特有种的保育策略提供了科学依据。     

Genome and population dynamics under selection and neutrality: an example of S-allele diversity in wild cherry (Prunus avium L.)

Self-incompatibility, a common attribute of plant development, forms a classical paradigm of balancing selection in natural populations, in particular negative frequency-dependent selection. Under negative frequency-dependent selection population genetics theory predicts that the S-locus, being in command of self-incompatibility, keeps numerous alleles in equal frequencies demonstrating a wide allelic range. Moreover, while natural populations exhibit a higher within population genetic diversity, a reduction of population differentiation and increase of effective migration rate is expected in comparison to neutral loci. Allelic frequencies were investigated in terms of distribution and genetic structure at the gametophytic self-incompatibility locus in five wild cherry (Prunus avium L.) populations. Comparisons were also made between the differentiation at the S-locus and at the SSR loci. Theoretical expectations under balancing selection were congruent to the results observed. The S-locus showed broad multiplicity (16 S-alleles), high genetic diversity, and allelic isoplethy. Genetic structure at the self-incompatibility locus was almost four times lower than at 11 nSSR loci. Analysis of molecular variance revealed that only 5?% of the total genetic variation concerns differentiation among populations. In conclusion, the wealth of S-allelic diversity found in natural wild cherry populations in Greece is useful not only in advancing basic population genetics research of self-incompatibility systems in wild cherry but also in the development of breeding programs.     

Rate of Adaptation in Sexuals and Asexuals: A Solvable Model of the Fisher–Muller Effect

The adaptation of large asexual populations is hampered by the competition between independently arising beneficial mutations in different individuals, which is known as clonal interference. In classic work, Fisher and Muller proposed that recombination provides an evolutionary advantage in large populations by alleviating this competition. Based on recent progress in quantifying the speed of adaptation in asexual populations undergoing clonal interference, we present a detailed analysis of the Fisher–Muller mechanism for a model genome consisting of two loci with an infinite number of beneficial alleles each and multiplicative (nonepistatic) fitness effects. We solve the deterministic, infinite population dynamics exactly and show that, for a particular, natural mutation scheme, the speed of adaptation in sexuals is twice as large as in asexuals. This result is argued to hold for any nonzero value of the rate of recombination. Guided by the infinite population result and by previous work on asexual adaptation, we postulate an expression for the speed of adaptation in finite sexual populations that agrees with numerical simulations over a wide range of population sizes and recombination rates. The ratio of the sexual to asexual adaptation speed is a function of population size that increases in the clonal interference regime and approaches 2 for extremely large populations. The simulations also show that the imbalance between the numbers of accumulated mutations at the two loci is strongly suppressed even by a small amount of recombination. The generalization of the model to an arbitrary number L of loci is briefly discussed. If each offspring samples the alleles at each locus from the gene pool of the whole population rather than from two parents, the ratio of the sexual to asexual adaptation speed is approximately equal to L in large populations. A possible realization of this scenario is the reassortment of genetic material in RNA viruses with L genomic segments.     

Match probabilities in a finite, subdivided population

We generalize a recently introduced graphical framework to compute the probability that haplotypes or genotypes of two individuals drawn from a finite, subdivided population match. As in the previous work, we assume an infinite-alleles model. We focus on the case of a population divided into two subpopulations, but the underlying framework can be applied to a general model of population subdivision. We examine the effect of population subdivision on the match probabilities and the accuracy of the product rule which approximates multi-locus match probabilities as a product of one-locus match probabilities. We quantify the deviation from predictions of the product rule by R, the ratio of the multi-locus match probability to the product of the one-locus match probabilities. We carry out the computation for two loci and find that ignoring subdivision can lead to underestimation of the match probabilities if the population under consideration actually has subdivision structure and the individuals originate from the same subpopulation. On the other hand, under a given model of population subdivision, we find that the ratio R for two loci is only slightly greater than 1 for a large range of symmetric and asymmetric migration rates. Keeping in mind that the infinite-alleles model is not the appropriate mutation model for STR loci, we conclude that, for two loci and biologically reasonable parameter values, population subdivision may lead to results that disfavor innocent suspects because of an increase in identity-by-descent in finite populations. On the other hand, for the same range of parameters, population subdivision does not lead to a substantial increase in linkage disequilibrium between loci. Those results are consistent with established practice.     

Diversity of Arabidobsis thaliana (L.) Heynh. natural populations at the northern limits of the species range: RAPD analysis

In natural populations of Arabidobsis thaliana (L.) Heynh., occupying northern limits of the species range (Karelia), the level of genetic diversity was evaluated. In two insular and one mainland population variability at 82 RAPD loci was tested. Considerable genetic diversity revealed (P = 4.5%; H _exp = 0.177) was not typical of self-pollinating plant species. It was demonstrated that genetic differentiation among the populations (G _ST = 0.680) was rather high, pointing to the low level of gene flow in the isolated insular populations. It was suggested that the high level of Arabidopsis population polymorphism in Karelia could be associated with extreme growing conditions at the northern limits of the species range.     

Contrasting dynamics of a mutator allele in asexual populations of differing size

Mutators have been shown to hitchhike in asexual populations when the anticipated beneficial mutation supply rate of the mutator subpopulation, NU(b) (for subpopulation of size N and beneficial mutation rate U(b)) exceeds that of the wild-type subpopulation. Here, we examine the effect of total population size on mutator dynamics in asexual experimental populations of Saccharomyces cerevisiae. Although mutators quickly hitchhike to fixation in smaller populations, mutator fixation requires more and more time as population size increases; this observed delay in mutator hitchhiking is consistent with the expected effect of clonal interference. Interestingly, despite their higher beneficial mutation supply rate, mutators are supplanted by the wild type in very large populations. We postulate that this striking reversal in mutator dynamics is caused by an interaction between clonal interference, the fitness cost of the mutator allele, and infrequent large-effect beneficial mutations in our experimental populations. Our work thus identifies a potential set of circumstances under which mutator hitchhiking can be inhibited in natural asexual populations, despite recent theoretical predictions that such populations should have a net tendency to evolve ever-higher genomic mutation rates.     

Genetic Divergence and Signatures of Natural Selection in Marginal Populations of a Keystone,Long-Lived Conifer,Eastern White Pine (Pinus strobus) from Northern Ontario

Marginal populations are expected to provide the frontiers for adaptation, evolution and range shifts of plant species under the anticipated climate change conditions. Marginal populations are predicted to show genetic divergence from central populations due to their isolation, and divergent natural selection and genetic drift operating therein. Marginal populations are also expected to have lower genetic diversity and effective population size (N _e) and higher genetic differentiation than central populations. We tested these hypotheses using eastern white pine (Pinus strobus) as a model for keystone, long-lived widely-distributed plants. All 614 eastern white pine trees, in a complete census of two populations each of marginal old-growth, central old-growth, and central second-growth, were genotyped at 11 microsatellite loci. The central populations had significantly higher allelic and genotypic diversity, latent genetic potential (LGP) and N _e than the marginal populations. However, heterozygosity and fixation index were similar between them. The marginal populations were genetically diverged from the central populations. Model testing suggested predominant north to south gene flow in the study area with curtailed gene flow to northern marginal populations. Signatures of natural selection were detected at three loci in the marginal populations; two showing divergent selection with directional change in allele frequencies, and one balancing selection. Contrary to the general belief, no significant differences were observed in genetic diversity, differentiation, LGP, and N _e between old-growth and second-growth populations. Our study provides information on the dynamics of migration, genetic drift and selection in central versus marginal populations of a keystone long-lived plant species and has broad evolutionary, conservation and adaptation significance.     

Natural Selection and Neutral Evolution Jointly Drive Population Divergence between Alpine and Lowland Ecotypes of the Allopolyploid Plant Anemone multifida (Ranunculaceae)

Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst  = 0.074–0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (F_ST  = 0.041–0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence.     

Selection-delayed population dynamics in baleen whales and beyond

While it is known that population cycles are driven by delayed density-dependent feedbacks, the search for a common feedback mechanism in natural populations with cyclic dynamics has remained unresolved for almost a century. To identify the existence and cause of delayed feedbacks I apply six age- and sex-structured population dynamics models to seven species of baleen whales (suborder Mysticeti) that were heavily depleted by past commercial whaling. The six models include a predator–prey model with killer whale (Orcinus orca) as the predator, and five singe-species models based on (1) exponential growth, (2) density-regulated growth, (3) density-regulated growth with depensation, (4) delayed density-regulated growth and (5) selection-delayed dynamics. The latter model has a density-regulated growth rate that is accelerated and decelerated by the intra-specific natural selection that arises from the density-dependent competitive interactions between the individuals in the population. Essential parameters are estimated by a Bayesian statistical framework, and it is shown that baleen whales have a delayed recovery relative to density-regulated growth. The time-lag is not explained by depensation, or by interactions with prey or predators. It is instead resolved by a selection-delayed acceleration of the intrinsic growth rate. The results are discussed in relation to the literature on cyclic dynamics, and it is noted (1) that selection-delayed dynamics is both theoretically and empirically sufficient for cyclic population dynamics, (2) that it is widespread in natural populations owing to the widespread occurrence of otherwise unexplained phenotypic cycles in populations with cyclic dynamics, and (3) that there is a lack of empirical evidence showing that predator–prey interactions is a sufficient cause for the cyclic dynamics of natural populations. The conclusion stresses the importance of intra-specific delays in cyclic dynamics, and suggests that it is the acceleration of the growth rate, and not the growth rate itself, that is determined by the density-dependent environment.     

Use of RAPD and ITE molecular markers in studying the genetic structure of the Crimean population of T. boeoticum Boiss

The influence of ecological factors on variation of random PCR markers (RAPD and inter-MITE polymorphism (IMP) primers) was evaluated in two wild Triticum boeoticum populations with contrasting climatic conditions in Crimea. The proportion of variation that undergoes natural selection was compared for these two types of molecular markers. The Sapun Mountain and Baidar Valley populations differed significantly in 24.7% of the analyzed loci, with a low Nei distance between these populations (0.0324). The number of significantly different RAPD and IMP markers in the two populations was nearly equal. Testing for evolutionary neutrality showed that 13 loci (17.8%) were influenced by natural selection. The Sapun Mountain population was more dependent on natural selection (ten loci, 13.7%) than the Baidar Valley population (four loci, 5.5%). Eleven out of the 13 loci undergoing selection were amplified with IMP primers.     

Long-run bacteria-phage coexistence dynamics under natural habitat conditions in an environmental biotechnology system

Bacterial viruses are widespread and abundant across natural and engineered habitats. They influence ecosystem functioning through interactions with their hosts. Laboratory studies of phage–host pairs have advanced our understanding of phenotypic and genetic diversification in bacteria and phages. However, the dynamics of phage–host interactions have been seldom recorded in complex natural environments. We conducted an observational metagenomic study of the dynamics of interaction between Gordonia and their phages using a three-year data series of samples collected from a full-scale wastewater treatment plant. The aim was to obtain a comprehensive picture of the coevolution dynamics in naturally evolving populations at relatively high time resolution. Coevolution was followed by monitoring changes over time in the CRISPR loci of Gordonia metagenome-assembled genome, and reciprocal changes in the viral genome. Genome-wide analysis indicated low strain variability of Gordonia, and almost clonal conservation of the trailer end of the CRISPR loci. Incorporation of newer spacers gave rise to multiple coexisting bacterial populations. The host population carrying a shorter CRISPR locus that contain only ancestral spacers, which has not acquired newer spacers against the coexisting phages, accounted for more than half of the total host abundance in the majority of samples. Phages genome co-evolved by introducing directional changes, with no preference for mutations within the protospacer and PAM regions. Metagenomic reconstruction of time-resolved variants of host and viral genomes revealed how the complexity at the population level has important consequences for bacteria-phage coexistence.Subject terms: Microbial ecology, Metagenomics, Bacteriophages     

Genetic diversity and differentiation of Siberian spruce populations at nuclear microsatellite loci

The results of the study of 21 populations of Siberian spruce (Picea obovata Ledeb.) from different parts of the species natural range by microsatellite (SSR) analysis of nuclear DNA are presented. Using nine loci developed for Picea abies (L.) Karst. and Picea glauca (Moench) Voss and detecting variation in Picea obovata, the parameters of intra- and interpopulation genetic diversity, as well as the degree of population differentiation, were determined. It was demonstrated that the population of Siberian spruce in the study was characterized by a relatively high average level of intrapopulation variability (H_o = 0.408; H_e = 0.423) and low interpopulation differentiation (F_st = 0.048, P = 0.001) at this class of DNA markers. The genetic distance between populations ranged from 0.009 to 0.167, averaging 0.039. The isolated Magadan population, located in the extreme Northeast of Russia at a considerable distance from the main species range and characterized by the lowest genetic diversity among the studied populations, was maximally differentiated from the rest of the spruce populations. In addition, the steppe Ubukun population from Buryatia and the population from the Bogd Khan Uul Biosphere Reserve, Mongolia, were considerably different in the genetic structure from most populations of Siberian spruce, although to a lesser extent than the Magadan population. These findings are consistent with the results of previous studies of this species carried out using allozyme and microsatellite loci of chloroplast DNA and point to the prospects of using nuclear microsatellites as DNA markers to analyze the population genetic structure of Siberian spruce.     

No genetic diversity at molecular markers and strong phenotypic plasticity in populations of Ranunculus nodiflorus, an endangered plant species in France

BACKGROUND AND AIMS: Although conservation biology has long focused on population dynamics and genetics, phenotypic plasticity is likely to play a significant role in population viability. Here, an investigation is made into the relative contribution of genetic diversity and phenotypic plasticity to the phenotypic variation in natural populations of Ranunculus nodiflorus, a rare annual plant inhabiting temporary puddles in the Fontainebleau forest (Paris region, France) and exhibiting metapopulation dynamics. METHODS: The genetic diversity and phenotypic plasticity of quantitative traits (morphological and fitness components) were measured in five populations, using a combination of field measurements, common garden experiments and genotyping at microsatellite loci. KEY RESULTS: It is shown that populations exhibit almost undetectable genetic diversity at molecular markers, and that the variation in quantitative traits observed among populations is due to a high level of phenotypic plasticity. Despite the lack of genetic diversity, the natural population of R. nodiflorus exhibits large population sizes and does not appear threatened by extinction; this may be attributable to large phenotypic plasticity, enabling the production of numerous seeds under a wide range of environmental conditions. CONCLUSIONS: Efficient conservation of the populations can only be based on habitat management, to favour the maintenance of microenvironmental variation and the resulting strong phenotypic plasticity. In contrast, classical actions aiming to improve genetic diversity are useless in the present case.     

Estimating the Gene Pool Condition in Natural Populations of Invertebrates in the Fragmented Landscape of Moscow and Moscow Region with Special Reference to Bush Snail Bradybaena fruticum Mull.

Using bush snail Bradybaena fruticum Mull (20 populations) as a model, we were the first in Russia and in the world to develop a system of urban ecological genetic monitoring of the gene pool of an invertebrate species. The results of isozyme polymorphism studies in bush snail populations showed a dramatic (up to 70%) reduction in genetic diversity in small isolates from the urbanized environment as compared to large natural populations. In urban populations, genetic diversity parameters were demonstrated to be lower than in natural ones: the mean heterozygosity per locus was reduced up to 0.08 (0.15–0.20 in natural populations); the mean allele number, to 1.9 (2.7 in natural populations); and the number of polymorphic loci, to four, i.e., 2.2-fold (nine in natural populations). In Moscow region, the number of polymorphic loci also decreased to five in the population subjected to anthropogenic pressure. The changes in the population gene pool (as shown by the number of polymorphic loci) were different in Moscow and Moscow region. The percentage of populations with the number of polymorphic loci as low as four to six was 76.9 in Moscow and 23.1% in Moscow region. The gene pool quality of 80% of the urban snail populations was estimated as unsatisfactory, and in half of them, as critical. The main reason for these changes seems to be genetic drift accompanied by inbreeding, caused by fragmentation of the range and reduction in the abundance of populations of the species, due to the anthropogenic pressure. The results of the study were employed in the program of the Moscow government for restoring the gene pools of endangered animals species on the preserved territories of the city.